1000 Sentences With "nucleic acids" | Random Sentence Generator

Is something that is in the nucleic acids, the RNA itself?

And now all suspected cases or unconfirmed cases can be tested for nucleic acids quickly.

They may consist of proteins, sugars, and-or nucleic acids, or they may involve entire living cells.

Many important classes of organic molecules in living organisms contain oxygen, including proteins, nucleic acids, carbohydrates, and fats.

Dr. Collins took a cell's normal reproductive "machinery" — including proteins, nucleic acids and ribosomes — and freeze-dried it on paper.

Polymerase, an enzyme that synthesizes polymers and nucleic acids, is essential in creating DNA and RNA, the molecules that are responsible for coding DNA.

Image: Lee et al, Nucleic Acids Research (2017)This all might sound pretty esoteric, but it could have some important implications for studying the flu virus.

Even similar strains of the flu could have different arrangements of these free loops, according to the paper published recently in the journal Nucleic Acids Research.

UVGI disinfects using UV light to kill or destroy microorganisms by targeting their nucleic acids or disrupting their DNA, which leaves them unable to perform their cellular functions.

ASOs are strands of nucleic acids—the same stuff as DNA and RNA—that can zipper up with RNA to either stop or enhance its protein-building activity.

DNA is made up of nucleic acids, and when a nucleic acid is incorrectly placed along the strand, this is referred to as a genetic mutation, noted Brawley.

In a paper last year, he and his colleagues speculated that methanol was originally a basic ingredient that was converted into amino acids, nucleic acids and other building blocks of biology.

Advice: Fauci told Axios that clinicians and patients should rely upon nasal swabs that look for influenza viral RNA or nucleic acids, or have their patient samples cultured for a couple days.

The celebrity trainer didn't hold back when asked about it in a video for Women's Health: "Your cells, your macro molecules, are literally made up of protein, fat, carbohydrates, nucleic acids," she said.

The nucleic acids would theoretically act as a sort of sensor than can be amplified, and the binding patterns analyzed, to reveal a kind of biochemical signature—a "fingerprint," as the researchers put it.

The relationships I value in life—with my wife, my friends, my editor—are emergent products of interacting with other people, other living systems comprising, principally, carbon-based molecules such as proteins and nucleic acids.

The relationships I value in life —with my wife, my friends, my editor—are emergent products of interacting with other people, other living systems comprising, principally, carbon-based molecules such as proteins and nucleic acids.

The effect of such infinitesimal pulses is so precise that they're already in use in applications such as cell nanosurgery, cell isolation, and cellular and embryo transfection (where nucleic acids are added to cells using light).

In the system that the researchers propose, a technique sometimes used in cancer detection called the "systematic evolution of ligands by exponential enrichment," researchers propose creating nucleic acids that can bind to organic molecules that are indicators of life.

Within that broad description, metabolism serves three main purposes: the conversion of food to energy to run cellular processes; the conversion of food to building blocks for proteins, lipids, nucleic acids, and some carbohydrates; and the elimination of waste.

Similar to the way Google searches and finds information online, Mammoth searches and finds nucleic acids indicative of disease and, with it, aims to democratize disease detection in health care as well as across industries such as agriculture, manufacturing, forensics and more.

Scientists at the Marine Biological Laboratory in Woods Hole, Massachusetts, and their colleagues reported on Monday in the journal Nucleic Acids Research that longfin inshore squid (Doryteuthis pealeii) are the first known animals that can edit messenger RNA outside the cell nucleus.

The working hypothesis is that the cells secrete exosomes, tiny vesicles that "contain a lot of nucleic acids, things like RNA, that can change patterns of the way the tissue responds to injury and the way genes are expressed in the tissue," Marbán said.

NFX thought the team could go bigger, so the team met with NFX every week and they collectively decided over time to look at another technology, CRISPR, the technique that allows scientists to make precision edits to any DNA, but that also acts like a search engine for nucleic acids — which has many business applications.

Figure 1. Three important classes of nucleic acids: one-dimensional linear, two-dimensional circular, and three-dimensional spherical. Spherical nucleic acids (SNAs)Cutler, J. I.; Auyeung, E.; Mirkin, C. A. “Spherical Nucleic Acids,” J. Am. Chem. Soc., 2012, 134, 1376–1391, doi: 10.1021/ja209351u.

Nucleotide (abbreviated "nt") is a common unit of length for single-stranded nucleic acids, similar to how base pair is a unit of length for double-stranded nucleic acids.

The quaternary structure of nucleic acids is similar to that of protein quaternary structure. Although some of the concepts are not exactly the same, the quaternary structure refers to a higher-level of organization of nucleic acids. Moreover, it refers to interactions of the nucleic acids with other molecules. The most commonly seen form of higher-level organization of nucleic acids is seen in the form of chromatin which leads to its interactions with the small proteins histones.

He also had a strong interest in the NMR and ESR of nucleic acids and other biological macromolecules.McDonald, C. C.; Phillips, W. D.; Penman, Sheldon. Nucleic acids; a nuclear magnetic resonance (NMR) study.

This led Stroun to explore if other methods could be developed to not only detect the overall abundance of nucleic acids in patients with disease (and specifically cancer) but to also detect the disease-specific components of such circulating nucleic acids themselves. Unlike bacterial transformations in plants and animal cells involving clear transfer of separately identifiable nucleic acids, it was not clear how malignancy in cancer arose, although there were many competing theories. Stroun’s postulate that neoplastic malignancy was associated with the presence of tumor specific nucleic acids, led to extensive research by his group of circulating nucleic acids in cancer patients in the late 1980s.

The recognition abilities of nucleic acids can be enhanced when arranged in a spherical geometry, which allows for polyvalent interactions to occur. This polyvalency, along with the high density and degree of orientation described above, helps explain why SNAs exhibit different properties than their lower-dimensional constituents (Fig. 2). Figure 2. Properties of spherical nucleic acids (SNAs) versus linear nucleic acids.

Folate is necessary for the cell to synthesize nucleic acids (nucleic acids are essential building blocks of DNA and RNA), and in its absence cells will be unable to divide. Hence the sulfonamide antibacterials exhibit a bacteriostatic rather than bactericidal effect.

All-atom molecular dynamics simulations showed that concentration of 1.5–2.2 molar, allow trehalose molecular clusters to percolate and form large, continuous aggregates. Trehalose directly interacts with nucleic acids, facilitates melting of double stranded DNA and stabilizes single-stranded nucleic acids.

Nucleic acid methods are the techniques used to study nucleic acids: DNA and RNA.

To control proteins and nucleic acids by light CEF scientists have designed and applied a range of photoswitchable tethers, ribonucleosides and nucleic acids, RNA aptamers and "beacons". They also developed an approach for the chemo‐enzymatic synthesis of position‐specifically modified RNA for biophysical studies including light control. Furthermore, light-activatable interaction of DNA nanoarchitectures, light-dependent conformational changes in nucleic acids, light-dependent RNA interference and light-dependent transcription were realized. Wavelength- selective light-triggering was established for nucleic acids as well as three-dimensional control of DNA hybridization by orthogonal two-colour two- photon uncaging.

Basic structure of an amino acid.Many biologically important molecules are acids. Nucleic acids, which contain acidic phosphate groups, include DNA and RNA. Nucleic acids contain the genetic code that determines many of an organism's characteristics, and is passed from parents to offspring.

RNA may be too complex to be the first nucleic acid, so before the RNA world several simpler nucleic acids that differ in the backbone, such as TNA and GNA and PNA, have been offered as candidates for the first nucleic acids.

Magnet-assisted transfection is a transfection method which uses magnetic interactions to deliver DNA into target cells. Nucleic acids are associated with magnetic nanoparticles, and magnetic fields drive the nucleic acid- particle complexes into target cells, where the nucleic acids are released.

Nucleic Acids in Chemistry and Biology. The Royal Society of Chemistry, 2006, p. 119-120.

Cystamine has been shown to interact with DNA and reversibly bind to it. Furthermore, cystamine is also able to bind to nucleoproteins. The nucleic acids that form from binding to DNA are more stable then unbound nucleic acids. Binding of cystamine to nucleoproteins makes them precipitate.

Nanoparticles used as carriers for nucleic acids are mostly iron oxides. These iron oxides can be generated by precipitation from acidic iron-salt solutions upon addition of appropriate bases. The magnetic nanoparticles have an approximate size of 100 nm and are additionally coated with biological polymers to allow loading of nucleic acids. Particles and nucleic acids form complexes by ionic interaction of the negatively charged nucleic acid and the positively charged surface of the magnetic nanoparticle.

Nair R., Carter,P. and Rost,B. (2003) NLSdb: database of nuclear localization signals. Nucleic Acids Res.

Kang, H.J. ( 1,2,3 ), et al. "FESD: A Functional Element Snps Database In Human." Nucleic Acids Research 33.

Since that time there have been regular descriptions of the resource in the journal Nucleic Acids Research.

Experimental approaches of determining the structure of nucleic acids, such as RNA and DNA, can be largely classified into biophysical and biochemical methods. Biophysical methods use the fundamental physical properties of molecules for structure determination, including X-ray crystallography, NMR and cryo-EM. Biochemical methods exploit the chemical properties of nucleic acids using specific reagents and conditions to assay the structure of nucleic acids. Such methods may involve chemical probing with specific reagents, or rely on native or analogue chemistry.

Cysteine proteases are used as feed additives for livestock to improve the digestibility of proteins and nucleic acids.

CRISPR-Cas prevents bacteriophage infection, conjugation and natural transformation by degrading foreign nucleic acids that enter the cell.

They did not recognise the contributions of Lindsey in their discovery of the molecular structure of nucleic acids.

DMBT1 has been shown to interact with Surfactant protein D. DMBT1-derived peptides also interacts with nucleic acids.

It opened up a research area eventually leading to the complete synthesis of other components of nucleic acids.

Reineke has published over 140 papers. Nucleic acids can have an unparalleled specificity for targets inside a cell, but need to be compacted into nanostructures (polyplexes) that can enter cells. Reineke designs polymer-based transportation systems for nucleic acids. These polymer vehicles can improve the solubility and bioavailability of drugs.

MODBASE, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Res 32, D217-D222, 2004.

J Chem Soc. 1947; 25: 1129-31JM Gulland; DO Jordan; HF Taylor; (1947) Deoxypentose nucleic acids; Part II electrometric titration of the acidic and the basic groups of the deoxypentose nucleic acid of calf thymus. J Chem Soc. 1947; 25:1131-41.Creeth, J.M., Gulland, J.M. and Jordan, D.O. (1947) Deoxypentose nucleic acids.

This first evidence for transfer of function between different nucleic acids could provide support for various pre-RNA World hypotheses.

Eric Westhof is executive editor of RNA journal (CSHP), Nucleic Acids Research (OUP), and the Journal of Molecular Recognition (Wiley).

Current living forms on Earth are essentially composed of four types of molecular entities: (i) nucleic acids, (ii) proteins, (iii) carbohydrates, and (iv) lipids. Nucleic acids (DNA and RNA) embody and express the genetic information and, together, constitute the genome and the apparatus for its expression (the genotype). Proteins, carbohydrates, and lipids form the structures, which harness and handle energy from the environment for organizing matter according to the instructions specified by the genotype, aiming to its conservation and transmission. The ensemble of proteins, carbohydrates, lipids and nucleic acids constitute the phenotype.

DNA sample separated using gel electrophoresis of nucleic acids and stained with ethidium bromide, which emits orange light after binding to DNA Ethidium bromide is commonly used to detect nucleic acids in molecular biology laboratories. In the case of DNA this is usually double- stranded DNA from PCRs, restriction digests, etc. Single-stranded RNA can also be detected, since it usually folds back onto itself and thus provides local base pairing for the dye to intercalate. Detection typically involves a gel containing nucleic acids placed on or under an ultraviolet lamp.

Schild regression is a radioligand binding assay. It is used for DNA labelling (5' and 3'), leaving the nucleic acids intact.

Phenol–chloroform extraction is a liquid-liquid extraction technique in molecular biology used to separate nucleic acids from proteins and lipids.

Lipoplexes are liposome structures characterized by a bilayer lipid membrane. Lastly, micelles result from electrostatic interaction between nucleic acids and copolymers.

Nucleic Acids Research. 42(7):e52, 2014. paper 5\. L. Sun, A.F. Johnson, J. Li, A.S. Lambdin, J. Cheng, J.A. Birchler.

The principle of detection was based on staining proteins and nucleic acids with fluorescent dyes within a liquid sample. As stained particles passed through the probe region and interacted with a laser, emissions were detected and recorded for analysis. This dual channel system established the concept of measuring intact virions through detection of co-localized protein and nucleic acids.

After agitation and centrifugal separation, the aqueous layer is extracted, and further processed with ether. Then the DNA is concentrated by ethanol precipitation. The phenol extraction technique is often used to purify samples of nucleic acids taken from cells. To obtain nucleic acid samples, the cell must be lysed and the nucleic acids separated from all other cell materials.

This is called translation because the protein's amino acid structure is determined by the mRNA's code. Information is hence translated from the language of nucleic acids to the language of amino acids. Some nucleic acids of RNA viruses function directly as mRNA without further modification. For this reason, these viruses are called positive-sense RNA viruses.

Nucleic acids RNA (left) and DNA (right). Nucleic acids are the biopolymers, or large biomolecules, essential to all known forms of life. The term nucleic acid is the overall name for DNA and RNA. They are composed of nucleotides, which are the monomers made of three components: a 5-carbon sugar, a phosphate group and a nitrogenous base.

Hydrogen and oxygen are found in water and organic molecules, both of which are essential to life. Carbon is found in all organic molecules, whereas nitrogen is an important component of nucleic acids and proteins. Phosphorus is used to make nucleic acids and the phospholipids that comprise biological membranes. Sulfur is critical to the three-dimensional shape of proteins.

Optical density of ribosome sample. The important wavelengths of 260nm and 280nm are labeled. In molecular biology, quantitation of nucleic acids is commonly performed to determine the average concentrations of DNA or RNA present in a mixture, as well as their purity. Reactions that use nucleic acids often require particular amounts and purity for optimum performance.

Russo Krauss, I. et al. Thrombin-aptamer recognition: a revealed ambiguity. Nucleic Acids Research 39, 7858-7867, doi:10.1093/nar/gkr522 (2011).

Eschenmoser developed synthetic pathways for artificial nucleic acids, specifically modifying the sugar backbone of the polymer. Having developed a number of structural alternatives to the naturally occurring nucleic acids, Eschenmoser and his colleagues were able to contrast the properties of these synthetic nucleic acids with naturally occurring ones to effectively determine the properties of RNA and DNA vital to modern biochemical processes. This work demonstrated that hydrogen-bonding interactions between the base-paring surfaces of the nucleobases alone might not have provided sufficient selection pressure to lead to the eventual rise of ribose in the structure of modern nucleic acids. He determined that pentose sugars, particularly ribose, conform to a geometry that contributes significantly to the helical structure of DNA by optimizing base-pair stacking distances in naturally occurring oligonucleotides.

This method relies on phase separation by centrifugation of a mixture of the aqueous sample and a solution containing water-saturated phenol and chloroform, resulting in an upper aqueous phase and a lower organic phase (mainly phenol). Guanidinium thiocyanate, a chaotropic agent, is added to the organic phase to aid in the denaturation of proteins (such as those that strongly bind nucleic acids or those that degrade RNA). The nucleic acids (RNA and/or DNA) partition into the aqueous phase, while protein partitions into the organic phase. The pH of the mixture determines which nucleic acids get purified.

Two- dimensional NMR methods are almost always used with nucleic acids. These include correlation spectroscopy (COSY) and total coherence transfer spectroscopy (TOCSY) to detect through-bond nuclear couplings, and nuclear Overhauser effect spectroscopy (NOESY) to detect couplings between nuclei that are close to each other in space. The types of NMR usually done with nucleic acids are 1H NMR, 13C NMR, 15N NMR, and 31P NMR. 19F NMR is also useful if nonnatural nucleotides such as 2'-fluoro-2'-deoxyadenosine are incorporated into the nucleic acid strand, as natural nucleic acids do not contain any fluorine atoms.

Evolutionary significance: From this evidence, it is clear that all living things have a common origin point or a common ancestor, which in turn had protoplasm. Its complexity increased due to changes in the mode of life and habitat. # Nucleic acids: DNA and RNA are the two types of nucleic acids present in all living organisms. They are present in the chromosomes.

Quinaldine red can exhibit fluorescence when it is bound to nucleic acids, which then emit radiation between 580-650 nm. Maximum fluorescence of QR is detected from 557 nm to 607 nm. QR and the nucleic acids react quickly under room temperature, and the resulting QR-nucleic acid complex is able to fluorescence. However, fluorescent activity decrease as time goes on.

Compounds that make up organisms may be divided into macromolecules and other, smaller molecules. The four groups of macromolecule are nucleic acids, proteins, carbohydrates and lipids. Nucleic acids (specifically deoxyribonucleic acid, or DNA) store genetic data as a sequence of nucleotides. The particular sequence of the four different types of nucleotides (adenine, cytosine, guanine, and thymine) dictate many characteristics that constitute the organism.

Robert W. Holley, left, poses with his research team. Research on RNA has led to many important biological discoveries and numerous Nobel Prizes. Nucleic acids were discovered in 1868 by Friedrich Miescher, who called the material 'nuclein' since it was found in the nucleus. It was later discovered that prokaryotic cells, which do not have a nucleus, also contain nucleic acids.

STING elicits powerful type I interferon immunity against viral infection. After viral entry, viral nucleic acids will be present in the cytosol of infected cells. Several DNA sensors, such as DAI, RNA polymerase III, IFI16, DDX41 and cGAS, can detect foreign nucleic acids. After recognizing viral DNA, DNA sensors initiate the downstream signaling pathways by activating STING-mediated interferon response.

NCBI Resource Coordinators. Database resources of the National Center for Biotechnology Information. Nucleic Acids Research. 2016;44(Database issue):D7-D19. doi:10.1093/nar/gkv1290.

"Stable nuclear expression of ATP8 and ATP6 genes rescues a mtDNA Complex V null mutant". Nucleic acids research. 44(19): 9342-9357. . . and MitoMouse.

A hybridization assay comprises any form of quantifiable hybridization i.e. the quantitative annealing of two complementary strands of nucleic acids, known as nucleic acid hybridization.

1992: 229. Print.through an exploitation of certain nucleic acids Weiler A.H. "'The Mutations,' British Sci-Fi, Arrives." The New York Times 26 Sept. 1974: 26.

The light from this UV laser is strongly absorbed by lipids, nucleic acids and proteins, making it useful for applications in medical therapy and surgery.

Nucleic Acids Research. 34(22). 6505-6520 GCM1 and FLYWCH are proposed ancestral proteins base on their crystal structural similarity to the WRKY domain.Babu, Iyer, Balaji and Aravind (2006) The natural history of the WRKY–GCM1 zinc fingers and the relationship between transcription factors and transposons. Nucleic Acids Research. 34(22). 6505-6520 Both GCM1 and FLYWCH belong to families of DNA-binding factors found in metazoan.

NAIL-MS (short for nucleic acid isotope labeling coupled mass spectrometry) is a technique based on mass spectrometry used for the investigation of nucleic acids and its modifications. It enables a variety of experiment designs to study the underlying mechanism of RNA biology in vivo. For example, the dynamic behaviour of nucleic acids in living cells, especially of RNA modifications, can be followed in more detail.

Extended bases using a natural DNA backbone could, likewise, be transliterated into natural DNA, although to a more limited extent. Aside being used as extensions to template DNA strands, XNA activity has been tested for use as genetic catalysts. Although proteins are the most common components of cellular enzymatic activity, nucleic acids are also used in the cell to catalyze reactions. A 2015 study found several different kinds of XNA, most notably FANA (2'-fluoroarabino nucleic acids), as well as HNA, CeNA and ANA (arabino nucleic acids) could be used to cleave RNA during post- transcriptional RNA processing acting as XNA enzymes, hence the name XNAzymes.

However, his research laboratory at Boston University continues to be active, and he works there frequently. He is also a co-founder and Director of Retrotope, a US-based company using heavier isotopes of carbon (C13) and hydrogen (deuterium) to stabilize essential compounds like amino acids, nucleic acids and lipids to target age-related diseases. Cantor held positions at Columbia University and the University of California, Berkeley. Cantor’s laboratory at Boston University has developed methods for separating large DNA molecules, for studying structural relationships in complex proteins and nucleic acids, and for sensitive detection of proteins and nucleic acids in a variety of settings.

The optical activity (absorption and scattering of light) and hydrodynamic properties (translational diffusion, sedimentation coefficients, and rotational correlation times) of formamide denatured nucleic acids are similar to those of heat-denatured nucleic acids. Therefore, depending on the desired effect, chemically denaturing DNA can provide a gentler procedure for denaturing nucleic acids than denaturation induced by heat. Studies comparing different denaturation methods such as heating, beads mill of different bead sizes, probe sonification, and chemical denaturation show that chemical denaturation can provide quicker denaturation compared to the other physical denaturation methods described. Particularly in cases where rapid renaturation is desired, chemical denaturation agents can provide an ideal alternative to heating.

In: Verna R, Shamoo A (eds) Biotechnology Today, Challenges of Modern Medicine, Ares-Serono Symposia Publications, 1994, Vol 5, pp 141–150. Stroun was also the first to demonstrate the successful detection of alterations beyond point mutations in plasma, such as microsatellite alterations, gene expression changes and copy-number alterations. Circulating Nucleic Acids in Plasma and Serum Congress The early work of Stroun and Anker spurred intense investigation into the relationship of circulating nucleic acids and human conditions, such as disease, trauma, and pregnancy. For example, Lo demonstrated that fetal-specific nucleic acids could be detected in maternal peripheral blood in the late 1990s.

For their groundbreaking work in the sequencing of nucleic acids, Gilbert and Sanger shared half the 1980 Nobel Prize in chemistry with Paul Berg (recombinant DNA).

Whitington, T., Frith, M. C., Johnson, J., & Bailey, T. L. (2011). Inferring transcription factor complexes from ChIP-seq data. Nucleic Acids Research, 39(15), e98-e98.

Development of biodegradable and biocompatible non-viral vectors with intrinsical multifunctional properties such as bioimaging ability for highly efficient nucleic acids delivery still remains a challenge.

There are three potential metal binding groups on nucleic acids: phosphate, sugar, and base moieties. Solid-state structure of complexes with alkali metal ions have been reviewed.

Metal salts can be used at low concentrations to precipitate enzymes and nucleic acids from solutions. Polyvalent metal ions frequently used are Ca2+, Mg2+, Mn2+ or Fe2+.

X-ray crystallography is not common for nucleic acids alone, since neither DNA nor RNA readily form crystals. This is due to the greater degree of intrinsic disorder and dynamism in nucleic acid structures and the negatively charged (deoxy)ribose-phosphate backbones, which repel each other in close proximity. Therefore, crystallized nucleic acids tend to be complexed with a protein of interest to provide structural order and neutralize the negative charge.

Aside from the genetic material of the cell, nucleic acids often play a role as second messengers, as well as forming the base molecule for adenosine triphosphate (ATP), the primary energy-carrier molecule found in all living organisms. Also, the nitrogenous bases possible in the two nucleic acids are different: adenine, cytosine, and guanine occur in both RNA and DNA, while thymine occurs only in DNA and uracil occurs in RNA.

The two nucleic acids, DNA and RNA, are polymers of nucleotides. Each nucleotide is composed of a phosphate attached to a ribose or deoxyribose sugar group which is attached to a nitrogenous base. Nucleic acids are critical for the storage and use of genetic information, and its interpretation through the processes of transcription and protein biosynthesis. This information is protected by DNA repair mechanisms and propagated through DNA replication.

388x388px In nucleic acids nanotechnology, artificial nucleic acids are designed to form molecular components that can self-assemble into stable structures for use ranging from targeted drug delivery to programmable biomaterials. DNA nanotechnology uses DNA motifs to build target shapes and arrangements. It has been used in a variety of situations, including nanorobotics, algorithmic arrays, and sensor applications. The future of DNA nanotechnology is filled with possibilities for applications.

Phosphoramidites derived from protected nucleosides are referred to as nucleoside phosphoramidites and are widely used in chemical synthesis of DNA, RNA, and other nucleic acids and their analogs.

Nucleic Acids Res. 2018 Nov 16;46(20):10535-10545. doi: 10.1093/nar/gky910. PMID:30307534 From 5 to 14 recombination events per genome occur at each replication cycle.

The energy parameters are also different for the two nucleic acids. The structure prediction methods can follow a completely theoretical approach, or a hybrid one incorporating experimental data.

Gallocyanin is a chemical compound classified as a phenoxazine dye. In combination with certain metals, it is used to prepare gallocyanin stains that are used in identifying nucleic acids.

Martin J, Abubucker S, Wylie T, Yin Y, Wang Z, Mitreva M. (2009) Nematode.net update 2008: improvements enabling more efficient data mining and comparative nematode genomics. Nucleic Acids Research.

Systematic names of hydrolases are formed as "substrate hydrolase." However, common names are typically in the form "substratease." For example, a nuclease is a hydrolase that cleaves nucleic acids.

Larsen N, Olsen GJ, Maidak BL, McCaughey MJ, Overbeek R, Macke TJ, Marsh TL, Woese CR. (1993) The ribosomal database project. Nucleic Acids Res. Jul 1;21(13):3021-3.

The hierarchical structure through which DNA is packaged into chromosomes. The first level of genome organization concerns how DNA is arranged linearly, and how it is packaged into chromosomes. DNA is composed of two antiparallel strands of nucleic acids, with two bound and opposing nucleic acids referred to as DNA base pairs. In order for DNA to pack inside the tiny cell nucleus, each strand is wrapped around histones, forming nucleosome structures.

BIND- The Biomolecular Interaction Network Database. Nucleic Acids Research 29: 242-245 (2001). BIND is based on a data specification written using Abstract Syntax Notation 1 (ASN.1) language. ASN.

MimoDB is a database of peptides that have been selected from random peptide libraries based on their ability to bind small compounds, nucleic acids, proteins, cells, tissues, ... through phage display.

Nucleic Acids Res. 39(Database issue):D576-82. # Viral g3p protein mediates pilus-mediated adsorption of the virus onto host cell. Pilus retraction pulls the virion to the host internal membrane.

Primary structure is the linear sequence of nucleotides, secondary structure involves small local folding motifs, and tertiary structure is the 3D folded shape of nucleic acid molecule. In general, quaternary structure refers to 3D interactions between multiple subunits. In the case of nucleic acids, quaternary structure refers to interactions between multiple nucleic acid molecules or between nucleic acids and proteins. Nucleic acid quaternary structure is important for understanding DNA, RNA, and gene expression because quaternary structure can impact function.

On the other hand, the discovery in 2009 that activated pyrimidine ribonucleotides can be synthesized under plausible prebiotic conditions suggests that it is premature to dismiss the RNA-first scenarios. Suggestions for 'simple' pre-RNA nucleic acids have included peptide nucleic acid (PNA), threose nucleic acid (TNA) or glycol nucleic acid (GNA). Despite their structural simplicity and possession of properties comparable with RNA, the chemically plausible generation of "simpler" nucleic acids under prebiotic conditions has yet to be demonstrated.

Nucleic Acids Research. 2011; 39. However site 2 requires the 3’-end of BoxA’ and U3 snoRNA for cleavage. Once site 2 is cleaved, 18S rRNA is liberated from the pre-rRNA.

A nucleosome is a combination of DNA + histone proteins.Nucleoproteins are any proteins that are structurally associated with nucleic acids, either DNA or RNA. Typical nucleoproteins include ribosomes, nucleosomes and viral nucleocapsid proteins.

Life cycle of a plastic product . Americanchemistry.com. Retrieved on 2011-07-01. Macromolecules are large molecules composed of thousands of covalently connected atoms. Carbohydrates, lipids, proteins, and nucleic acids are all macromolecules.

Wang, Shuya; Qin, L.; Yamankurt, G.; Skakuj, K.; Huang, Z.; Chen, P.-C.; Dominquez, D.; Lee, A.; Zhang, B.; Mirkin, C. A. “Rational Vaccinology with Spherical Nucleic Acids,” Proc. Natl. Aca. Sci.

Data are contributed by participating scientists or downloaded from public resources. Maddatu TP, Grubb SC, Bult CJ, Bogue MA. Mouse Phenome Database (MPD). Nucleic Acids Res. 2012 Jan;40(Database issue):D887-94.

VCD spectra of nucleotides, synthetic polynucleotides and several nucleic acids, including DNA, have been reported and assigned in terms of the type and number of helices present in A-, B-, and Z-DNA.

Intramolecular hydrogen bonding is partly responsible for the secondary, tertiary, and quaternary structures of proteins and nucleic acids. It also plays an important role in the structure of polymers, both synthetic and natural.

Fixed nitrogen sources are required for most organisms to synthesize proteins, nucleic acids and other cellular components. Depending on the enzyme capabilities of the organism, nitrogen may be provided as bulk protein, such as soy meal; as pre-digested polypeptides, such as peptone or tryptone; or as ammonia or nitrate salts. Cost is also an important factor in the choice of a nitrogen source. Phosphorus is needed for production of phospholipids in cellular membranes and for the production of nucleic acids.

Glycol nucleic acid (left) is an example of a xeno nucleic acid because it has a different backbone than DNA (right). Xeno nucleic acids (XNA) are synthetic nucleic acid analogues that have a different sugar backbone than the natural nucleic acids DNA and RNA. As of 2011, at least six types of synthetic sugars have been shown to form nucleic acid backbones that can store and retrieve genetic information. Research is now being done to create synthetic polymerases to transform XNA.

Nucleic Acids Are Not Boring Long Polymers of Only Four Types of Nucleotides: A Guided Tour. Landes Bioscience. This report was severely criticized because their identification based solely on the optical properties of the crystalline picrate, and other scientists failed to reproduce the same result. But its existence was ultimately proven in 1948, when Hotchkiss separated the nucleic acids of DNA from calf thymus using paper chromatography, by which he detected a unique methylated cytosine, quite distinct from conventional cytosine and uracil.

In biochemistry, diamino acids are of particular interest. Diamino acids are used for the synthesis of specific peptide nucleic acids, such as daPNA. Artificial peptide nucleic acids are capable of forming duplex structures with individual DNA- and RNA-strands and are, therefore, not only called DNA-analog, but also they are considered as candidates for the first genetic material on Earth. The corresponding diamino acids such as 2,3-diaminopropanoic acid were detected in the Murchison meteorite and in a simulated comet.

Structure of a G-quadruplex. Left: a G-tetrad. Right: an intramolecular G4 complex. In molecular biology, G-quadruplex secondary structures (G4) are formed in nucleic acids by sequences that are rich in guanine.

Advantages of this technique are higher yields of proteins and nucleic acids from small, hard tissue samples - especially when used as a preliminary step to mechanical or chemical/solvent cell disruption methods mentioned above.

In 2018, trade between both nations totaled US$815,000 dollars. Mexico's main exports to Syria include: raw pepper and nucleic acids and their salts. Syria's main exports to Mexico include: leather, plants and Anise seeds.

Senapathy has published his other scientific findings in journals including Science', Nucleic Acids Research, PNAS, Journal of Biological Chemistry, and Journal of Molecular Biology, and is the author of several patents in the genomics field.

Coccoid Symbiodinium cells are metabolically active, as they photosynthesize, undergo mitosis, and actively synthesize proteins and nucleic acids. While most dinoflagellates undergo mitosis as a mastigote, in Symbiodinium, mitosis occurs exclusively in the coccoid cell.

123-126 With Pascal Auffinger, the importance and specificity of halogen atom-mediated bonds in biological macromolecules and nucleic acids was established.Auffinger, P., et al., « Halogen bonds in biological molecules. », Nature, (2004), 101(48), p.

The S-particles are mainly used in ring structures whereas the T-particles are currently used in nucleic acids only. Bonded interactions (bonds, angles, dihedrals, and impropers) are derived from atomistic simulations of crystal structures.

Nobel Prize Site for Nobel Prize in Physiology or Medicine 1962. The results were based partly on fundamental studies done by Rosalind Franklin, Raymond Gosling and Wilkins. Crick was an important theoretical molecular biologist and played a crucial role in research related to revealing the helical structure of DNA. He is widely known for the use of the term "central dogma" to summarise the idea that once information is transferred from nucleic acids (DNA or RNA) to proteins, it cannot flow back to nucleic acids.

DNA coils and winds around histone proteins to condense into chromatin. Nucleic acid quaternary structure refers to the interactions between separate nucleic acid molecules, or between nucleic acid molecules and proteins. The concept is analogous to protein quaternary structure, but as the analogy is not perfect, the term is used to refer to a number of different concepts in nucleic acids and is less commonly encountered. Similarly other biomolecules such as proteins, nucleic acids have four levels of structural arrangement: primary, secondary, tertiary, and quaternary structure.

Nucleic acids play important roles as cellular information storage and gene regulation machinery. In efforts to regulate this machinery by light, DNA and RNA have been modified with photocleavable groups at the backbone (in an approach called ‘statistical backbone caging’, the protection groups react mainly with backbone phosphate groups). In the organism, modified nucleic acids are ‘silent’ and only upon irradiation with light can their activity be turned on. This approach finds use in developmental biology, where the chronology of gene activity is of particular interest.

In 1953 James Watson and Francis Crick, building on the work of Maurice Wilkins and Rosalind Franklin, suggested that the structure of DNA was a double helix. In their famous paper "Molecular structure of Nucleic Acids", Watson and Crick noted coyly, "It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material."Watson, James D. and Francis Crick. "Molecular structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid", Nature, vol. 171, no.

NPM1 is associated with nucleolar ribonucleoprotein structures and binds single- stranded and double-stranded nucleic acids, but it binds preferentially G-quadruplex forming nucleic acids. It is involved in the biogenesis of ribosomes and may assist small basic proteins in their transport to the nucleolus. Its regulation through SUMOylation (by SENP3 and SENP5) is another facet of the protein's regulation and cellular functions. It is located in the nucleolus, but it can be translocated to the nucleoplasm in case of serum starvation or treatment with anticancer drugs.

The central dogma of molecular biology outlines the mechanism by which proteins are constructed using information contained in nucleic acids. DNA is transcribed into mRNA molecules, which travels to the ribosome where the mRNA is used as a template for the construction of the protein strand. Since nucleic acids can bind to molecules with complementary sequences, there is a distinction between "sense" sequences which code for proteins, and the complementary "antisense" sequence which is by itself nonfunctional, but can bind to the sense strand.

Nucleic acids have an important range of interactions with Mg2+. The binding of Mg2+ to DNA and RNA stabilises structure; this can be observed in the increased melting temperature (Tm) of double-stranded DNA in the presence of Mg2+. In addition, ribosomes contain large amounts of Mg2+ and the stabilisation provided is essential to the complexation of this ribo-protein. A large number of enzymes involved in the biochemistry of nucleic acids bind Mg2+ for activity, using the ion for both activation and catalysis.

In order to study the virome, virus- like particles are separated from cellular components, usually using a combination of filtration, density centrifugation, and enzymatic treatments to get rid of free nucleic acids. The nucleic acids are then sequenced and analyzed using metagenomic methods. Alternatively, there are recent computational methods that use directly metagenomic assembled sequences to discover viruses. The Global Ocean Viromes (GOV) is a dataset consisting of deep sequencing from over 150 samples collected across the world's oceans in two survey periods by an international team.

RiboGreen is a proprietary fluorescent dye that is used in the detection and quantification of nucleic acids, including both RNA and DNA. It is synthesized and marketed by Molecular Probes/Invitrogen (a division of Life Technologies, now part of Thermo Fisher Scientific) of Eugene, Oregon, United States. In its free form, RiboGreen exhibits little fluorescence and possesses a negligible absorbance signature. When bound to nucleic acids, the dye fluoresces with an intensity that, according to the manufacturer, is several orders of magnitude greater than the unbound form.

Additionally, electroporation can be used to increase permeability of cells during in Utero injections and surgeries. Particularly, the electroporation allows for a more efficient transfection of DNA, RNA, shRNA, and all nucleic acids into the cells of mice and rats. The success of in vivo electroporation depends greatly on voltage, repetition, pulses, and duration. Developing central nervous systems are most effective for in vivo electroporation due to the visibility of ventricles for injections of nucleic acids, as well as the increased permeability of dividing cells.

Defects in certain nucleases can cause genetic instability or immunodeficiency. Nucleases are also extensively used in molecular cloning. There are two primary classifications based on the locus of activity. Exonucleases digest nucleic acids from the ends.

Boom method (aka Boom nucleic acid extraction method) is a solid phase extraction method for isolating nucleic acid from a biological sample. This method is characterized by "absorbing the nucleic acids (NA) to the silica beads".

A slower rate of change occurs in TFBS than in other, less critical, parts of the non- coding genome.Neph, S. and Tompa, M. 2006. MicroFootPrinter: a tool for phylogenetic footprinting in prokaryotic genomes. Nucleic Acids Research.

They play an important role as source of nitrogen and precursor for the synthesis of hormones, alkaloids, nucleic acids, proteins, amines and food aroma components. However, food containing high amounts of biogenic amines may have toxicological effects.

The term "gel" in this instance refers to the matrix used to contain, then separate the target molecules. In most cases, the gel is a crosslinked polymer whose composition and porosity are chosen based on the specific weight and composition of the target to be analyzed. When separating proteins or small nucleic acids (DNA, RNA, or oligonucleotides) the gel is usually composed of different concentrations of acrylamide and a cross- linker, producing different sized mesh networks of polyacrylamide. When separating larger nucleic acids (greater than a few hundred bases), the preferred matrix is purified agarose.

This comes at the cost of slightly less accurate and detailed structures than crystallography. Nucleic acid NMR uses techniques similar to those of protein NMR, but has several differences. Nucleic acids have a smaller percentage of hydrogen atoms, which are the atoms usually observed in NMR, and because nucleic acid double helices are stiff and roughly linear, they do not fold back on themselves to give "long-range" correlations. Nucleic acids also tend to have resonances distributed over a smaller range than proteins, making the spectra potentially more crowded and difficult to interpret.

Schematic structure of DEAE-C: positively charged diethylaminoethanol groups can bind negative ions Diethylaminoethyl cellulose (DEAE-C) is a positively charged resin used in ion-exchange chromatography, a type of column chromatography, for the separation and purification of proteins and nucleic acids. Gel matrix beads are derivatized with diethylaminoethanol (DEAE) and lock negatively charged proteins or nucleic acids into the matrix. The proteins are released from the resin by increasing the salt concentration of the solvent or changing the pH of the solution as to change the charge on the protein.

Brand, Fischer, Harter, Kohlbacher and Wanke (2013) Elucidating the evolutionary conserved DNA-binding specificities of WRKY transcription factors by molecular dynamics and in vitro binding assays. Nucleic Acids Research. 41(21). 9764-9778 Additionally, contrary to early reports, both WRKY domains of group I family members can bind DNA.Brand, Fischer, Harter, Kohlbacher and Wanke (2013) Elucidating the evolutionary conserved DNA-binding specificities of WRKY transcription factors by molecular dynamics and in vitro binding assays. Nucleic Acids Research. 41(21). 9764-9778 Implications of these results are still being resolved.

The virino was described partially to protect the central dogma of molecular biology, which was threatened by the existence of a series of degenerative neurological TSE diseases including kuru, CJD, scrapie in sheep, and BSE in cattle. The central dogma states that nucleic acids act as the information carriers, and DNA and RNA make proteins. Proteins alone cannot make DNA. However, studies searching for the transmission agent of scrapie and other TSEs have failed to culture bacteria, and tests attacking nucleic acids strands have little effect on the infectivity of TSE solutions.

Immunoaffinity media (detailed below) utilizes antigens' and antibodies' high specificity to separate; immobilized metal affinity chromatography is detailed further below and uses interactions between metal ions and proteins (usually specially tagged) to separate; nucleotide/coenzyme that works to separate dehydrogenases, kinases, and transaminases. Nucleic acids function to trap mRNA, DNA, rRNA, and other nucleic acids/oligonucleotides. Protein A/G method is used to purify immunoglobulins. Speciality media are designed for a specific class or type of protein/co enzyme; this type of media will only work to separate a specific protein or coenzyme.

Negative image of an ethidium bromide-stained DGGE gel Temperature gradient gel electrophoresis (TGGE) and denaturing gradient gel electrophoresis (DGGE) are forms of electrophoresis which use either a temperature or chemical gradient to denature the sample as it moves across an acrylamide gel. TGGE and DGGE can be applied to nucleic acids such as DNA and RNA, and (less commonly) proteins. TGGE relies on temperature dependent changes in structure to separate nucleic acids. DGGE separates genes of the same size based on their different denaturing ability which is determined by their base pair sequence.

Nucleic Acids Research is an open-access peer-reviewed scientific journal published since 1974 by the Oxford University Press. The journal covers research on nucleic acids, such as DNA and RNA, and related work. According to the Journal Citation Reports, the journal's 2019 impact factor is 11.501.. The journal publishes two yearly special issues, the first issue of each year is dedicated to biological databases, published in January since 1993, and the other is devoted to papers describing web-based software resources of value to the biological community (web servers), published in July since 2003.

In living cells, signals are processed by networks of proteins that can act as complex computational devices. These networks rely on the ability of single proteins to exist in a variety of functionally different states achieved through multiple mechanisms, including post-translational modifications, ligand binding, conformational change, or formation of new complexes. Similarly, nucleic acids can undergo a variety of transformations, including protein binding, binding of other nucleic acids, conformational change and DNA methylation. In addition, several types of modifications can co-exist, exerting a combined influence on a biological macromolecule at any given time.

It has been suggested that double-walled "bubbles" of lipids like those that form the external membranes of cells may have been an essential first step. Experiments that simulated the conditions of the early Earth have reported the formation of lipids, and these can spontaneously form liposomes, double-walled "bubbles," and then reproduce themselves. Although they are not intrinsically information-carriers as nucleic acids are, they would be subject to natural selection for longevity and reproduction. Nucleic acids such as RNA might then have formed more easily within the liposomes than they would have outside.

Most organic substances are molecules. The substances of life are molecules, e.g. proteins, the amino acids they are made of, the nucleic acids (DNA & RNA), sugars, carbohydrates, fats, and vitamins. The nutrient minerals ordinarily are not molecules, e.g.

Nucleic acid structure refers to the structure of nucleic acids such as DNA and RNA. Chemically speaking, DNA and RNA are very similar. Nucleic acid structure is often divided into four different levels: primary, secondary, tertiary, and quaternary.

More recently a database that contains all SNPSTRs in five model genomes, including human, has been created.AGRAFIOTI I AND STUMPF MPH (2007) "SNPSTR: a database of compound microsatellite-SNP markers" Nucleic Acids Research 35(Database issue): 71–75.

Damha is a member of the Nicaraguan Academy of Science (2017–present) and President of the International Society of Nucleosides, Nucleotides, Nucleic Acids (IS3NA)(2019-2020). During 2012-2014, Damha served as President of the Oligonucleotide Therapeutic Society.

Electrophoresis is a peer-reviewed scientific journal covering all aspects of electrophoresis, including new or improved analytical and preparative methods, development of theory, and innovative applications of electrophoretic methods in the study of proteins, nucleic acids, and other compounds.

SnpEff has been used for various applicationsMedina, Ignacio, et al. "VARIANT: Command Line, Web service and Web interface for fast and accurate functional characterization of variants found by Next-Generation Sequencing." Nucleic Acids Research 40.W1 (2012): W54-W58.

Thus, it protects the genome from harmful changes induced by chemical and environmental agents. Its crystal structure was described in 2008. It is the first HEAT repeat protein identified to interact with nucleic acids or to contain enzymatic activity.

The Diatom EST Database. Nucleic Acids Research 33: D344-D347. Phaeodactylum tricornutum has emerged as a potential microalgal energy source. It grows rapidly and storage lipids constitute about 20-30% of its dry cell weight under standard culture conditions.

Her work will also lead to prenatal screening and early diagnosis of autism. Penn has been published in Cell, Genome Research, Molecular Biology and Evolution, Nucleic Acids Research, Systematic Biology, BMC Evolutionary Biology, PLoS Computational Biology, Bioinformatics, and Proteins.

J Mol Biol. 1994 Oct 7;242(5):670-82. Electrophoretic characterization of the denatured states of staphylococcal nuclease. Creighton TE, Shortle D. Similar looking patterns are produced by proteins and nucleic acids, but the fundamental principles are quite different.

Wylie T, Martin J, Dante M, Mitreva M, Clifton SC, Chinwalla A, Waterston RH, Wilson RK, McCarter JP. (2004) Nematode.net: a tool for navigating sequences from parasitic and free- living nematodes Nucleic Acids Research. 32 (suppl 1): D423-D426.

A number of factors can affect the migration of nucleic acids: the dimension of the gel pores, the voltage used, the ionic strength of the buffer, and the concentration intercalating dye such as ethidium bromide if used during electrophoresis.

In addition to labelling pure nucleic acids, SYBR Green can also be used for labelling of DNA within cells for flow cytometry and fluorescence microscopy. In these cases RNase treatment may be required to reduce background from RNA in the cells.

Proteins have many different functions. There are proteins that are used for structural support, storage, transport, cellular communication, movement, defense against foreign substances, and more. Nucleic acids transmit and help express hereditary information. They are made up of monomers called nucleotides.

Phosphodiester bonds, when hydrolyzed, release a considerable amount of free energy. Therefore, nucleic acids tend to spontaneously hydrolyze into mononucleotides. The precursors for RNA are GTP, CTP, UTP and ATP, which is a major source of energy in group-transfer reactions.

Organic carbon forms the backbone of key component of organic compounds such as – proteins, lipids, carbohydrates, and nucleic acids. Inorganic carbon is found primarily in simple compounds such as carbon dioxide, carbonic acid, bicarbonate, and carbonate (CO2, H2CO3, HCO3−, CO32− respectively).

WHAT IF is a computer program used in a wide variety of computational (in silico) macromolecular structure research fields. The software provides a flexible environment to display, manipulate, and analyze small and large molecules, proteins, nucleic acids, and their interactions.

In 2015, Jain et. al. described a trans-acting DNA-based amphiphatic delivery system for convenient delivery of poly A tailed uncharged nucleic acids (UNA) such as PNAs and morpholinos, so that several UNA’s can be easily screened ex vivo.

Its true function has yet to be elucidated, but it is a suspected androgen receptor because it is up-regulated in the presence of androgens, but not glucocorticoids.Marchler-Bauer A et al. (2015), "CDD: NCBI's conserved domain database.", Nucleic Acids Res.

To date, there are two main approaches used by scientists to quantitate, or establish the concentration, of nucleic acids (such as DNA or RNA) in a solution. These are spectrophotometric quantification and UV fluorescence tagging in presence of a DNA dye.

Scaffold hopping: exploration of acetanilide-containing uracil analogues as potential NNRTIs. Bioorg Med Chem. 2015;23(5):1069‐1081. # Seley-Radtke KL, Sunkara NK. Carbocyclic thymidine analogues for use as potential therapeutic agents. Nucleosides Nucleotides Nucleic Acids. 2009;28(5):633‐641.

For example, TNA has been evaluated in a model system for antisense technology.Liu, L. S. et al. alpha-l-Threose Nucleic Acids as Biocompatible Antisense Oligonucleotides for Suppressing Gene Expression in Living Cells. ACS Appl Mater Interfaces 10, 9736-9743, (2018).

Zinc finger proteins (ZNFs), such as ZNF101, bind nucleic acids and perform many key functions, the most important of which is regulating transcription (summary by Bellefroid et al., 1993 [PubMed 8467795]). See ZNF91 (MIM 603971) for general information on ZNFs.

Hierarchically clustered heat map using aa-dUTPs The goal of combining fluorescence and nucleic acids has been to provide a non-isotopic tag that is detectable to study DNA or RNA. This type of labeling allows scientists to study DNA or RNA in their structure, function, or formation with other nucleic acids. The first base modification for fluorescent labeling occurred in 1971 with a 4-thiouridine and 4-thiouracil. This research along with others, which included various types of direct and non-direct labeling via: analogs, addition via enzymes, or other methods made labeling of nucleotides much safer for scientist to study DNA.

Nucleic acid structures can be made to incorporate molecules other than nucleic acids, sometimes called heteroelements, including proteins, metallic nanoparticles, quantum dots, and fullerenes. This allows the construction of materials and devices with a range of functionalities much greater than is possible with nucleic acids alone. The goal is to use the self-assembly of the nucleic acid structures to template the assembly of the nanoparticles hosted on them, controlling their position and in some cases orientation.Overview: Many of these schemes use a covalent attachment scheme, using oligonucleotides with amide or thiol functional groups as a chemical handle to bind the heteroelements.

CRISPR associated nucleases have shown to be useful as a tool for molecular testing due to their ability to specifically target nucleic acid sequences in a high background of non-target sequences. In 2016, the Cas9 nuclease was used to deplete unwanted nucleotide sequences in next-generation sequencing libraries while requiring only 250 picograms of initial RNA input. Beginning in 2017, CRISPR associated nucleases were also used for direct diagnostic testing of nucleic acids, down to single molecule sensitivity. By coupling CRISPR-based diagnostics to additional enzymatic processes, the detection of molecules beyond nucleic acids is possible.

A satellite is a subviral agent that depends on the coinfection of a host cell with a helper virus for its replication. Satellites can be divided into two major classes: satellite viruses and satellite nucleic acids. Satellite viruses, which are most commonly associated with plants, but are also found in mammals, arthropods, and bacteria, encode structural proteins to enclose their genetic material, which are therefore distinct from the structural proteins of their helper viruses. Satellite nucleic acids, in contrast, do not encode their own structural proteins, but instead are encapsulated by proteins encoded by their helper viruses.

In the biological sciences, nitrogenous bases are increasingly termed nucleobases because of their role in nucleic acids - their flat shape is particularly important when considering their roles as the building blocks of DNA and RNA. A set of five nitrogenous bases is used in the construction of nucleotides, which in turn build up nucleic acids like DNA and RNA. These nitrogenous bases are adenine (A), uracil (U), guanine (G), thymine (T), and cytosine (C). Thymine and uracil are distinguished by merely the presence or absence of a methyl group on the fifth carbon (C5) of these heterocyclic six-membered rings.

Structure of molecular beacons in their native conformations (top) or hybridized with a DNA strand (bottom) Molecular beacons, or molecular beacon probes, are oligonucleotide hybridization probes that can report the presence of specific nucleic acids in homogenous solutions. Molecular beacons are hairpin-shaped molecules with an internally quenched fluorophore whose fluorescence is restored when they bind to a target nucleic acid sequence. This is a novel non-radioactive method for detecting specific sequences of nucleic acids. They are useful in situations where it is either not possible or desirable to isolate the probe-target hybrids from an excess of the hybridization probes.

Polyvalent DNA gold nanoparticles, now more commonly referred to as spherical nucleic acids,Cutler, J. I.; Auyeung, E.; Mirkin, C. A. “Spherical Nucleic Acids,” Journal of the American Chemical Society, 2012, 134, 1376–1391, doi: 10.1021/ja209351u. (Fig. 1) are colloidal gold particles densely modified with short (typically ~30-mer or less), highly oriented, synthetic DNA strands. They were invented by Chad Mirkin et al. at Northwestern University in 1996.Mirkin, C. A.; Letsinger, R. L.; Mucic, R. C; Storhoff, J. J. “A DNA- based method for rationally assembling nanoparticles into macroscopic materials,” Nature, 1996, 382, 607-609, doi: 10.1038/382607a0.

A depiction of the genetic code, by which the information contained in nucleic acids are translated into amino acid sequences in proteins. In biological systems, nucleic acids contain information which is used by a living cell to construct specific proteins. The sequence of nucleobases on a nucleic acid strand is translated by cell machinery into a sequence of amino acids making up a protein strand. Each group of three bases, called a codon, corresponds to a single amino acid, and there is a specific genetic code by which each possible combination of three bases corresponds to a specific amino acid.

One of the more commonly used practices to quantitate DNA or RNA is the use of spectrophotometric analysis using a spectrophotometer. A spectrophotometer is able to determine the average concentrations of the nucleic acids DNA or RNA present in a mixture, as well as their purity. Spectrophotometric analysis is based on the principles that nucleic acids absorb ultraviolet light in a specific pattern. In the case of DNA and RNA, a sample is exposed to ultraviolet light at a wavelength of 260 nanometres (nm) and a photo-detector measures the light that passes through the sample.

Next a series of chemical treatments must be applied to achieve transparency, in which the lipid content of the sample is removed, while almost all of the original proteins and nucleic acids are left in place. The purpose of this is to make the tissue transparent and thus amenable to detailed microscopic investigation of its constituent functional parts (which are predominantly proteins and nucleic acids). To accomplish this, the preexisting protein structure has to be placed in a transparent scaffolding which preserves it, while the lipid components are removed. This 'scaffolding' is made up of hydrogel monomers such as acrylamide.

The general chemical formula of an unmodified monosaccharide is (C•H2O)n, literally a "carbon hydrate". Monosaccharides are important fuel molecules as well as building blocks for nucleic acids. The smallest monosaccharides, for which n=3, are dihydroxyacetone and D- and L-glyceraldehydes.

Nucleic Acids Research, 1994. 22(24): p. 5204-5210.Odegrip, R. and E. Haggård-Ljungquist, The two active-site tyrosine residues of the A protein play non-equivalent roles during initiation of rolling circle replication of bacteriophage P2. Journal of Molecular Biology, 2001.

139 : 1635-1648. Nitrogen is found in chlorophyll and is often a limiting nutrient for plants because plants need large quantities of N to form amino acids, nucleic acids, proteins, and certain plant hormones.Hopkins, W.G. and N.P.A. Huner. 2009. Introduction to Plant Physiology.

Feigon's research specializes in nuclear magnetic resonance spectroscopy (NMR) studies of the structure and dynamics of nucleic acids. Her research group has invested significant effort in determining the structure of telomerase, using NMR, X-ray crystallography, and more recently cryo-electron microscopy.

Biological databases are stores of biological information. The journal Nucleic Acids Research regularly publishes special issues on biological databases and has a list of such databases. The 2018 issue has a list of about 180 such databases and updates to previously described databases.

Nucleic Acids Res. 2003 Oct 15;31(20):5877-85. # Aravin AA, Lagos-Quintana M, Yalcin A, Zavolan M, Marks D, Snyder B, Gaasterland T, Meyer J, Tuschl T. The small RNA profile during D. melanogaster development. Dev Cell. 2003 5(2):337-50.

In Kaplan's lab, working with lactate and malate dehydrogenases, Wilson was first introduced to the nascent field of molecular evolution.A.C.Wilson and N.O.Kaplan (1963) Enzymes and nucleic acids in systematics. Proceedings of the XVI International Congress of Zoology Vol.4, pp.125–127.

Several labs have reported sequence-specific polymerization of peptide nucleic acids from DNA or RNA templates. Liu and coworkers used these polymerization methods to evolve functional PNAs with the ability to fold into three-dimensional structures, similar to proteins, aptamers and ribozymes.

The phosphorus from the male ejaculate is incorporated into the female ovaries and traceable in RNA and DNA. Inside the female, phosphorus is then used to synthesize nucleic acids necessary in egg production. Reduced phosphorus levels in mature female diets slowed oogenesis.

The Biological Magnetic Resonance Data Bank (BioMagResBank or BMRB) is sponsored by the Department of Biochemistry at the University of Wisconsin–Madison; it is dedicated to Proteins, Peptides, Nucleic Acids, and other Biomolecules. It stores a large variety of raw NMR data.

According to the University of Nevada, Reno's official website, Czarnik's research interests include "chemical product improvement using deuterium substitution, combinatorial chemistry as a tool for drug discovery, nucleic acids as targets for small molecule intervention, and fluorescent chemosensors of ion and molecule recognition".

P. and Wolfe-Simon,F. Signatures of a Shadow Biosphere (2009) Astrobiology. 9(2): 241-249. . having a different genetic code, or even another kind of chemical for its genetic material that are not nucleic acids (DNA nor RNA) chains or biopolymers.

CCDC37 has a predicted nuclear localization via Reinhard's methodA. Reinhardt and T. Hubbard, Nucleic Acids Res. 26, 2230, 1998 (reliability 94.1%) using a bipartite nuclear localization signal peptide starting at amino acid 155: KRQMFLLQYALDVKRRE.Dingwall C, Robbins J, Dilworth SM, Roberts B, Richardson WD (Sep 1988).

Nucleic Acids Res 2008; 36:2219-29.He N, Jahchan NS, Hong E, Li Q, Bayfield MA, Maraia RJ, et al. A La-related protein modulates 7SK snRNP integrity to suppress P-TEFb-dependent transcriptional elongation and tumorigenesis. Mol Cell 2008; 29:588-99.

BEI is very hazardous since it attacks nucleic acids and proteins as described above. It can be neutralised by sodium thiosulfate; the thiosulfate is a nucleophile which opens the three-membered ring. The presence of BEI can be tested for using silver nitrate solution.

In biochemistry, a ribonucleotide is a nucleotide containing ribose as its pentose component. It is considered a molecular precursor of nucleic acids. Nucleotides are the basic building blocks of DNA and RNA. The monomer itself from ribonucleotides forms the basic building blocks for RNA.

Amino acids are the building blocks of protein. Amino acids are necessary nutrients. Present in every cell, they are also precursors to nucleic acids, co-enzymes, hormones, immune response, repair and other molecules essential for life. Proteins are essential nutrients for the human body.

Zinc-finger proteins bind nucleic acids and play important roles in various cellular functions, including cell proliferation, differentiation, and apoptosis. This gene encodes a zinc-finger protein, and belongs to the Krüppel C2H2-type zinc-finger protein family. It may be involved in transcriptional regulation.

This work became later the basis for his development of the genetic fingerprinting technology that is nowadays used in paternity testing, forensics and population geneticsTautz, D. (1989). Hypervariability of simple sequences as a general source for polymorphic DNA markers. Nucleic Acids Research, 17, 6463-6471.

Nucleic Acids Res 36:D768. To facilitate use of the zebrafish as a model of human biology, ZFIN links these data to corresponding information about other model organisms (e.g., mouse) and to human disease databases.The Zebrafish Database Project Abundant links to external sequence databases (e.g.

Rockport virus was first isolated in archival tissues of four Eastern moles found in and around Rockport, Texas.Hall T. A. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp. Ser. (Oxf.) 41:95–98.

C1orf198 has the highest composition of serine, glutamic acid, proline, alanine, and arginine; It has the lowest composition of histidine. Relative to the average human protein, C1orf198 is serine-rich, proline-rich, and tyrosine-poor.B. Rost, J. Liu, The PredictProtein server. Nucleic Acids Res.

Taking the cell culture example, a hyperspectral image could show the distribution of cholesterol, as well as proteins, nucleic acids, and fatty acids. Sophisticated signal- and image-processing techniques can be used to ignore the presence of water, culture media, buffers, and other interference.

Nematode.net is a publicly available resource dedicated to the study of parasitic nematodes.Martin J, Abubucker S, Heizer E, Taylor CM, Mitreva M. (2012) Nematode.net update 2011: addition of data sets and tools featuring next-generation sequencing data. "Nucleic Acids Research." 40 (Database issue): D720-D728.

Macromolecular components of respiratory secretions (proteins, glycoproteins, lipids, nucleic acids) are converted to nutrients (e.g. carbohydrates, amino acids). Thus, the metabolic activity of present bacteria allow for the colonization of new species. The commensal bacteria are nonpathogenic and defend our airways against the pathogens.

Exosomes contain different cargoes; proteins, lipids, and nucleic acids. These cargoes are specifically sorted and packaged into exosomes. The contents packaged into exosomes are cell type specific and also influenced by cellular conditions. Exosomal microRNAs (exomiRs) and proteins are sorted and packaged in exosomes.

For this reason, the nucleic acid sequence is also termed the primary structure. The sequence has capacity to represent information. Biological deoxyribonucleic acid represents the information which directs the functions of a living thing. Nucleic acids also have a secondary structure and tertiary structure.

For example, high energy metabolites such as ATP and PEP are alkyl phosphates, as are nucleic acids such as DNA and RNA. Alkyl phosphates are also important medicinally, for example the HIV drug AZT is inactive until it becomes an alkyl phosphate in vivo.

They target molecules such as phospholipids, nucleic acids, and ATP. Class B metals are metals that form soft acids. Soft acids are acids with relatively covalent bonds. These metals, such as lead, gold, palladium, platinum, mercury, and rhodium, would rather bond with iodine than fluorine.

The catalytic conversion of uridine triphosphate (UTP) to cytidine triphosphate (CTP) is accomplished by the enzyme cytidine-5-prime-triphosphate synthetase. This enzyme is important in the biosynthesis of phospholipids and nucleic acids, and plays a key role in cell growth, development, and tumorigenesis.

While most flow cytometers do not have sufficient sensitivity, there are a few commercially available flow cytometers that can be used for virus quantification. A virus counter quantifies the number of intact virus particles in a sample using fluorescence to detect colocalized proteins and nucleic acids. Samples are stained with two dyes, one specific for proteins and one specific for nucleic acids, and analyzed as they flow through a laser beam. The quantity of particles producing simultaneous events on each of the two distinct fluorescence channels is determined, along with the measured sample flow rate, to calculate a concentration of virus particles (vp/mL).

Despite the primary distribution method at the time being via magnetic tape, by 1987, the EMBL Data Library was being used by an estimated 10,000 scientists internationally. The same year, the EMBL File Server was introduced to serve database records over BITNET, EARN and the early Internet. In May 1988 the journal Nucleic Acids Research introduced a policy stating that "manuscripts submitted to [Nucleic Acids Research] and containing or discussing sequence data must be accompanied by evidence that the data have been deposited with the EMBL Data Library." The EBI at the Wellcome Trust Genome Campus in Hinxton, UK which hosts the European Nucleotide Archive.

Digital polymerase chain reaction (digital PCR, DigitalPCR, dPCR, or dePCR) is a biotechnological refinement of conventional polymerase chain reaction methods that can be used to directly quantify and clonally amplify nucleic acids strands including DNA, cDNA, or RNA. The key difference between dPCR and traditional PCR lies in the method of measuring nucleic acids amounts, with the former being a more precise method than PCR, though also more prone to error in the hands of inexperienced users. A "digital" measurement quantitatively and discretely measures a certain variable, whereas an “analog” measurement extrapolates certain measurements based on measured patterns. PCR carries out one reaction per single sample.

Transient expression, more frequently referred to "transient gene expression", is the temporary expression of genes that are expressed for a short time after a nucleic acid, most frequently plasmid DNA encoding an expression cassette, has been introduced into eukaryotic cells. The majority of transient gene expressions are done with cultivated animal cells. The technique is also used in plant cells; however, the transfer of nucleic acids into these cells requires different methods than those with animal cells. In both plants and animals, transient expression should result in a time-limited use of transferred nucleic acids, since any long-term expression would be called "stable expression".

Typically the analogue nucleobases confer, among other things, different base pairing and base stacking properties. Examples include universal bases, which can pair with all four canonical bases, and phosphate-sugar backbone analogues such as PNA, which affect the properties of the chain (PNA can even form a triple helix). Nucleic acid analogues are also called Xeno Nucleic Acid and represent one of the main pillars of xenobiology, the design of new-to-nature forms of life based on alternative biochemistries. Artificial nucleic acids include peptide nucleic acid (PNA), Morpholino and locked nucleic acid (LNA), as well as glycol nucleic acid (GNA), threose nucleic acid (TNA) and hexitol nucleic acids (HNA).

These chain-joins of sugar and phosphate molecules create a 'backbone' strand for a single- or double helix. In any one strand, the chemical orientation (directionality) of the chain-joins runs from the 5'-end to the 3'-end (read: 5 prime-end to 3 prime-end)—referring to the five carbon sites on sugar molecules in adjacent nucleotides. In a double helix, the two strands are oriented in opposite directions, which permits base pairing and complementarity between the base-pairs, all which is essential for replicating or transcribing the encoded information found in DNA. Nucleic acids then are polymeric macromolecules assembled from nucleotides, the monomer-units of nucleic acids.

In biological systems, oxocarbenium ions are mostly seen during reactions of carbohydrates. Since sugars are present in the structure of nucleic acids, with a ribose sugar present in RNA and a deoxyribose present in the structure of DNA, their chemistry plays an important role in wide range of cellular functions of nucleic acids. In addition to their functions in nucleotides, sugars are also used for structural components of organisms, as energy storage molecules, cell signaling molecules, protein modification and play key roles in the immune system, fertilization, preventing pathogenesis, blood clotting, and development. The abundance of sugar chemistry in biological processes leads many reaction mechanisms to proceed through oxocarbenium ions.

This pathogen reduction process involves adding riboflavin (vitamin B2) to the blood component, which is then placed into an illuminator where it is exposed to UV light for about five to ten minutes. Exposure to UV light activates riboflavin and when it is associated with nucleic acids (DNA and RNA), riboflavin causes a chemical alteration to functional groups of the nucleic acids thereby making pathogens unable to replicate. In this way the process prevents viruses, bacteria, parasites and white blood cells, from replicating and causing disease. :::::::UV Light + Riboflavin → Irreversible Inactivation This method using riboflavin and UV light renders pathogens harmless by using a non-mutagenic, non-toxic method.

These constraints stem from the basic structure of nucleic acids, mainly that the double helix formed by nucleic acid duplexes has a fixed helicity of about 10.4 base pairs per turn, and is relatively stiff. Because of these constraints, the nucleic acid complexes are sensitive to the relative orientation of the major and minor grooves at junction points. Geometrical modeling can detect strain stemming from misalignments in the structure, which can then be corrected by the designer. Geometric models of nucleic acids for DNA nanotechnology generally use reduced representations of the nucleic acid, because simulating every atom would be very computationally expensive for such large systems.

1982 Apr;121(2):382-7. This was later improved using guanidinium thiocyanate or guanidinium hydrochloride as the chaotropic agent.Boom R, Sol CJ, Salimans MM, Jansen CL, Wertheim-van Dillen PM, van der Noordaa J. Rapid and simple method for purification of nucleic acids. J Clin Microbiol.

Erdeniz N., Mortensen UH., Rothstein R. (1997) Cloning-free PCR-based allele replacement methods. Genome Res. 7:1174-83.Langle-Rouault F., Jacobs E. (1995) A method for performing precise alterations in the yeast genome using a recyclable selectable marker. Nucleic Acids Res. 23:3079-81.

Cancer mutanomes can be defined by comparing exome sequencing data obtained by NGS of individual healthy tissue with sequences from tumor-derived nucleic acids. As the vast majority of cancer- associated mutations are patient specific, shared mutations are rare, even within the same type of cancer.

Homeobox protein notochord (NOTO) is a transcription factorThe UniProt Consortium; UniProt: the universal protein knowledgebase. Nucleic Acids Res 2017; 45 (D1): D158-D169. doi: 10.1093/nar/gkw1099. encoded by the gene notochord homeobox (NOTO) located on the short arm of chromosome 2 (2p13.2) in humans (Homo sapiens).

PMAP integrates five databases. ProteaseDB and SubstrateDB, are driven by an automated annotation pipeline that generates dynamic ‘Molecule Pages’, rich in molecular information. CutDBIgarashi Y, Eroshkin A, Gramatikova S, Gramatikoff K, Zhang Y, Smith JW, Osterman AL, Godzik A. CutDB: a proteolytic event database. Nucleic Acids Research.

Presently, some of the agents used in the fixation process include two variations of formaldehyde (formalin and paraformaldehyde), 70% ethanol, glutaraldehyde and TCA. It is presumed that the best fixation agent for protein and nucleic acids is paraformaldehyde due to its ability to swiftly enter cells.

Drude particles are model oscillators used to simulate the effects of electronic polarizability in the context of a classical molecular mechanics force field. They are inspired by the Drude model of mobile electrons and are used in the computational study of proteins, nucleic acids, and other biomolecules.

These domains contain a few basic modular units. Comparing with a single motif, RBPs can recognize a much longer stretch of nucleic acids with those multiple motifs. Meanwhile, RBPs bind to RNA by forming weak interactions. The weak interaction surface is largely increased by these motifs.

D. P. Malenov, G. V. Janjić, D. Ž. Veljković, S. D. Zarić, "Mutual influence of parallel, CH/O, OH/π and lone pair/π interactions in water/benzene/water system", Computational and Theoretical Chemistry, (2013), vol. 1018, 59 - 65. DOI: 10.1016/j.comptc.2013.05.030 and nucleic acids.

The focus of his research is on developing methods for controlling the architecture of molecules and materials on the 1 – 100 nm length scale and utilizing such structures in the development of analytical tools that can be used in the areas of chemical and biological sensing, lithography, catalysis, and optics. Mirkin has pioneered the use of DNA and nanoparticles as synthons in materials science and the development of nanoparticle-based biodiagnostics. A common strategy used by Mirkin's group is the use of the unique properties of spherical nucleic acids (SNAs), spherical arrangements of nucleic acids with or without organic or inorganic nanoparticle cores, to enable the synthesis of novel materials and colloidal crystals, the development of high sensitivity probes for chemical and medical diagnostic purposes, and single-entity structures capable of intracellular gene regulation. His 1996 work with SNA-gold nanoparticle conjugates introduced the concept of a nanoparticle as an atom and nucleic acids as bonds, and it laid the ground work for the fields of colloidal crystal engineering with DNA and molecular diagnostics based upon well-defined nanoparticle and nanocrystal bioconjugates.

SNA properties, such as enhanced cellular uptake, multivalent binding, and endosomal delivery, are desirable for the delivery of immunomodulatory nucleic acids. In particular, SNAs have been used deliver nucleic acids that agonize or antagonize toll-like receptors (proteins involved in innate immune signaling). The use of immunostimulatory SNAs has been shown to result in an 80-fold increase in potency, 700-fold higher antibody titers, 400-fold higher cellular responses to a model antigen, and improved treatment of mice with lymphomas compared to free oligonucleotides (not in SNA form).Radovic-Moreno, A. F.; Chernyak, N.; Mader, C. C.; Nallagatla, S.; Kang, R.; Hao, L.; Walker, D. A.; Halo, T. L.; Merkel, T. J.; Rische, C.; Ananatatmula, S.; Burkhart, M.; Mirkin, C. A.; Gryaznov, S. M. “Immunomodulatory Spherical Nucleic Acids,” Proc. Natl. Aca. Sci. USA, 2015, 112, 3892-3897, doi: 10.1073/pnas.1502850112. SNAs have also been used by Mirkin to introduce the concept of “rational vaccinology,” that the chemical structure of an immunotherapy, as opposed to just the components alone, dictates its efficacy.

Jennifer Margaret Heemstra (née Cary) is an Associate Professor of Chemistry at Emory University. Her research makes use of the ability of nucleic acids to self-assemble and recognise other molecules. Alongside her research, Heemstra is a science communicator and writes a regular column for Chemical & Engineering News.

Xenarios I, Salwinski L, Duan XJ, Higney P, Kim SM, et al. (2002). "Dip, the database of interacting proteins: a research tool for studying cellular networks of protein interactions". Nucleic Acids Res 30: 303–305.Farkas IJ, Korcsmaros T, Kovacs IA, Mihalik A, Palotai R, et al. (2011).

When purifying protein from a biological extract, streptomycin sulfate is sometimes added as a means of removing nucleic acids. Since it binds to ribosomes and precipitates out of solution, it serves as a method for removing rRNA, mRNA, and even DNA if the extract is from a prokaryote.

66 (1997). Gel electrophoresis of large DNA or RNA is usually done by agarose gel electrophoresis. See the "Chain termination method" page for an example of a polyacrylamide DNA sequencing gel. Characterization through ligand interaction of nucleic acids or fragments may be performed by mobility shift affinity electrophoresis.

Hung, Mien-Chie, and Pieter C. Wensink. "Different Restriction Enzyme- generated Sticky DNA Ends Can Be Joined in Vitro." Nucleic Acids Research 12.4 (1984): 1863-874. Print. For this reason, most restriction enzymes used in DNA cloning make staggered cuts in the DNA strands to create sticky ends.

Genus can be also calculated for the graph spanned by the net of chemical interactions in nucleic acids or proteins. In particular, one may study the growth of the genus along the chain. Such a function (called the genus trace) shows the topological complexity and domain structure of biomolecules.

Because the specific proteins, mRNAs, and miRNAs in microvesicles are highly variable, it is likely that these molecules are specifically packaged into vesicles using an active sorting mechanism. At this point, it is unclear exactly which mechanisms are involved in packaging soluble proteins and nucleic acids into microvesicles.

Nucleotides serve as the building blocks for nucleic acids, DNA and RNA. They are composed of a nitrogenous base, a pentose sugar, and at least one phosphate group. Nucleotides contain either a purine or a pyrimidine nitrogenous base. All intermediates in purine biosynthesis are constructed on a R5P "scaffold".

Version 2.0 was released in 2001 and included the capability to link to information available in other databases. Version 3.0 (2002) expanded the database from physical/biochemical interactions to also include genetic interactions.Bader, GD, et al.. BIND: the Biomolecular Interaction Network Database. Nucleic Acids Research 31: 248-250 (2003).

Multiscale modeling or multiscale mathematics is the field of solving problems which have important features at multiple scales of time and/or space. Important problems include multiscale modeling of fluids, solids, polymers, proteins, nucleic acids as well as various physical and chemical phenomena (like adsorption, chemical reactions, diffusion).

He is also involved in the development of the Cellosaurus a knowledge resource on cell lines. According to Google Scholar and Scopus, his most highly cited peer reviewed papers in scientific journals have been published in Nucleic Acids Research, the Biochemical Journal, Nature, Briefings in Bioinformatics, and Database.

NaOH) have been shown to denature DNA by changing pH and removing hydrogen-bond contributing protons. These denaturants have been employed to make Denaturing Gradient Gel Electrophoresis gel (DGGE), which promotes denaturation of nucleic acids in order to eliminate the influence of nucleic acid shape on their electrophoretic mobility.

The BMRB has archived sets of raw time-domain data collected from NMR experiments carried out to calculate restraints and chemical shifts in peptides, proteins and nucleic acids. This collection contains over 200 entries and in many cases the pulse-sequences and the acquisition parameters used are also available.

His research area concerns the structural biology of nucleic acids (stereochemistry, topology, modelling and bioinformatics) and especially ribonucleic acid molecules (RNA). He has developed computer tools dedicated to crystallographic refinement and computer manipulation of nucleic acids.Westhof E, et al., « Crystallographic Refinement of Yeast Aspartic Transfer RNA, », J. Mol. Biol.

Proc. Natl. Acad. Sci. USA 94, pp. 8928-8935 He also developed the now popular His-tag expression system,Hoffmann, A. and Roeder, R.G. 1991. Purification of his-tagged proteins in non-denaturing conditions suggests a convenient method for protein interaction studies. Nucleic Acids Research 19, No.22, pp.

Vitamin C and other reducing agents combine with chromate to give chromium(III) products inside the cell. The resultant chromium(III) forms stable complexes with nucleic acids and proteins. This causes strand breaks and Cr–DNA adducts which are responsible for mutagenic damage. According to Shi et al.

A heteroduplex is a double-stranded (duplex) molecule of nucleic acid originated through the genetic recombination of single complementary strands derived from different sources, such as from different homologous chromosomes or even from different organisms. One such example is the heteroduplex DNA strand formed in hybridization processes, usually for biochemistry-based phylogenetic analyses. Another is the heteroduplexes formed when non-natural analogs of nucleic acids are used to bind with nucleic acids; these heteroduplexes result from performing antisense techniques using single- stranded peptide nucleic acid, 2'-O-methyl phosphorothioate or Morpholino oligos to bind with RNA. In meiosis, the process of crossing-over occurs between non-sister chromatids, which results in new allelic combinations in the gametes.

In later years, Stroun promoted the development and validation through large clinical studies of cancer diagnostics based on circulating nucleic acid detection. Stroun and Anker would later set up a company, OncoXL, in Geneva to commercialize a cancer diagnostic test, or liquid biopsy, as it later become known, based on the fruits of their multiple decades of research into circulating nucleic acids. In 2005, Stroun’s semi-forgotten pioneering work in circulating nucleic acids was later acknowledged in a compilation of scientists that gave rise to various groundbreaking fields. Maurice Stroun currently serves as an advisor to Guardant Health, a company that has commercialized a comprehensive liquid biopsy based on circulating DNA in peripheral blood.

Natural DNA is a molecule carrying the genetic instructions used in the growth, development, functioning, and reproduction of all known living organisms and many viruses. DNA and ribonucleic acid (RNA) are nucleic acids; alongside proteins, lipids and complex carbohydrates (polysaccharides), nucleic acids are one of the four major types of macromolecules that are essential for all known forms of life. DNA is a polynucleotide as it is composed of simpler monomeric units called nucleotides; when double-stranded, the two chains coil around each other to form a double helix. In natural DNA, each nucleotide is composed of one of four nucleobases (cytosine [C], guanine [G], adenine [A] or thymine [T]), a sugar called deoxyribose, and a phosphate group.

Silica in a spin column with water and with DNA sample in chaotropic buffer Spin column-based nucleic acid purification is a solid phase extraction method to quickly purify nucleic acids. This method relies on the fact that nucleic acid will bind to the solid phase of silica under certain conditions.

Heemstra is working on new approaches to monitor RNA editing, through the use of fluorescence labelling, as well as ways to manipulate these modifications for genetic engineering. She has worked on threose nucleic acids (TNAs) which can be used to confer genetic information and in the detection of small molecule toxins.

MUltiple Sequence Comparison by Log-Expectation (MUSCLE) is computer software for multiple sequence alignment of protein and nucleotide sequences. It is licensed as public domain. The method was published by Robert C. Edgar in two papers in 2004. The first paper, published in Nucleic Acids Research, introduced the sequence alignment algorithm.

Bombyx huttoni, or the chocolate-tipped silk moth, is a moth belonging to the silk moth family, Bombycidae.Bombyx huttoni in "UniProt: a worldwide hub of protein knowledge", Nucleic Acids Res. 47: D506–515 (2019) at [www.uniprot.org The UniProt Consortium] It is closely related to the domestic silk moth (Bombyx mori).

One specific three dimensional structure that is commonly observed in rRNA is the A-minor motif. There are four types of A-minor motifs, all of which include many unpaired adenosines. These lone adenosines extend from outward and allow RNA molecules to bind other nucleic acids in the minor groove.

Desalting is used to remove salts from protein solutions, phenol or unincorporated nucleotides from nucleic acids or excess crosslinking or labeling reagents from conjugated proteins. Buffer exchange is used to transfer a protein solution into a buffer system appropriate for downstream applications such as ion exchange, electrophoresis or affinity chromatography.

Aclara received 96 patents during its history. Its best-known product was its proprietary eTag (short for "electrophoretic tag") assay technology designed for use on proteins and nucleic acids. In October 2004, Aclara entered into an arrangement with GlaxoSmithKline to test these assays for potential use in cancer drug development.

TAE buffer is a buffer solution containing a mixture of Tris base, acetic acid and EDTA. In molecular biology it is used in agarose electrophoresis typically for the separation of nucleic acids such as DNA and RNA.Ogden, R.C., and Adams, D.A., (1987) Electrophoresis in agarose and acrylamide gels. Methods Enzymol.

Tautz's research covers a broad interest area in the fields of molecular evolution and developmental genetics. His thesis dealt with the first generic description of simple sequences (now often called microsatellites). Tautz, D., Renz, M. (1984). Simple sequences are ubiquitous repetitive components of eukaryotic genomes. Nucleic Acids Research, 12, 4127-4138.

Emil Paleček (3 October 1930 – 30 October 2018) was a Czech biochemist, who researched how DNA can be used to diagnose genetic diseases. Paleček discovered that nucleic acids could be analysed by electrochemical research, contradicting previous assumptions from the 1950s that DNA molecules were too large to be affected by electrochemistry.

Saenger (1984), p. 84. Structural elements of common nucleic acid constituents. Because they contain at least one phosphate group, the compounds marked nucleoside monophosphate, nucleoside diphosphate and nucleoside triphosphate are all nucleotides (not simply phosphate-lacking nucleosides). The most common nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA).

Common methods of DNA extraction include Phenol, Chelex, Silica, and Magnetic beads. The Phenol process is toxic and is "not open to automation". This method is primarily used to extract, from the cells, the nucleic acids necessary for purification. The Chelex process is safe and is "not open to automation".

The expression of CD16a and CD32a in a subset of activated CD4+ T cells is now confirmed. FcRs on the cell surface upon binding to ICs composed of nucleic acids trigger cytokine production and upregulate nucleic acid sensing pathways. FcRs are present both on the cell surface and in the cytosol.

Heterocycles are commonly found in a wide range of products including aniline dyes and medicines. Additionally, they are prevalent in a wide range of biochemical compounds such as alkaloids, vitamins, steroids, and nucleic acids (e.g. DNA, RNA). Rings can fuse with other rings on an edge to give polycyclic compounds.

The American Society for Neurochemistry (ASN) is a professional society for neurochemists and neuroscientists from North, Central, and South America and the Caribbean, whose research concerns the role and interactions of small molecules (proteins, peptides, nucleic acids, lipids, sugars) in the development, growth, function, and pathology of the nervous system.

Nifurtimox forms a nitro- anion radical metabolite that reacts with nucleic acids of the parasite causing significant breakdown of DNA. Its mechanism is similar to that proposed for the antibacterial action of metronidazole. Nifurtimox undergoes reduction and creates oxygen radicals such as superoxide. These radicals are toxic to T. cruzi.

Protein quaternary structure is the number and arrangement of multiple folded protein subunits in a multi-subunit complex. It includes organizations from simple dimers to large homooligomers and complexes with defined or variable numbers of subunits. It can also refer to biomolecular complexes of proteins with nucleic acids and other cofactors.

Circuit topology relations in a chain with two binary contacts. The circuit topology of a linear polymer refers to arrangement of its intra-molecular contacts. Examples of linear polymers with intra-molecular contacts are nucleic acids and proteins. For defining the circuit topology, contacts are defined depending on the context.

R.W. Li), Nova Science Publishers, p.61-78.Solovyev VV, Shahmuradov IA, Salamov AA. (2010) Identification of promoter regions and regulatory sites. Methods Mol. Biol. 674, 57-83.Shahmuradov I, V. V. Solovyev and A. J. Gammerman (2005) Plant promoter prediction with confidence estimation. Nucleic Acids Research 33(3):1069-1076.

He then began his independent career at Yale University. Among his major accomplishments is the discovery of riboswitches. His current research is focused on understanding advanced functions of nucleic acids, including the discovery and analysis of riboswitches and ribozymes. He has been a Howard Hughes Medical Institute (HHMI) Investigator since 2005.

Connolly M. (1983) Solvent-accessible surfaces of proteins and nucleic acids. Science 221:709-713 Chakravarty S, Varadarajan R. (1999) Residue depth: a novel parameter for the analysis of protein structure and stability. Structure Fold. Des. 7:723-732. Pintar A, Carugo O, Pongor S. (2003) Atom depth in protein structure and function.

Several systems have been proposed which combine MRI capability with lanthanides probes in dual assays. The luminescent probe may for instance serve to localize the MRI contrast agent. This has helped to visualize the delivery of nucleic acids into cultured cells. Lanthanides are not used for their fluorescence but their magnetic qualities.

In virology, the International Committee on Taxonomy of Viruses's virus classification includes fifteen taxa: realm, subrealm, kingdom, subkingdom, phylum, subphylum, class, subclass, order, suborder, family, subfamily, genus, subgenus, and species, to be applied for viruses, viroids and satellite nucleic acids. There are currently fourteen viral orders, each ending in the suffix -virales.

Contrary to early assumptions that ethylenimines only modified nucleic acids, it was found that trimeric ethylenimine also alters proteins in virus preparations, especially at higher pH values. The modification of the proteins affected viral particle uptake into cells. This should be taken into consideration when using BEI and other ethyleneimines as well.

Common uses for this carbodiimide include peptide synthesis, protein crosslinking to nucleic acids, but also in the preparation of immunoconjugates. EDC is often used in combination with N-hydroxysuccinimide (NHS) for the immobilisation of large biomolecules. Recent work has also used EDC to assess the structure state of uracil nucleobases in RNA.

3-Deoxyglucosone, a common RCS, rapidly reacts with protein amino groups to form AGEs. Reactive carbonyl species (RCS) are molecules with highly reactive carbonyl groups, and often known for their damaging effects on proteins, nucleic acids, and lipids. They are often generated as metabolic products. Important RCSs include 3-deoxyglucosone, glyoxal, and methylglyoxal.

Research work by the faculty has led to several publications in international journals such as Cell, Nature Biotechnology, Nucleic Acids Research, PLoS One, Journal of Medicinal Chemistry, Journal of Biological Chemistry, BMC Genomics, Bioinformatics, Drug Discovery Today and FEBS Journal. It has also led to bioinformatics tools, such as ExPrimer for primer design.

The first are dehydration synthesis reactions; these involve the joining of smaller molecules together to form larger, more complex molecules. These include the formation of carbohydrates, proteins, lipids and nucleic acids. The second are reduction reactions, in which hydrogens and electrons are added to a molecule. Whenever that is done, molecules gain energy.

Unlike NAPPA, PISAHe, M. and M. J. Taussig (2001). "Single step generation of protein arrays from DNA by cell-free expression and in situ immobilisation (PISA method)." Nucleic Acids Res 29(15): E73-3. completely bypasses DNA immobilization as the DNA template is added as a free molecule in the reaction mixture.

Comparison of alignment software for genome-wide bisulphite sequence data. Nucleic Acids Research 40(10): e79. sequencing (also known as bisulphite sequencing) is the use of bisulfite treatment of DNA before routine sequencing to determine the pattern of methylation. DNA methylation was the first discovered epigenetic mark, and remains the most studied.

The sequence of the bases determine the genetic code. Nucleotides are nucleosides that are phosphorylated by specific kinases via a phosphodiester bond. Nucleotides are the repeating structural units of nucleic acids. The nucleotides are made of a nitrogenous base, a pentose (ribose for RNA or deoxyribose for DNA), and three phosphate groups.

Morpholinos targeted to "slippery" mRNA sequences within protein coding regions can induce translational frameshifts. Morpholinos can block RNA editing, poly-A tailing and translocation sequences. Morpholino activities against this variety of targets suggest that Morpholinos can be used as a general-purpose tool for blocking interactions of proteins or nucleic acids with mRNA.

MEGARes is a hand-curated antibiotic resistance database for approximately 4000 resistant genes., Lakin, S.M., Dean, C., Noyes, N.R., Dettenwanger, A., Spencer Ross, A., Doster, E., Rovira, P., Abdo, Z., Jones, K.L., Ruiz, J., Belk, K.E., Morley, P.S., Boucher, C. (2016) MEGARes: an antimicrobial database for high throughput sequencing. Nucleic Acids Res., 45.

The majority of Canto curation use bio-ontologies: current CANTO uses Gene Ontology (GO) Gene Ontology Consortium, Blake, J. A., Dolan, M., Drabkin, H., Hill, D. P., Li, N., … Westerfield, M. (2013). Gene Ontology annotations and resources. Nucleic acids research, 41(Database issue), D530–D535. doi:10.1093/nar/gks1050 and PSI-MOD.

He has published a large number of papers and books concerning insulin, nucleic acids, proteins and vitamin B6 deficiency. On 20 July 2004 he was elected one of the 14 Vice-Presidents of the European Parliament, ending his mandate on 15 January 2007. He is the brother of Demetrios, Archbishop of America.

Lange P.F., Huesgen P.F., Overall C.M. TopFIND 2.0 — Linking protein termini with proteolytic processing and modifications altering protein function. Nucleic Acids Res. 40 ,D351 – 361 (2012). By combining research literature and other biological databases including UniProt, MEROPS, Ensembl, and TisDB, the database comprehensively renders protein termini modifications accessible to a broad scientific community.

Rangel, A. E., Chen, Z., Ayele, T. M. & Heemstra, J. M. In vitro selection of an XNA aptamer capable of small-molecule recognition. Nucleic Acids Res. 46, 8057-8068, (2018). Such experiments demonstrate that the properties of heredity and evolution are not limited to the natural genetic polymers of DNA and RNA.

Type I interferon activity was originally described over 50 years ago as a soluble factor produced by cells treated with inactivated, non-replicating viruses that blocked subsequent infection with live virus. Although the rapid induction and amplification of the type I interferon system is highly adaptive in terms of virus eradication, aberrant stimulation or unregulated control of the system could lead to inappropriate and / or excessive interferon output. Studies of the AGS-related proteins TREX1, the RNase H2 complex, SAMHD1 and ADAR1, suggest that an inappropriate accumulation of self-derived nucleic acids can induce type I interferon signaling. The findings of IFIH1 mutations in the similar context implicates the aberrant sensing of nucleic acids as a cause of immune upregulation.

Since there were no known chemical pathways for the abiogenic synthesis of nucleotides from pyrimidine nucleobases cytosine and uracil under prebiotic conditions, it is thought by some that nucleic acids did not contain these nucleobases seen in life's nucleic acids. The nucleoside cytosine has a half-life in isolation of 19 days at and 17,000 years in freezing water, which some argue is too short on the geologic time scale for accumulation. Others have questioned whether ribose and other backbone sugars could be stable enough to find in the original genetic material, and have raised the issue that all ribose molecules would have had to be the same enantiomer, as any nucleotide of the wrong chirality acts as a chain terminator.

For example, because cell-free nucleic acids exist in human plasma, a simple blood sample can be enough to sample genetic information from tumours, transplants or an unborn fetus. Many, but not all, molecular diagnostics methods based on nucleic acids detection use polymerase chain reaction (PCR) to vastly increase the number of nucleic acid molecules, thereby amplifying the target sequence(s) in the patient sample. PCR is a method that a template DNA is amplified using synthetic primers, a DNA polymerase, and dNTPs. The mixture is cycled between at least 2 temperatures: a high temperature for denaturing double-stranded DNA into single-stranded molecules and a low temperature for the primer to hybridize to the template and for the polymerase to extend the primer.

Oligonucleotide synthesis is the chemical synthesis of sequences of nucleic acids. The majority of biological research and bioengineering involves synthetic DNA, which can include oligonucleotides, synthetic genes, or even chromosomes. Today, all synthetic DNA is custom-built using the phosphoramidite method by Marvin H. Caruthers. Oligos are synthesized from building blocks which replicate natural bases.

A PCR primer bank for quantitative gene expression analysis. Nucleic Acids Research, 31(24), e154; 1-8 From these studies, it was concluded that the STX17 gene and the NR4A3 gene are both being over-expressed in gray horses, which is responsible for the increased incidences of melanoma in horses with the gray gene.

In addition, glucose metabolites produce all nonessential amino acids, sugar alcohols such as mannitol and sorbitol, fatty acids, cholesterol and nucleic acids. Finally, glucose is used as a building block in the glycosylation of proteins to glycoproteins, glycolipids, peptidoglycans, glycosides and other substances (catalyzed by glycosyltransferases) and can be cleaved from them by glycosidases.

MBs can serve as drug delivery vehicles in a variety of methods. The most notable of these include: (1) incorporating a lipophilic drug to the lipid monolayer, (2) attaching nanoparticles and liposomes to the microbubble surface, (3) enveloping the microbubble within a larger liposome, and (4) electrostatically bonding nucleic acids to the MB surface.

CrRNAs associate with Cas proteins to form ribonucleotide complexes that recognize foreign nucleic acids. CrRNAs show no preference between the coding and non-coding strands, which is indicative of an RNA-guided DNA-targeting system. The type I-E complex (commonly referred to as Cascade) requires five Cas proteins bound to a single crRNA.

Chromosome 9 is one of the 23 pairs of chromosomes in humans. Humans normally have two copies of this chromosome, as they normally do with all chromosomes. Chromosome 9 spans about 138 million base pairs of nucleic acids (the building blocks of DNA) and represents between 4.0 and 4.5% of the total DNA in cells.

This allows water treatment plants to greatly improve the removal of total organic content (TOC) from raw water. Polyacrylamide is also often used in molecular biology applications as a medium for electrophoresis of proteins and nucleic acids in a technique known as PAGE. It was also used in the synthesis of the first Boger fluid.

These chips haves been developed for ribosomal RNA (rRNA) targets, commonly used for detecting bacteria. rRNA are very abundant in the cell comprising about 80% of the RNA content of the typical eukaryotic cell.Zlatanova, J., and Mirzabekov, A., “Gel-Immobilized Microarrays of Nucleic Acids and Proteins. Production and Application for Macromolecular Research,” Methods Mol. Biol.

This raises the interesting question in how far these properties can be utilized to assemble nucleic acidpeptide nano-complexes and whether this can be exploited to modulate the pharmacological properties of nucleic acids and/or for nucleic acid delivery to target cells Recently, DMBT1-derived peptides have been successfully harnessed for siRNA intracellular delivery.

Nucleic Acids Research. (Database issue) 41: D1228-D1233. including the Pseudomonas aeruginosa Community Annotation Project and Pseudomonas Genome Database. She chairs the Scientific Advisory Board for The European Nucleotide Archive (EMBL-EBI) and serves as a member of several other boards, including the Genome Canada Board of Directors and the Scientific Advisory Board for REACTOME.

Oxygen radicals react with plant cell lipids, proteins, and nucleic acids, damaging and killing affected cells, and nutrients released during the cell rupture and death feed the Cercospora fungus. A study of mutant Cercospora lacking the gene responsible for cercosporin production demonstrates that, though unnecessary for infection, cercosporin increases the virulence of Cercospora fungi.

Inside the mycelium, hexose is converted to trehalose and glycogen. Trehalose and glycogen are carbon storage forms that can be rapidly synthesized and degraded and may buffer the intracellular sugar concentrations. The intraradical hexose enters the oxidative pentose phosphate pathway, which produces pentose for nucleic acids. Lipid biosynthesis also occurs in the intraradical mycelium.

This is less accurate but also much less computationally costly. Software for thermodynamic modeling of nucleic acids includes Nupack, mfold/UNAFold, and Vienna. A related approach, inverse secondary structure prediction, uses stochastic local search which improves a nucleic acid sequence by running a structure prediction algorithm and the modifying the sequence to eliminate unwanted features.

Dr. Kolodny has been a featured guest on hundreds of national television shows, from Good Morning America and the David Susskind Show to Larry King Live, Nightline, Crossfire, and the MacNeil-Lehrer Report. In 1997, he joined the board of directors of Advanced Viral Research Corporation, a biotechnology company specializing in peptide nucleic acids.

Within minutes, bacterial ribosomes start translating viral mRNA into protein. For RNA-based phages, RNA replicase is synthesized early in the process. Proteins modify the bacterial RNA polymerase so it preferentially transcribes viral mRNA. The host's normal synthesis of proteins and nucleic acids is disrupted, and it is forced to manufacture viral products instead.

Traces of many aldehydes are found in essential oils and often contribute to their favorable odors, e.g. cinnamaldehyde, cilantro, and vanillin. Possibly because of the high reactivity of the formyl group, aldehydes are not common in several of the natural building blocks: amino acids, nucleic acids, lipids. Most sugars, however, are derivatives of aldehydes.

SPR imaging is used to study the multiple adsorption interactions in an array format under same experimental conditions. Nelson and his coworkers introduced a multistep procedure to create DNA arrays on gold surfaces for use with SPR imaging. Affinity interactions can be studied for a variety of target molecules e.g. proteins and nucleic acids.

The methods in which the program specializes can return quantitative calculations of the energy balance which occurs in proteins and nucleic acids. It can provide insight into key problems in biochemistry such as, energetic details on parts of the translation mechanism in mitochondrial ribosomes (Lind et al. 2013), or details in enzymatic reactions (Mones et al. 2013), among others.

In sexually active men, tests for sexually transmitted diseases may be done. These may include microscopy and culture of a first void urine sample, Gram stain and culture of fluid or a swab from the urethra, nucleic acid amplification tests (to amplify and detect microbial DNA or other nucleic acids) or tests for syphilis and HIV.

Phosphorus-32 is widely used for labeling nucleic acids and phosphoproteins. It has the highest emission energy (1.7 MeV) of all common research radioisotopes. This is a major advantage in experiments for which sensitivity is a primary consideration, such as titrations of very strong interactions (i.e., very low dissociation constant), footprinting experiments, and detection of low-abundance phosphorylated species.

The two tautomers of an amino acid: (1) neutral and (2) zwitterionic forms. Tautomers () are structural isomers (constitutional isomers) of chemical compounds that readily interconvert. This reaction commonly results in the relocation of a proton. Tautomerism is for example relevant to the behavior of amino acids and nucleic acids, two of the fundamental building blocks of life.

Polymerases all are involved with DNA replication in some capacity, synthesizing chains of nucleic acids. DNA replication is a vital aspect of a cell's proliferation. Without replicating its DNA, a cell cannot divide and share its genetic information to progeny. In prokaryotes, like E. coli, DNA Pol III is the major polymerase involved with DNA replication.

Most ucfDNA is derived from urogenital tract cells. Approximately over 3×106 urogenital tract cells are exfoliated into urine per day. These cells undergo apoptosis (primarily) or necrosis to release fragmented nucleic acids. Necrotic lymphocytes, kidney, prostate, and urinary bladder contribute to high-molecular-weight DNA, while apoptotic cells from the urogenital tract contribute to low-molecular-weight DNA.

Some common features of protein-RNA interfaces were deduced based on known structures. For example, RNP in snRNPs have an RNA-binding motif in its RNA-binding protein. Aromatic amino acid residues in this motif result in stacking interactions with RNA. Lysine residues in the helical portion of RNA- binding proteins help to stabilize interactions with nucleic acids.

Here, he set out to confirm the furanose chemical structure of the sugar part of nucleosides in natural nucleic acids, which had only been inferred at the time. He and Basil Lythgoe proved this to be the case. He gained his second PhD in 1952. He later worked on the selective phosphorylation of nucleosides to form nucleotides.

Afterwards, they are blended (homogenize) with sodium sulfite. Then the extract is filtered and clarified by centrifugation (10.000 g during 10 minutes). The next step is to add polyethylene glycol (PEG). Finally, after nearly two hours of incubation at 4 °C, and after another centrifugation (at low speed) the nucleic acids can be extracted by chloroform procedures, for example.

Michal Hocek (born 11 December 1969 in Benešov, Czechoslovakia) is a Czech chemist. He is a group leader at the Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and a professor of organic chemistry at Charles University in Prague. He specializes in the chemistry and chemical biology of nucleosides, nucleotides, and nucleic acids.

This annotation and prediction software can be compared to ANNOVAR and Variant Effect Predictor, but each use different nomenclatures Wang K, Li M, Hakonarson H. ANNOVAR: Functional annotation of genetic variants from next-generation sequencing data Nucleic Acids Research, 38:e164, 2010"Variant Effect Predictor." Variant Effect Predictor. EMBL-EBI, Dec. 2016. Web. 28 Feb. 2017. .

Demethylases are enzymes that remove methyl (CH3-) groups from nucleic acids, proteins (in particular histones), and other molecules. Demethylase enzymes are important in epigenetic modification mechanisms. The demethylase proteins alter transcriptional regulation of the genome by controlling the methylation levels that occur on DNA and histones and, in turn, regulate the chromatin state at specific gene loci within organisms.

Proteins and nucleic acids are defined by their sequences and any modifications that may be present. Polymers are defined by their structural repeating units and physical properties such as molecular weight or properties related to molecular weight (e.g. viscosity). Structurally diverse material (e.g., botanicals), are defined by taxonomic information along with a part or fraction of the material.

In other words, the binding of B molecules to the different sites on A do not constitute mutually independent events. Cooperativity can be positive or negative. Cooperative binding is observed in many biopolymers, including proteins and nucleic acids. Cooperative binding has been shown to be the mechanism underlying a large range of biochemical and physiological processes.

Todd's group did fundamental work on the chemistry of nucleosides, nucleotides and nucleic acids. This formed the base for subsequent work on the role of these compounds in cell biology and heredity. In 1944 he moved with Todd to Cambridge University and was awarded an ICI research fellowship. His work culminated in the first synthesis of adenosine triphosphate (ATP).

These classic molecular biology papers are identified as: Watson J.D. and Crick F.H.C. "A Structure for Deoxyribose Nucleic Acid" Nature 171, 737–738 (1953); Wilkins M.H.F., Stokes A.R. & Wilson, H.R. "Molecular Structure of Deoxypentose Nucleic Acids" Nature 171, 738–740 (1953); Franklin R. and Gosling R.G. "Molecular Configuration in Sodium Thymonucleate" Nature 171, 740–741 (1953).

IMG Registered User count These include systems for data management and curation of genome projects and their associated metadata, such as the Genomes OnLine Database (GOLD),Bernal A, et al. (2001) Genomes OnLine Database (GOLD): a monitor of genomes projects worldwide. Nucleic Acids Research 29, 126-127. and comparative-genomics systems such as ERGOOverbeek R, et al.

Kyrpides's early work focused on the origins and evolution of the genetic code. In collaboration with Christos Ouzounis, he developed a series of hypotheses for the transfer of information from proteins to nucleic acids known as reverse interpretation.Kyrpides N., and Ouzounis C. (1993) Mechanisms of specificity in mRNA degradation: autoregulation and cognate interactions. J.Theor.Biology 163: 373-392.

Unlike other endonucleases, the MmeI (type IIS) and EcoP15I (type III) restriction endonucleases cut downstream of their target binding sites. MmeI cuts 18/20 base pairs downstream Morgan RD, Bhatia TK, Lovasco L, Davis TB. 2008. MmeI: A minimal Type II restriction-modification system that only modifies one DNA strand for host protection. Nucleic Acids Res. 36:6558–6570.

Lynne Regan was a professor of chemistry and Molecular and Biophysics and Biochemistry at Yale University. In 2018, she moved to the University of Edinburgh. She was the president of the Protein Society for the 2013–2014 term and has earned many awards throughout her career. Her research mainly concerns interactions between proteins and nucleic acids.

Juli Feigon is a Distinguished Professor of Biochemistry at the University of California, Los Angeles, where she has been a faculty member since 1985. She was elected to the United States National Academy of Sciences in 2009. Her research focuses on structural studies of nucleic acids by nuclear magnetic resonance spectroscopy along with other biophysical techniques.

Xenbase is a Model Organism Database (MOD), providing informatics resources, as well as genomic and biological data on Xenopus frogs.K. Karimi et al. (2017) Xenbase: a genomic, epigenomic and transcriptomic model organism database, Nucleic Acids Research (NAR), gkx936 Xenbase has been available since 1999, and covers both X. laevis and X. tropicalis Xenopus varieties.P.D. Vize et al.

A biosensor is an analytical device, used for the detection of a chemical substance, that combines a biological component with a physicochemical detector. The sensitive biological element, e.g. tissue, microorganisms, organelles, cell receptors, enzymes, antibodies, nucleic acids, etc., is a biologically derived material or biomimetic component that interacts with, binds with, or recognizes the analyte under study.

Phenol is a useful compound for breaking down superfluous cell materials that would otherwise contaminate the nucleic acid sample. There are two reasons why phenol makes such an effective purifier for nucleic acid samples. The first is that it is a non-polar compound. Because nucleic acids are highly polar, they do not dissolve in the presence of phenol.

This gene encodes a Kruppel-associated box (KRAB) zinc- finger protein, which belongs to a large group of transcriptional regulators in mammals. These proteins bind nucleic acids and play important roles in various cellular functions, including cell proliferation, differentiation and apoptosis, and in regulating viral replication and transcription. A pseudogene of this gene was identified on chromosome 1.

TEMED is used with ammonium persulfate to catalyze the polymerization of acrylamide when making polyacrylamide gels, used in gel electrophoresis, for the separation of proteins or nucleic acids. Although the amounts used in this technique may vary from method to method, 0.1–0.2% v/v TEMED is a "traditional" range. TEMED can also be a component of hypergolic propellants.

The quaternary structure refers to the number and arrangement of multiple protein molecules in a multi-subunit complex. For nucleic acids, the term is less common, but can refer to the higher-level organization of DNA in chromatin, including its interactions with histones, or to the interactions between separate RNA units in the ribosome or spliceosome.

Hypoxanthine is a naturally occurring purine derivative. It is occasionally found as a constituent of nucleic acids, where it is present in the anticodon of tRNA in the form of its nucleoside inosine. It has a tautomer known as 6-hydroxypurine. Hypoxanthine is a necessary additive in certain cell, bacteria, and parasite cultures as a substrate and nitrogen source.

Alpha- hemolysin has been used extensively in academic research as a single molecule nanopore sensor. In 1996 it was first shown that single-stranded nucleic acids can be detected by electrophysiology measurements as they translocate through an alpha-hemolysin pore embedded in a lipid bilayer. This was an important milestone in the development of nanopore sequencing.

From antibody labeling, the applications have spread to nucleic acids thanks to carboxyfluorescein (FAM), TET, ...). Other historically common fluorophores are derivatives of rhodamine (TRITC), coumarin, and cyanine. Newer generations of fluorophores, many of which are proprietary, often perform better, being more photostable, brighter, and/or less pH-sensitive than traditional dyes with comparable excitation and emission.

Ed. Stephen A. Krawetz and David D. Womble; Humana Press Inc., Totowa, NJ. pp. 345-361. The first papers describing this software were published in 1989 and 1990,Wojciech Rychlik and Robert E. Rhoads (1989) A Computer Program for Choosing Optimal Oligonucleotides for Filter Hybridization, Sequencing and in vitro Amplification of DNA; Nucleic Acids Research 17, 8543-8551.

Integrated DNA Technologies, Inc. (IDT), headquartered in Coralville, Iowa, is a supplier of custom nucleic acids, serving the areas of academic research, biotechnology, clinical diagnostics, and pharmaceutical development. IDT's primary business is the manufacturing of custom DNA and RNA oligonucleotides (oligos) for research applications. Joseph A. Walder, M.D., Ph.D. (Northwestern University), founded Integrated DNA Technologies, Inc.

IDT's mission is to enable discovery in biology and medicine. The company strives to achieve this by improving nucleic acid synthesis technology and developing new applications for the use of DNA- and RNA-based compounds. IDT's advanced synthesis group combines expertise in chemistry, molecular biology, and engineering to produce and purify complex nucleic acids of all kinds.

The chemical structure of gallocyanin The gallocyanin stain, also known as the gallocyanin-chromalum stain, is a stain of the oxazine group for total nucleic acids. It is prepared from gallocyanin and is an ideal method for numerous slides that need to be stained serially, equivalently, and reproducible. Structures containing basophilic compounds take on a bluish color.

DEAD box proteins are involved in an assortment of metabolic processes that typically involve RNAs, but in some cases also other nucleic acids. They are highly conserved in nine motifs and can be found in most prokaryotes and eukaryotes, but not all. Many organisms, including humans, contain DEAD-box (SF2) helicases, which are involved in RNA metabolism.

Protein segment finder,Samson A. O., and Levitt M., "Protein segment finder: an online search engine for segment motifs in the PDB", 2009, Nucleic Acids Research, 37 (Database issue), D224-8 or PSF, is a search engine to quickly identify protein segments obeying a set of primary, secondary and tertiary structure constraints in the Protein Data Bank.

An oligosaccharide is an oligomer of monosaccharides (simple sugars). An oligonucleotide is a short single-stranded fragment of nucleic acid such as DNA or RNA, or similar fragments of analogs of nucleic acids such as peptide nucleic acid or Morpholinos. A pentamer unit of the major capsid protein VP1. Each monomer is in a different color.

Simplified diagram of mRNA synthesis and processing. Enzymes not shown. Transcription is the first of several steps of DNA based gene expression in which a particular segment of DNA is copied into RNA (especially mRNA) by the enzyme RNA polymerase. Both DNA and RNA are nucleic acids, which use base pairs of nucleotides as a complementary language.

Treatise on Basic Philosophy, vol. 4. Ontology II: A World of Systems, p. 61-2. link. Biomolecules include large macromolecules (or polyanions) such as proteins, carbohydrates, lipids, and nucleic acids, as well as small molecules such as primary metabolites, secondary metabolites and natural products. A more general name for this class of material is biological materials.

Biochemistry is closely related to molecular biology, the study of the molecular mechanisms of biological phenomena.Astbury (1961), p. 1124. Much of biochemistry deals with the structures, functions, and interactions of biological macromolecules, such as proteins, nucleic acids, carbohydrates, and lipids, which provide the structure of cells and perform many of the functions associated with life.Eldra (2007), p. 45.

A DNA-binding domain (DBD) is an independently folded protein domain that contains at least one structural motif that recognizes double- or single- stranded DNA. A DBD can recognize a specific DNA sequence (a recognition sequence) or have a general affinity to DNA. Some DNA-binding domains may also include nucleic acids in their folded structure.

Structural biology is concerned with the biomolecular structure of macromolecules, particularly proteins and nucleic acids. The function of these molecules is determined by their shape as well as their composition, and their structure has multiple levels. Protein structure has a four-level hierarchy. The primary structure is the sequence of amino acids that make it up.

Nucleofection is an electroporation-based transfection method which enables transfer of nucleic acids such as DNA and RNA into cells by applying a specific voltage and reagents. Nucleofection, also referred to as nucleofector technology, was invented by the biotechnology company Amaxa. "Nucleofector" and "nucleofection" are trademarks owned by Lonza Cologne AG, part of the Lonza Group.

Kuijpers, W.H.A. e.a. (1990) "Synthesis of well-defined phosphate- methylated DNA fragments: the application of potassium carbonate in methanol as deprotecting agent", Nucleic Acids Research, Vol. 18, pp. 5197-5205 In May 1989 he invited one of Bucks research assistants to test their material on HPLC equipment in the lab of Organon, a Dutch pharmaceutical company.

From 2006 to 2011, he was Deputy Director of the Laboratory of Molecular Biology, Medical Research Council, acting Director from 2007 to 2008 and Head of the Division of Protein and Nucleic Acids Chemistry from 1994 to 2006. He was also Deputy Director of the MRC Centre for Protein Engineering from 1990 to its closure in 2010.

Molecules directly encoded by the genome, such as nucleic acids, proteins and peptides derived from proteins by proteolytic cleavage, are not as a rule included in ChEBI. ChEBI uses nomenclature, symbolism and terminology endorsed by the International Union of Pure and Applied Chemistry (IUPAC) and Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB).

6-Carboxyfluorescein (6-FAM) is a fluorescent dye with an absorption wavelength of 495 nm and an emission wavelength of 517 nm. A carboxyfluorescein molecule is a fluorescein molecule with a carboxyl group added. They are commonly used as a tracer agents. It is used in the sequencing of nucleic acids and in the labeling of nucleotides.

In eutactic macromolecules, substituents may occupy any specific (but potentially complex) sequence of positions along the chain. Isotactic and syndiotactic polymers are instances of the more general class of eutactic polymers, which also includes heterogeneous macromolecules in which the sequence consists of substituents of different kinds (for example, the side-chains in proteins and the bases in nucleic acids).

In a phenol–chloroform extraction, addition of a phenol/chloroform mixture will dissolve protein and lipid contaminants, leaving the nucleic acids in the aqueous phase. It also denatures proteins, like DNase, which is especially important if the plasmids are to be used for enzyme digestion. Otherwise, smearing may occur in enzyme restricted form of plasmid DNA.

DNA tetrahedron described in Goodman, 2005. Models of this type are useful for ensuring that tertiary structure constraints do not cause excessive strain to the molecule. Geometrical models of nucleic acids are used to predict tertiary structure. This is important because designed nucleic acid complexes usually contain multiple junction points, which introduces geometric constraints to the system.

The binary structure of a TNA reverse transcriptase has also been solved by X-ray crystallography, revealing the importance of structural plasticity as a possible mechanism for template recognition.Jackson, L. N., Chim, N., Shi, C. & Chaput, J. C. Crystal structures of a natural DNA polymerase that functions as an XNA reverse transcriptase. Nucleic Acids Res., (2019).

Frederick Sanger (; 13 August 1918 – 19 November 2013) was a British biochemist who twice won the Nobel Prize in Chemistry, one of only two people to have done so in the same category (the other is John Bardeen in physics), the fourth person overall with two Nobel Prizes, and the third person overall with two Nobel Prizes in the sciences. In 1958, he was awarded a Nobel Prize in Chemistry "for his work on the structure of proteins, especially that of insulin". In 1980, Walter Gilbert and Sanger shared half of the chemistry prize "for their contributions concerning the determination of base sequences in nucleic acids". The other half was awarded to Paul Berg "for his fundamental studies of the biochemistry of nucleic acids, with particular regard to recombinant DNA".

Solid state nanopore sequencing approaches, unlike biological nanopore sequencing, do not incorporate proteins into their systems. Instead, solid state nanopore technology uses various metal or metal alloy substrates with nanometer sized pores that allow DNA or RNA to pass through. These substrates most often serve integral roles in the sequence recognition of nucleic acids as they translocate through the channels along the substrates.

Coarse-grained modeling, coarse-grained models, aim at simulating the behaviour of complex systems using their coarse-grained (simplified) representation. Coarse-grained models are widely used for molecular modeling of biomolecules at various granularity levels. A wide range of coarse-grained models have been proposed. They are usually dedicated to computational modeling of specific molecules: proteins, nucleic acids, lipid membranes, carbohydrates or water.

These relatively simple molecules may be then used to further synthesise more complicated molecules, including proteins, complex carbohydrates, lipids, and nucleic acids, or be respired to perform work. Consumption of primary producers by heterotrophic organisms, such as animals, then transfers these organic molecules (and the energy stored within them) up the food web, fueling all of the Earth's living systems.

All life forms require certain core chemical elements needed for biochemical functioning. These include carbon, hydrogen, nitrogen, oxygen, phosphorus, and sulfur—the elemental macronutrients for all organisms—often represented by the acronym CHNOPS. Together these make up nucleic acids, proteins and lipids, the bulk of living matter. Five of these six elements comprise the chemical components of DNA, the exception being sulfur.

The program Coot (Crystallographic Object-Oriented Toolkit) is used to display and manipulate atomic models of macromolecules, typically of proteins or nucleic acids, using 3D computer graphics. It is primarily focused on building and validation of atomic models into three-dimensional electron density maps obtained by X-ray crystallography methods, although it has also been applied to data from electron microscopy.

The most common being, for nucleic acids Tris/Acetate/EDTA (TAE), Tris/Borate/EDTA (TBE). Many other buffers have been proposed, e.g. lithium borate, which is rarely used, based on Pubmed citations (LB), isoelectric histidine, pK matched goods buffers, etc.; in most cases the purported rationale is lower current (less heat) matched ion mobilities, which leads to longer buffer life.

The magnetofection principle is to associate nucleic acids with cationic magnetic nanoparticles: these molecular complexes are then concentrated and transported into cells supported by an appropriate magnetic field. In this way, the magnetic force allows a very rapid concentration of the entire applied vector dose onto cells, so that 100% of the cells get in contact with a significant vector dose.

The high density of the caesium ion makes solutions of caesium chloride, caesium sulfate, and caesium trifluoroacetate () useful in molecular biology for density gradient ultracentrifugation.Manfred Bick, Horst Prinz, "Cesium and Cesium Compounds" in Ullmann's Encyclopedia of Industrial Chemistry 2005, Wiley-VCH, Weinheim. . This technology is used primarily in the isolation of viral particles, subcellular organelles and fractions, and nucleic acids from biological samples.

ENU, also known as N-ethyl-N-nitrosourea (chemical formula C3H7N3O2), is a highly potent mutagen. For a given gene in mice, ENU can induce 1 new mutation in every 700 loci. It is also toxic at high doses. The chemical is an alkylating agent, and acts by transferring the ethyl group of ENU to nucleobases (usually thymine) in nucleic acids.

Sucrose gradients are typically used for separation of cellular organelles. Gradients of caesium salts are used for separation of nucleic acids. After the sample has spun at high speed for sufficient time to produce the separation, the rotor is allowed to come to a smooth stop and the gradient is gently pumped out of each tube to isolate the separated components.

This process, while preserving the structural integrity of the cells and tissue can damage the biological functionality of proteins, particularly enzymes. Formalin fixation leads to degradation of mRNA, miRNA, and DNA as well as denaturation and modification of proteins in tissues. However, extraction and analysis of nucleic acids and proteins from formalin- fixed, paraffin-embedded tissues is possible using appropriate protocols.

The SENS Research Foundation recently reported success in expressing the ATP6 gene allotopically in vitro. As of 6 September 2016 and as a result of funds raised at lifespan.io SENS Research Foundation showed ATP6 and ATP8 could be successfully expressed and their published research appears in Nucleic Acids Research providing proof of concept for the MitoSENS repair approach for repairing age related damage.

G2Cdb integrates information curated from the scientific literature and numerous online databases about genes and diseases of interest to Genes to Cognition.G2Cdb: the Genes to Cognition database. Nucleic Acids Research. 37(Database issue):D846-51 (2009) It also provides access to lists of genes derived from proteomics experiments characterising the composition of the complex of proteins present at the postsynaptic density.

Nussinov was made a Fellow of the Biophysical Society in 2011, for her "extraordinary contributions to advances in computational biology on both nucleic acids and proteins". She became a Fellow of the International Society for Computational Biology (ISCB) in 2013. In 2018, Nussinov was awarded the ISCB Senior Scientist Award. In 2020, Nussinov was elected Fellow of the American Physical Society.

Diagnostic qualitative PCR is applied to rapidly detect nucleic acids that are diagnostic of, for example, infectious diseases, cancer and genetic abnormalities. The introduction of qualitative PCR assays to the clinical microbiology laboratory has significantly improved the diagnosis of infectious diseases, and is deployed as a tool to detect newly emerging diseases, such as new strains of flu and coronavirus, in diagnostic tests.

Biochemistry is the science of the chemical processes which takes place within living organisms. Living organisms need essential elements to survive, among which are carbon, hydrogen, nitrogen, oxygen, calcium, and phosphorus. These elements make up the four macromolecules that living organisms need to survive: carbohydrates, lipids, proteins, and nucleic acids. Carbohydrates, made up of carbon, hydrogen, and oxygen, are energy-storing molecules.

Zinc finger proteins have been shown to interact with nucleic acids and to have diverse functions. The zinc finger domain is a conserved amino acid sequence motif containing two specifically positioned cysteines and two histidines that are involved in coordinating zinc. Kruppel- related proteins form one family of zinc finger proteins. See MIM 604749 for additional information on zinc finger proteins.

Nucleic Acids Res. 37 1152–1159 In support of this model, TERRA expression has also been shown relate to cellular ALT-status. Cells that have been experimentally confirmed to utilize the ALT pathway have markedly higher levels of TERRA expression compared to non-ALT cells. The specific nature of the complex interactions involved in this proposed model remain an area of active research.

Working independently, Dr. Holley (Cornell University) had discovered the exact chemical structure of transfer-RNA, and Dr. Khorana (University of Wisconsin in Madison) had mastered the synthesis of nucleic acids. Dr. Nirenberg showed - excluding nonsense codons - every combination of a triplet (i.e. a codon) composed of four different nitrogen-containing bases found in DNA and in RNA produces a specific amino acid.

The European Collection of Authenticated Cell Cultures houses and supplies cell lines. It is part of the Culture Collections of Public Health England. The collection is held in Porton Down. ECACC, which was established in 1985, consists of a team with specialist knowledge which supply authenticated cell lines, induced Pluripotent stem cells (iPSCs) and nucleic acids to provide stock for the research community.

Zhijian "James" Chen (; born 1966) is a Chinese-American biochemist and Professor in the Department of Molecular Biology at University of Texas Southwestern Medical Center. He is best known for his discovery of mechanisms by which nucleic acids trigger innate and autoimmune responses from the interior of a cell, work for which he received the 2019 Breakthrough Prize in Life Sciences.

Adenosine deaminase (also known as adenosine aminohydrolase, or ADA) is an enzyme () involved in purine metabolism. It is needed for the breakdown of adenosine from food and for the turnover of nucleic acids in tissues. Its primary function in humans is the development and maintenance of the immune system. However, the full physiological role of ADA is not yet completely understood.

Uncoating is the removal of viral capsid, which makes the viral nucleic acids available for transcription. The capsid could have been degraded by either host or viral enzymes, releasing the viral genome into the cell. Replication is the multiplication of virus's genetic material. The process includes the transcription of mRNA, synthesis, and assembly of viral proteins and is regulated by protein expression.

Nucleic Acids Research. 35(4). 1145-1154 and nuclear magnetic resonance spectroscopy.Yamasaki, Kigawa, Inoue, Tateno, Yamasaki, et al. (2005) Solution Structure of an Arabidopsis WRKY DNA Binding Domain. The Plant Cell. 17(3). 944-956, Yamasaki, Kigawa, Watanabe, Inoue, Yamasaki, et al. (2012) Structural Basis for Sequence-specific DNA Recognition by an Arabidopsis WRKY Transcription Factor. Journal of Biological Chemistry. 287(10).

The Plant Cell Online. 15(9). 2076-2092 Since then, WRKYs have been found to bind a more generic GAC core cis-element with flanking sequences dictating DNA-protein interactions.Brand, Fischer, Harter, Kohlbacher and Wanke (2013) Elucidating the evolutionary conserved DNA-binding specificities of WRKY transcription factors by molecular dynamics and in vitro binding assays. Nucleic Acids Research. 41(21).

The virino is a hypothetical infectious particle that was once theorized to be the cause of scrapie and other degenerative diseases of the central nervous system; it was thought to consist of nucleic acids in a protective coat of host cell proteins. The hypothesis was never widely accepted, and the causative agents responsible for these diseases are now widely accepted to be prions.

In the virino model, the host protein protects the scrapie agent nucleic acids from degradation and prevents the host from raising an immune response, since the protein/nucleic acid complex is seen as a legitimate part of the host. However, the presumed scrapie-associated nucleic acid has not been identified, and physical or chemical evidence for its presence is lacking.

TSE or Tris/Saline/EDTA, is a buffer solution containing a mixture of Tris base, Sodium chloride and EDTA. In molecular biology, TSE buffers are often used in procedures involving nucleic acids. Tris-acid solutions are effective buffers for slightly basic conditions, which keep DNA deprotonated and soluble in water. The concentration of tris in the solution is kept near 25 mM.

Fig. 5. A Nicholson model, showing a short part of protein backbone (white) with side chains (grey). Note the snipped stubs representing hydrogen atoms. A good example of composite models is the Nicholson approach, widely used from the late 1970s for building models of biological macromolecules. The components are primarily amino acids and nucleic acids with preformed residues representing groups of atoms.

This can be done by means of polymerase chain reaction (PCR) testing for HRSV nucleic acids in peripheral blood samples if all other infectious processes have been ruled out or if it is highly suspicious for RSV such as a recent exposure to a known source of HRSV infection. The incubation period is 2–8 days but is usually 4–6 days.

Kethoxal, as with other 1,2-dicarbonyl compounds, reacts with nucleic acids. It has high specificity for guanine over other ribonucleotides. In whole RNA, it reacts preferentially with guanine residues that are not involved in hydrogen-bonding. It can thus be used to probe the interactions involved with the secondary structure and other binding interactions of RNA and help with nucleic acid sequence analysis.

C1orf198’s longest isoform has a sequence length of 327 amino acids. The entire sequence is as follows: MASMAAAIAASRSAVMSGNRPLDDRERKRFTYFSSLSPMARKIMQDKEKIREKYGPEWARLPPAQQDEII DRCLVGPRAPAPRDPGDSEELTRFPGLRGPTGQKVVRFGDEDLTWQDEHSAPFSWETKSQMEFSISALSI QEPSNGTAASEPRPLSKASQGSQALKSSQGSRSSSLDALGPTRKEEEASFWKINAERSRGEGPEAEFQSL TPSQIKSMEKGEKVLPPCYRQEPAPKDREAKVERPSTLRQEQRPLPNVSTERERPQPVQAFSSALHEAAP SQLEGKLPSPDVRQDDGEDTLFSEPKFAQVSSSNVVLKTGFDFLDNW The entire protein has a theoretical molecular weight of 36.346 kDa and its isoelectric point is 5.6.S. Chojnacki, A. Cowley, J. Lee, A. Foix, R. Lopez, Programmatic access to bioinformatics tools from EMBL-EBI update: 2017. Nucleic Acids Res.

Fast internal conversion reduces the excited state lifetime, and thereby prevents bimolecular reactions. Bimolecular electron transfer always produces a reactive chemical species, free radicals. Nucleic acids (precisely the single, free nucleotides, not those bound in a DNA/RNA strand) have an extremely short lifetime due to a fast internal conversion. Both melanin and DNA have some of the fastest internal conversion rates.

Valency and Molecular Structure (4th ed.). . The principle of polyvalency also applies to larger species, such as antibodies, medical drugs, and even nanoparticles surface- functionalized with ligands, like spherical nucleic acids, which can show enhanced or cooperative binding compared to their monovalent counterparts.Crothers, D.; Metzger, H. (1972). “The influence of polyvalency on the binding properties of antibodies”. Immunochemistry. 9 (3): 341-357.

Jordan worked with John Masson Gulland, Michael Creeth and others on a series of experiments in 1947 which firstly created high quality DNA, then measured its viscocity, and finally demonstrated the hydrogen bonds within the molecule.Gulland JM, Jordan D. O., and Threlfall C. J., (1947) Deoxypentose nucleic acids. Part I. Preparation of the tetrasodium salt of the deoxypentose nucleic acid of calf thymus.

Synthetically produced nitrates are key ingredients of industrial fertilizers, and also key pollutants in causing the eutrophication of water systems. Nitrogen is a constituent element of amino acids and thus of proteins, and of nucleic acids (DNA and RNA). It resides in the chemical structure of almost all neurotransmitters, and is a defining component of alkaloids, biological molecules produced by many organisms.

Lysine can be methylated up to three times on its terminal ammonium group. Methylation is the addition of a -CH3, or methyl group, to another molecule. In biology, methylation is typically catalyzed by enzymes, and methyl groups are commonly added to either proteins or nucleic acids. In EZH2-catalyzed methylation, the amino acid lysine in the histone h3 is methylated.

Pseudomonas aeruginosa Genome Database and PseudoCAP: Facilitating community-based, continually updated, genome annotation. Nucleic Acids Research. 33:D338-343.Lynn, D.J., C. Chan, M. Naseer, M. Yau, R. Lo, A. Sribnaia, G. Ring, J. Que, K. Wee, G.L. Winsor, M.R. Laird, K. Breuer, A.K. Foroushani, F.S.L. Brinkman, R.E.W. Hancock (2010). Curating the Innate Immunity Interactome. BMC Systems Biology 4:117.

19 In parallel with Henri Grosjean, a new representation of the genetic code anchored in ribosome structures related to messenger RNA and transfer RNA and integrating the very numerous observations on the effects of changes in transfer RNAs is of great interest.Grosjean, H., et al., « An integrated, structure- and energy-based view of the genetic code », Nucleic Acids Res, (2016) 44, p.

If DNA from any of the agent of primer panel is present, it will be amplified. Each amplified product will carry its specific Masscodes. The PCR product is then purified to remove unbound primers, dNTPs, enzyme and other impurities. Finally, the purified PCR products are subjected to UV light as the chemical bond between the nucleic acids and primers is photolabile.

Very dilute solutions of aluminium-haematein, used at pH 3.2 (higher than is usual for staining), contain a cationic dye-metal complex and will slowly stain nucleic acids. Haemalum solutions used for routine staining are more concentrated and more acidic (pH 2-2.5) and are able to stain nuclei after chemical or enzymatic extraction of DNA and RNA from the tissue.

Enzymes used in decellularization treatments are used to break the bonds and interactions between nucleic acids, interacting cells through neighboring proteins, and other cellular components. Lipases, thermolysin, galactosidase, nucleases, and trypsin have all been used in the removal of cells. After a cell is lysed with a detergent, acid, physical pressure, etc., endonucleases and exonucleases can begin the degradation of the genetic material.

Alexander Sergeevich Spirin (Russian: Александр Сергеевич Спирин) (born September 4, 1931) is a Russian biochemist, Distinguished Professor at the Lomonosov Moscow State University (since 1999), a former Director of Institute of Protein Research Russian Academy of Sciences, Puschino (Пущино-на-Оке), Moscow Region (Московская Область), Academician of Russian Academy of Sciences. His primary scientific interests in biochemistry include nucleic acids and protein biosynthesis.

A deoxyribonucleotide is a nucleotide that contains deoxyribose. They are the monomeric units of the informational biopolymer, deoxyribonucleic acid (DNA). Each deoxyribonucleotide comprises three parts: a deoxyribose sugar (monosaccharide), a nitrogenous base, and one phosphoryl group. The nitrogenous bases are either purines or pyrimidines, heterocycles whose structures support the specific base-pairing interactions that allow nucleic acids to carry information.

Klein, TM et al (1987) High-velocity microprojectiles for delivering nucleic acids into living cells. Nature 327:70-73. He is the co-inventor of the Pathogen-derived Resistance (PDR) process and the co-inventor of the genetic vaccination process. In 1998 he retired on the proceeds from the sale of his biotech companies and continued at Cornell as a courtesy associate professor.

Foldamers are classified into three different categories: peptidomimetic foldamers, nucleotidomimetic foldamers, and abiotic foldamers. Peptidomimetic foldamers are synthetic molecules that mimic the structure of proteins, while nucleotidomimetic foldamers are based on the interactions in nucleic acids. Abiotic foldamers are stabilized by aromatic and charge- transfer interactions which are not generally found in nature."Foldamers: Structure, Properties, and Applications" Stefan Hecht, Ivan Huc Eds.

The viriome of a habitat or environment is the total virus content within it. A viriome may relate to the viruses that inhabit a multicellular organism as well as the phages that are residing inside bacteria and archaea. This term exists in contrast to the virome, which more commonly refers to the collection of nucleic acids contained by viruses in a microbiome.

The glycol unit has just three carbon atoms and still shows Watson-Crick base pairing. The Watson-Crick base pairing is much more stable in GNA than its natural counterparts DNA and RNA as it requires a high temperature to melt a duplex of GNA. It is possibly the simplest of the nucleic acids, making it a hypothetical precursor to RNA.

The binding of the negatively charged nucleic acids to the positively charged iron particles occurs relatively fast. After complex formation, the loaded particles are incubated together with the target cells on a magnetic plate. The magnetic field causes the iron particles to be rapidly drawn towards the surface of the cell membrane. Cellular uptake occurs by either endocytosis or pinocytosis.

Reverse transfection is a technique for the transfer of genetic material into cells. As DNA is printed on a glass slide for the transfection process (the deliberate introduction of nucleic acids into cells) to occur before the addition of adherent cells, the order of addition of DNA and adherent cells is reverse that of conventional transfection. Hence, the word “reverse” is used.

Hydrogen cyanide has been discussed as a precursor to amino acids and nucleic acids, and is proposed to have played a part in the origin of life. Although the relationship of these chemical reactions to the origin of life theory remains speculative, studies in this area have led to discoveries of new pathways to organic compounds derived from the condensation of HCN.

However, nucleic acids are unusual because, in the absence of counterions (low salt) to neutralize the high charges on opposing phosphate groups, the nucleic acid duplex dissociates into single chains. Early tides, driven by a close moon, could have generated rapid cycles of dilution (high tide, low salt) and concentration (dry-down at low tide, high salt) that exclusively promoted the replication of nucleic acids through a process dubbed tidal chain reaction (TCR). This theory has been criticized on the grounds that early tides may not have been so rapid, although regression from current values requires an Earth–Moon juxtaposition at around two Ga, for which there is no evidence, and early tides may have been approximately every seven hours. Another critique is that only 2–3% of the Earth's crust may have been exposed above the sea until late in terrestrial evolution.

The Qubit fluorometer uses fluorescent dyes to determine the concentration of either nucleic acids or proteins in a sample. The other common method of measuring the concentration of nucleic acids and protein is the UV-absorbance method, which uses a spectrophotometer to measure the natural absorbance of light at 260 nm (for DNA and RNA) or 280 nm (for proteins). Because so many molecules absorb light at 260 nm, this measurement is subject to inaccuracy due to potential contamination of the sample with these other molecules and is unable to distinguish between DNA, RNA, protein or free nucleotides or amino acids in the sample. On the other hand, Qubit system is supplied with fluorescent dyes that bind specifically to analytes of interest such as double-stranded DNA (dsDNA), single-stranded DNA (ssDNA), RNA, miRNA or protein providing more accurate quantification.

Nucleic Acids Res. 1986;14(18):7379-7390 and the phage gene 39 protein shares homology with the gyrB subunit.Huang WM. Nucleotide sequence of a type II DNA topoisomerase gene. Bacteriophage T4 gene 39. Nucleic Acids Res. 1986;14(19):7751-7765. doi:10.1093/nar/14.19.7751 Since the host E. coli DNA gyrase can partially compensate for the loss of the phage gene products, mutants defective in either genes 39, 52 or 60 do not completely abolish phage DNA replication, but rather delay its initiation. Mutants defective in genes 39, 52 or 60 show increased genetic recombination as well as increased base-substitution and deletion mutation suggesting that the host compensated DNA synthesis is less accurate than that directed by wild-type phage.Mufti S, Bernstein H. The DNA-delay mutants of bacteriophage T4. J Virol. 1974;14(4):860-871. doi:10.1128/JVI.14.4.

Depiction of the restriction enzyme (endonuclease) HindIII cleaving a double- stranded DNA molecule at a valid restriction site (). A nuclease (also archaically known as nucleodepolymerase or polynucleotidase) is an enzyme capable of cleaving the phosphodiester bonds between nucleotides of nucleic acids. Nucleases variously effect single and double stranded breaks in their target molecules. In living organisms, they are essential machinery for many aspects of DNA repair.

In 2018, trade between Jordan and Mexico totaled $44 million USD.Mexican Ministry of the Economy: Jordan (in Spanish) Jordan's main exports to Mexico include: natural calcium phosphates, mineral or chemical fertilizers, mechanical appliances, and tailor suits. Mexico's main exports to Jordan include: vehicles for the transport of goods; tubes; antibiotics; nucleic acids and their salts; and passenger cars. Jordan is Mexico's 95th largest trading partner globally.

The Mouse genome Database (MGD) is the international community resource for integrated genetic, genomic and biological data about the laboratory mouse. MGD provides full annotation of phenotypes and human disease associations for mouse models (genotypes) using terms from the Mammalian Phenotype Ontology and disease names from OMIM.C. Bult and J. Eppig, "The Mouse genome Database (MGD): mouse biology and model systems," Nucleic Acids Research, vol. 36, no.

Tobramycin works by binding to a site on the bacterial 30S and 50S ribosome, preventing formation of the 70S complex. As a result, mRNA cannot be translated into protein, and cell death ensues. Tobramycin also binds to RNA- aptamers, artificially created molecules to bind to certain targets. However, there seems to be no indication that Tobramycin binds to natural RNAs or other nucleic acids.

Single-stranded DNA or RNA tends to fold up into molecules with complex shapes and migrate through the gel in a complicated manner based on their tertiary structure. Therefore, agents that disrupt the hydrogen bonds, such as sodium hydroxide or formamide, are used to denature the nucleic acids and cause them to behave as long rods again.Troubleshooting DNA agarose gel electrophoresis. Focus 19:3 p.

Zinc finger protein 331 is a protein that in humans is encoded by the ZNF331 gene. Zinc finger proteins have been shown to interact with nucleic acids and to have diverse functions. The zinc finger domain is a conserved amino acid sequence motif containing 2 specifically positioned cysteines and 2 histidines that are involved in coordinating zinc. Kruppel-related proteins form one family of zinc finger proteins.

Guanine (; or G, Gua) is one of the four main nucleobases found in the nucleic acids DNA and RNA, the others being adenine, cytosine, and thymine (uracil in RNA). In DNA, guanine is paired with cytosine. The guanine nucleoside is called guanosine. With the formula C5H5N5O, guanine is a derivative of purine, consisting of a fused pyrimidine-imidazole ring system with conjugated double bonds.

Hydrophobic silica is used as a defoamer component. In its capacity as a refractory, it is useful in fiber form as a high-temperature thermal protection fabric. Silica is used in the extraction of DNA and RNA due to its ability to bind to the nucleic acids under the presence of chaotropes. Silica aerogel was used in the Stardust spacecraft to collect extraterrestrial particles.

Figure 5. Proposed cascade mechanism for the PCR-mimic in the context of acetate detection. The polymerase chain reaction (PCR) is utilized in biochemistry and molecular biology for exponentially amplifying nucleic acids by making copies of a specific region of a nucleic acid target. When coupled with diagnostic probes, this technique allows one to detect a small collection of molecules under very dilute conditions.

Thus, these subdomains may move dynamically when the substrate enters the cleft. The size of the cleft suggests that the substrate is large, e.g., the substrate may be a nucleic acid or protein. However, the inner side of the cleft is not filled with positively charged residues, and therefore it is unlikely that negatively charged nucleic acids such as DNA or RNA interact at this site.

Viral infectivity factor, or Vif, is an accessory protein found in HIV and other lentiviruses. Its role is to disrupt the antiviral activity of the human enzyme APOBEC (specifically APOBEC3G, "A3G" in short) by targeting it for ubiquitination and cellular degradation. APOBEC is a cytidine deaminase enzyme that mutates viral nucleic acids. Vif is a 23-kilodalton protein that is essential for viral replication.

MBs also serve a non-viral vector for gene transfection through electrostatic bonds between a positively charged MB outer shell and negatively charged nucleic acids. The transient pores formed by microbubble collapse allow the genetic material to pass into the target cells in a safer and more specific manner than current treatment methods. MBs have been used to deliver microRNAs, plasmids, and small interfering RNA.

Multiple stereocenters may give rise to additional stereoisomers. On the other hand, a molecule with an even number of stereocenters may have one or more stereoisomers which are not chiral. Chirality is an important concept for stereochemistry and biochemistry. Most substances relevant to biology are chiral, such as carbohydrates (sugars, starch, and cellulose), the amino acids that are the building blocks of proteins, and the nucleic acids.

It labels all individual chromosomes at every stage of cell division to display structural and numerical abnormalities that may arise throughout the cycle. This is done with a probe that can be locus specific, centromeric, telomeric, and whole-chromosomal. This technique is typically preformed on interphase cells and paraffin block tissues. FISH maps out single copy or repetitive DNA sequences through localization labeling of specific nucleic acids.

The aqueous phase is always on top of the organic because, as mentioned above, phenol is denser than water. Nucleic acids are polar, and therefore stay in the aqueous phase, whereas non- polar cellular components move into the organic phase. After phenol has been added to the sample it is centrifuged and the aqueous and organic (“Phenol”) phases form. Phenol is often used in combination with chloroform.

Bah A, Wischnewski H, Shchepachev V, Azzalin CM. The telomeric transcriptome of Schizosaccharomyces pombe. Nucleic Acids Res 2012, 40:2995–3005. Both of these post-transcriptional modifications contribute to stabilizing TERRA within the cell (half-life ~8 hours) compared to non-modified transcripts (half-life ~3 hours). Additionally, the presence of a polyadenylated tail also appears to act as a determinant of TERRA localization within the nucleus.

This model of TERRA-telomerase interaction is supported by experimental evidence where TERRA-mimicking (UUAGGG)3 oligonucleotides have been shown to lead to complete inhibition of telomerase activity in vitro;Redon S, Reichenbach P, Lingner J. The non-coding RNA TERRA is a natural ligand and direct inhibitor of human telomerase. Nucleic Acids Res 2010, 38:5797–5806. however evidence of this relationship in vivo remains elusive.

Nucleic Acids Research. 34(22). 6505-6520 Such a model is plausible as WRKY family members are part of numerous phytohormone, developmental, and defense signaling transcriptional networks. Furthermore, W-box elements for WRKY binding occur in promoters of many other WRKY transcription factors Dong, Chen and Chen (2003) Expression profiles of the Arabidopsis WRKY gene superfamily during plant defense response. Plant Molecular Biology. 51(1).

Alexander Meissner, Andreas Gnirke, George W. Bell, Bernard Ramsahoye, Eric S. Lander and Rudolf Jaenisch. 2005. "Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis". Nucleic Acids Res. 33(18):5868-77 The fragments that comprise the reduced genome still include the majority of promoters, as well as regions such as repeated sequences that are difficult to profile using conventional bisulfite sequencing approaches.

At high pH (about 10) the dye binds to nucleic acids and all proteins. Although everything in the tissue is stained, structural details are clearly visible because of the thinness of the sections. Semi-thin sections are used in conjunction with ultra-thin sections examined by electron microscopy. Toluidine blue is also commonly used to stain frozen sections (rapid microscopic analysis of a specimen).

The Helicos patent applications (US Patent application 12/709,057 and 12/727,824) cover methods for detecting fetal nucleic acids and diagnosing fetal abnormalities. In July 2012, The United States District Court denied Sequenom's motion for a preliminary injunction motion against Ariosa Diagnostics. In August 2013, The Court of Appeals for the Federal Circuit vacated the District Court decision and remanded that case to the District Court.

Finally, tetraspanin proteins, including CD9, CD37, CD63 and CD81 are one of the most abundant protein families found in microvesicle membranes. Many of these proteins may be involved in the sorting and selection of specific cargos to be loaded into the lumen of the microvesicle or its membrane. Other than lipids and proteins, microvesicles are enriched with nucleic acids (e.g., messenger RNA (mRNA) and microRNA (miRNA).

The endoplasm, along with its granules, contains water, nucleic acids amino acids, carbohydrates, inorganic ions, lipids, enzymes, and other molecular compounds. It is the site of most cellular processes as it houses the organelles that make up the endomembrane system, as well as those that stand alone. The endoplasm is necessary for most metabolic activities, including cell division. The endoplasm, like the cytoplasm, is far from static.

Entrance to host cells begins infection, and is largely controlled by the US 2 viral protein. Envelope fusion with the plasma membrane of the host cell causes separation of the nucleocapsid from viral DNA and proteins. Multiple necessary viral proteins are located within the envelope. DNA and proteins enter the host cell nucleus and turn-off host cell synthesis of nucleic acids, proteins, and other macro molecules.

More generally they are covalently bonded to a macromolecule, serving as a marker (or dye, or tag, or reporter) for affine or bioactive reagents (antibodies, peptides, nucleic acids). Fluorophores are notably used to stain tissues, cells, or materials in a variety of analytical methods, i.e., fluorescent imaging and spectroscopy. Fluorescein, via its amine-reactive isothiocyanate derivative fluorescein isothiocyanate (FITC), has been one of the most popular fluorophores.

Prions are infectious pathogens that do not contain nucleic acids. Prions are abnormal proteins whose presence causes some diseases such as scrapie, bovine spongiform encephalopathy (mad cow disease), and Creutzfeldt–Jakob disease.The prion diseases STANLEY B. PRUSINER, Scientific American The discovery of prion as a new class of pathogen allowed Stanley B. Prusiner to receive the Nobel Prize in Physiology or Medicine in 1997.

The different types of topologies in G-quadruplex, propeller, lateral, and diagonal. G-quadruplexes, also known as G4 DNA are secondary structures found in nucleic acids that are rich in guanine. These structures are normally located at the telomeres (the ends of the chromosomes). The G-quadruplex can either be parallel or antiparallel depending on the loop configuration, which is a component of the structure.

Taq DNA polymerase A polymerase is an enzyme (EC 2.7.7.6/7/19/48/49) that synthesizes long chains of polymers or nucleic acids. DNA polymerase and RNA polymerase are used to assemble DNA and RNA molecules, respectively, by copying a DNA template strand using base-pairing interactions or RNA by half ladder replication. A DNA polymerase from the thermophilic bacterium, Thermus aquaticus (Taq) (PDB 1BGX, EC 2.7.

Nucleic acids are macromolecules that consist of DNA and RNA which are biopolymers consisting of chains of biomolecules. These two molecules are the genetic code and template that make life possible. Manipulation of these molecules and structures causes major changes in function and expression of other macromolecules. Nucleosides are glycosylamines containing a nucleobase bound to either ribose or deoxyribose sugar via a beta-glycosidic linkage.

Elsinochromes were proven to kill cells of the host plant and even cause necrotic legions on live tissue by reactions of a singlet oxygen species from the pigment. The singlet oxygen breaks down proteins, lipids, and nucleic acids in the plant cells. Toxicity has been demonstrated to decrease in the addition of singlet oxygen quenchers, as they prevent the interaction of the oxygen species with plant cells.

Virosomes are vehicles that have a spherical shape with a phospholipid mono/bilayer membrane. Inside of the virosome, there is a central cavity that holds the therapeutic molecules such as nucleic acids, proteins, and drugs. On the surface of the virosome, there can be different types of glycoproteins. Glycoproteins are a type of protein that have an oligosaccharide chain bonded to amino acid chains.

Animal metabolism of nitrogen in proteins, in general, results in excretion of urea, while animal metabolism of nucleic acids results in excretion of urea and uric acid. The characteristic odour of animal flesh decay is caused by the creation of long-chain, nitrogen-containing amines, such as putrescine and cadaverine, which are breakdown products of the amino acids ornithine and lysine, respectively, in decaying proteins.

ASO-based drugs employ highly modified, single-stranded chains of synthetic nucleic acids that achieve wide tissue distribution with very long half-lives.Weiss, B. (ed.): Antisense Oligodeoxynucleotides and Antisense RNA : Novel Pharmacological and Therapeutic Agents, CRC Press, Boca Raton, FL, 1997. For instance, many ASO- based drugs contain phosphorothioate substitutions and 2' sugar modifications to inhibit nuclease degradation enabling vehicle-free delivery to cells.

Nucleic acids are generally very large molecules. Indeed, DNA molecules are probably the largest individual molecules known. Well-studied biological nucleic acid molecules range in size from 21 nucleotides (small interfering RNA) to large chromosomes (human chromosome 1 is a single molecule that contains 247 million base pairs). In most cases, naturally occurring DNA molecules are double-stranded and RNA molecules are single-stranded.

In certain functions Pur-alpha interacts with family member Pur-beta. Several cell cycle regulatory functions may be mediated by Pur-alpha binding to Cyclin/Cdk protein kinases, which phosphorylate proteins regulating cell cycle transition points. Requirements for Pur-alpha in all organisms are united by Pur-alpha's ability to bind nucleic acids coupled to its ability to interact with regulatory and transport proteins.

Fixation is done to not only preserve sample, but also to increase permeability of cells to stains. However, most common fixation agents have the capacity to alter cells by changing certain aspects such as size, how light is scattered, autofluorescence and nucleic acids. This is problematic as flow cytometric distinction of cells relies on these qualities. Some fixatives also lead to complete loss of cells.

After purification of the nucleic acids, most often RNA, analysis is done by mass spectrometry. Mass spectrometry is an analytical technique that measures the mass-to-charge ratio of ions. Pairs of chemically identical nucleosides of different stable-isotope composition can be differentiated in a mass spectrometer due to their mass difference. Unlabeled nucleosides can therefore be distinguished from their stable isotope labeled isotopologues.

Schematic representation of a transfer stack. Electroblotting is a method in molecular biology/biochemistry/immunogenetics to transfer proteins or nucleic acids onto a membrane by using PVDF or nitrocellulose, after gel electrophoresis. The protein or nucleic acid can then be further analyzed using probes such as specific antibodies, ligands like lectins, or stains. This method can be used with all polyacrylamide and agarose gels.

Mrinalini Puranik is lead scientist at Unilever Limited. Her areas of research include biomolecular spectroscopy, Raman spectroscopy of proteins, and nucleic acids. She started her career as associate professor at Indian Institute of Science Education and Research, Pune (IISER). In 2015, her article "Solution structures of purine base analogues 9-deazaguanine and 9-deazahypoxanthine" was published by the Journal of Biomolecular Structure and Dynamics.

Nonionic detergents are produced by alkylation of phenol to give the alkylphenols, e.g., nonylphenol, which are then subjected to ethoxylation. Phenol is also a versatile precursor to a large collection of drugs, most notably aspirin but also many herbicides and pharmaceutical drugs. Phenol is a component in liquid–liquid phenol–chloroform extraction technique used in molecular biology for obtaining nucleic acids from tissues or cell culture samples.

The DNA ligase from bacteriophage T4 (a bacteriophage that infects Escherichia coli bacteria). The T4 ligase is the most-commonly used in laboratory research. It can ligate either cohesive or blunt ends of DNA, oligonucleotides, as well as RNA and RNA-DNA hybrids, but not single-stranded nucleic acids. It can also ligate blunt-ended DNA with much greater efficiency than E. coli DNA ligase.

Once the model of a molecule's structure has been finalized, it is often deposited in a crystallographic database such as the Cambridge Structural Database (for small molecules), the Inorganic Crystal Structure Database (ICSD) (for inorganic compounds) or the Protein Data Bank (for protein and sometimes nucleic acids). Many structures obtained in private commercial ventures to crystallize medicinally relevant proteins are not deposited in public crystallographic databases.

This protein is a member of the RUNX family of transcription factors and has a Runt DNA-binding domain. It is essential for osteoblastic differentiation and skeletal morphogenesis. It acts as a scaffold for nucleic acids and regulatory factors involved in skeletal gene expression. The protein can bind DNA both as a monomer or, with more affinity, as a subunit of a heterodimeric complex.

Lehn and coworkers in Helv. Chim. Acta, 2003, 86, 1598–1624. Dynamic view of an alpha-beta foldamer In chemistry, a foldamer is a discrete chain molecule or oligomer that folds into a conformationally ordered state in solution. They are artificial molecules that mimic the ability of proteins, nucleic acids, and polysaccharides to fold into well-defined conformations, such as helices and β-sheets.

Angelicin derivatives are used to treat psoriasis and cancer. One way of treating these diseases is by photochemotherapy (PUVA) which combines UV irradiation with photosensitizing chemical. In most cases the 4,5’-dimethylangelicin is applied owing to its firm binding and specificity to DNA. Also, it was shown that it is actively inhibits the synthesis of nucleic acids in tumor cells thereby decreasing their growth.

His research is on nucleic acids. He and his research group developed methods for the phosphoramidite synthesis of DNA. Using this technique, his group was able to incorporate nucleotide analogs for functional group mutagenesis for a deeper understanding of nucleic acid biochemistry. In addition to DNA, he developed methods of RNA synthesis and also for DNA analogues and the applications of the resulting molecules.

Pneumoviruses are pleomorphic, capable of producing spherical and filamentous enveloped virions (virus particles) that vary in size from 150 to 200 nm in diameter. The nucleocapsid consisting of a protein shell and viral nucleic acids has a helical symmetry. Nucleocapsids have a diameter of 13.5 nm and a helical pitch of 6.5 nm. The genome is composed of negative-sense single-stranded RNA that is non-segmented.

Bio-FETs couple a transistor device with a bio-sensitive layer that can specifically detect bio-molecules such as nucleic acids and proteins. A Bio-FET system consists of a semiconducting field-effect transistor that acts as a transducer separated by an insulator layer (e.g. SiO2) from the biological recognition element (e.g. receptors or probe molecules) which are selective to the target molecule called analyte.

The fluorescence can be detected by a sensor and the nucleic acid can be quantified. The presence of protein contaminants in the sample of nucleic acids to be tested does not make significant contributions to the absorbance, and thus allows for the addition of deoxyribonucleases to the protocol in order to degrade DNA, in the instances where one is only interested in detecting or quantifying RNA.

A major component of soil respiration is from the decomposition of litter which releases CO2 to the environment while simultaneously immobilizing or mineralizing nutrients. During decomposition, nutrients such as nitrogen are immobilized by microbes for their own growth. As these microbes are ingested or die, nitrogen is added to the soil. Nitrogen is also mineralized from the degradation of proteins and nucleic acids in litter.

Phoebus Levene Prior to James Watson and Francis Crick's landmark paper that detailed the structure of DNA from Rosalind Franklin's X-ray crystallography image, there were several historical scientists that also contributed to its discovery. Friedrich Miescher, a Swiss physician, who, in 1869, was first to isolate and identify nucleic substance from the nuclei of white blood cells he later called “nuclein”, paving the way for the discovery of DNA. Following Mieschers work, was the German biochemist, Albrecht Kossel, who, in 1878, isolated the non-protein components of “nuclein”, and discovered the five nucleobases present in nucleic acids: adenine, cytosine, guanine, thymine and uracil. Although some fundamental facts were known about nucleic acids due to these early discoveries, its structure and function remained a mystery. It wasn’t until the discovery of nucleotides in 1919 by Phoebus Levene, a Russian-Lithuanian biochemist that re-opened the gates of the DNA discovery.

Structure validation concept: model of a protein (each ball is an atom), and magnified region with electron density data and 3 bright flags for problems Macromolecular structure validation is the process of evaluating reliability for 3-dimensional atomic models of large biological molecules such as proteins and nucleic acids. These models, which provide 3D coordinates for each atom in the molecule (see example in the image), come from structural biology experiments such as x-ray crystallography or nuclear magnetic resonance (NMR). The validation has three aspects: 1) checking on the validity of the thousands to millions of measurements in the experiment; 2) checking how consistent the atomic model is with those experimental data; and 3) checking consistency of the model with known physical and chemical properties. Proteins and nucleic acids are the workhorses of biology, providing the necessary chemical reactions, structural organization, growth, mobility, reproduction, and environmental sensitivity.

A hypercycle with translation. Analysis of potential molecules that could form the first hypercycles in nature prompted the idea of coupling an information carrier function with enzymatic properties. At the time of the hypercycle theory formulation, enzymatic properties were attributed only to proteins, while nucleic acids were recognized only as carriers of information. This led to the formulation of a more complex model of a hypercycle with translation.

Sulfur-35 is used to label proteins and nucleic acids. Cysteine is an amino acid containing a thiol group which can be labeled by S-35. For nucleotides that do not contain a sulfur group, the oxygen on one of the phosphate groups can be substituted with a sulfur. This thiophosphate acts the same as a normal phosphate group, although there is a slight bias against it by most polymerases.

During or immediately following transcription of pre-rRNA from rDNA in the nucleolus, the ribosomal RNA precursor (pre-rRNA) is modified and associates with a few ribosomal proteins.Marmier-Gourrier N, Cle´ry A, Schlotter F, Branlant C. A second base pair interaction between U3 small nucleolar RNA and the 5’-ETS region is required for early cleavage of the yeast pre-ribosomal RNA. Nucleic Acids Research. 2011; 39.

Some DNA molecules are circular and are topologically constrained. More recently circular RNA was described as well to be a natural pervasive class of nucleic acids, expressed in many organisms (see CircRNA). A covalently closed, circular DNA (also known as cccDNA) is topologically constrained as the number of times the chains coiled around one other cannot change. This cccDNA can be supercoiled, which is the tertiary structure of DNA.

In biochemistry, the molar attenuation coefficient of a protein at depends almost exclusively on the number of aromatic residues, particularly tryptophan, and can be predicted from the sequence of amino acids. Similarly, the extinction coefficient of nucleic acids at 260 nm can be predicted given the nucleotide sequence. If the molar attenuation coefficient is known, it can be used to determine the concentration of a protein in solution.

Cherries contain many different phenolic compounds and anthocyanins, which are indicators of being rich in antioxidants. Recent research has linked the phenolic compounds of the sweet cherry (Prunus avium) with antitumor properties. Reactive oxygen species (ROS) include superoxide radicals, hydrogen peroxide, hydroxyl radicals, and singlet oxygen; they are the byproducts of metabolism. High levels of ROS lead to oxidative stress, which causes damage to lipids, proteins, and nucleic acids.

The 15.5-kDa protein also exists as one of the four core proteins of the C/D small nucleolar ribonucleoprotein that mediates methylation of pre-ribosomal RNAs. Structural evidence supporting the idea that fibrillarin is the snoRNA methyltransferase has been reviewed.The structure and function of small nucleolar ribonucleoproteins by Steve L. Reichow, Tomoko Hamma, Adrian R. Ferré-D'Amaré and Gabriele Varani in Nucleic Acids Research (2007) Volume 35, pages 1452–1464.

Magnetofection has been adapted to all types of nucleic acids (DNA, siRNA, dsRNA, shRNA, mRNA, ODN), non viral transfection systems (transfection reagents) and viruses. It has been successfully tested on a broad range of cell lines, hard-to-transfect and primary cells. Several optimized and efficient magnetic nanoparticle formulations have been specifically developed for several types applications such as DNA, siRNA, and primary neuron transfection as well as viral applications.

Wilma K. Olson (born c. 1945) is the Mary I. Bunting professor at the Rutgers Center for Quantitative Biology (CQB) (formerly known as BioMaPS institute for Quantitative Biology) at Rutgers University. Olson has her own research group on the New Brunswick campus. Although she is a polymer chemist by training, her research aims to understand the influence of chemical architecture on the conformation, properties, and interactions of nucleic acids.

The Virus Pathogen Database and Analysis Resource (ViPR) Virus Pathogen Database and Analysis Resource (ViPR)Pickett B.E., Sadat E.L., Zhang Y., et al. ViPR:also called bacterioghoages an open bioinformatics database and analysis resource for virology research. Nucleic Acids Research 2011 doi:10.1093/nar/gkr859Pickett B.E., Greer D.S., Zhang Y., et al. Virus Pathogen Database and Analysis Resource (ViPR): A Comprehensive Bioinformatics Database and Analysis Resource for the Coronavirus Research Community. Viruses.

Figure 1 illustrates the alignment result when one protein sequence and one DNA sequence was aligned using normal protein-DNA alignment algorithm. The frame used was frame 1 for the DNA sequence. As shown in the picture, there was a gap of 2 amino acids (6 nucleic acids) in the alignment, which results the total low score of -2. Figure 1 Figure 2 illustrates the aligned result using PairWise.

Many of the questions surrounding neuroscience attempt to answer and understand molecules and wiring in neural circuits. However, mapping these structures across the large scales of neural circuits is difficult. In these cases, ExM magnifies biological specimens such as brain circuits and allows them to be more easily mapped. Biomolecules, such as proteins and nucleic acids, are anchored to the polymer, which is then swelled in order to expand the biomolecules.

Examples include macromolecules such as proteins and nucleic acids, biomolecular complexes such as a ribosome, and structures such as membranes, and organelles. While the majority of cellular components are located within the cell itself, some may exist in extracellular areas of an organism. Cellular components may also be called biological matter or biological material. Most biological matter has the characteristics of soft matter, being governed by relatively small energies.

However, the mutants which form the genetic basis for a variety of human diseases are usually slightly different from the normal nucleic acids. Often, they are only different in a single base, e.g., insertions, deletions, and single-nucleotide polymorphisms (SNPs). In this case, imperfect probe-target binding can easily occur, resulting in false-positive outcomes such as mistaking a strain that is commensal for one that is pathogenic.

FISH images of chromosomes from dividing orangutan (left) and human (right) cells. Yellow probe shows 4 copies of a region in the orangutan genome and only 2 copies in human. Fluorescence In Situ Hybridization maps out single copy or repetitive DNA sequences through localization labeling of specific nucleic acids. The technique utilizes different DNA probes labeled with fluorescent tags that bind to one or more specific regions of the genome.

DNA nanotechnology is one important example of bionanotechnology. The utilization of the inherent properties of nucleic acids like DNA to create useful materials is a promising area of modern research. Another important area of research involves taking advantage of membrane properties to generate synthetic membranes. Proteins that self-assemble to generate functional materials could be used as a novel approach for the large-scale production of programmable nanomaterials.

3,3'-Diaminobenzidine (DAB) is an organic compound with the formula (C6H3(NH2)2)2. This derivative of benzidine is a precursor to polybenzimidazole, which forms fibers that are renowned for their chemical and thermal stability.Hans Schwenecke, Dieter Mayer "Benzidine and Benzidine Derivatives" in Ullmann’s Encyclopedia of Industrial Chemistry, 2005, Wiley- VCH, Weinheim. As its water-soluble tetrahydrochloride, DAB has been used in immunohistochemical staining of nucleic acids and proteins.

PCNA (PDB ), a sliding DNA clamp protein that is part of the DNA replication complex and serves as a processivity factor for DNA polymerase. The three individual polypeptide chains that make up the trimer are shown. In biochemistry, a protein trimer is a macromolecular complex formed by three, usually non-covalently bound, macromolecules like proteins or nucleic acids. A homo-trimer would be formed by three identical molecules.

Though the mechanism is as of yet unclear, RNA-dependent RNA polymerase RrpC has been shown to post-transcriptionally silence retrotransposons in Dictyostelium.Wiegand, S., Meier, D., Seehafer, C., Malicki, M., Hofmann, P., Schmith, A., et al. (2014). The Dictyostelium discoideum RNA-dependent RNA polymerase RrpC silences the centromeric retrotransposon DIRS-1 post- transcriptionally and is required for the spreading of RNA silencing signals. [Article]. Nucleic Acids Research, 42(5), 3330-3345.

Nucleic acids are a key component of DNA, the main genetic information-storing substance, found oftentimes in the cell nucleus, and controls the metabolic processes of the cell. DNA consists of two complementary antiparallel strands consisting of varying patterns of nucleotides. RNA is a single strand of DNA, which is transcribed from DNA and used for DNA translation, which is the process for making proteins out of RNA sequences.

Together p33 and p92 comprise the viral replicase complex. P33 is smaller and p92 is produced through ribosomal read-through of the p33 stop codon, resulting in a shared N-terminal amino acid sequence and a large excess of p33 relative to p92. P33 proteins cooperatively bind single- stranded nucleic acids, while the p92 protein is a RNA-dependent RNA polymerase (RdRp). Both are essential to viral proliferation.

Another example related to aging is the Free Radical theory. Free Radical Theory suggests that the free radicals, which are being produced by aerobic respiration, are causing oxidative stress to be put on the body. This oxidative stress will result in aging and lead to death. Oxygen centered radicals are very reactive and can cause the accumulation of damage on lipids, nucleic acids as well as proteins within the body.

His first work there was investigating DNA damage caused by radiation. Paleček later worked with the Masaryk Memorial Cancer Institute, part of Masaryk University. In 1960, Paleček discovered that nucleic acids could be analysed through electrochemical research, which allowed him to explore how DNA can be used to diagnose genetic diseases. His discovery contradicted previous assumptions from the 1950s that DNA molecules were too large to be analysed by electrochemical research.

S-Adenosyl methionine (SAM-e) is a common cosubstrate involved in methyl group transfers, transsulfuration, and aminopropylation. Although these anabolic reactions occur throughout the body, most SAM-e is produced and consumed in the liver. More than 40 methyl transfers from SAM-e are known, to various substrates such as nucleic acids, proteins, lipids and secondary metabolites. It is made from adenosine triphosphate (ATP) and methionine by methionine adenosyltransferase.

An important resource for finding biological databases is a special yearly issue of the journal Nucleic Acids Research (NAR). The Database Issue of NAR is freely available, and categorizes many of the publicly available online databases related to biology and bioinformatics. A companion database to the issue called the Online Molecular Biology Database Collection lists 1,380 online databases. Other collections of databases exist such as MetaBase and the Bioinformatics Links Collection.

The research interests of V. Šikšnys include structure-function relationships of enzymes involved in nucleic acids metabolism. V. Šikšnys and members of his laboratory perform biochemical, biophysical and structural studies of proteins involved in bacterial antiviral defense, including restriction endonucleases and CRISPR-Cas systems. V. Šikšnys has co-authored more than 90 scientific publications and filled 5 patent applications. For more than two decades Šikšnys’ lab was focused on restriction endonucleases.

There are several techniques to produce peptides chemically, generally it is by solid-phase protection chemistry. This means that any (protected) amino acid can be added into the nascent sequence. In November 2017, a team from the Scripps Research Institute reported having constructed a semi-synthetic E. coli bacteria genome using six different nucleic acids (versus four found in nature). The two extra 'letters' form a third, unnatural base pair.

Singer was born in New York City. After attending Midwood High School in Brooklyn, she majored in chemistry (and minored in biology) at Swarthmore College. She went on to earn a Ph.D. in 1957 at Yale University, researching protein chemistry under Joseph Fruton. Fruton encouraged her to specialize in nucleic acids, and in 1956 she joined the Laboratory of Biochemistry of Leon Heppel at the National Institutes of Health.

When a sequence motif appears in the exon of a gene, it may encode the "structural motif" of a protein; that is a stereotypical element of the overall structure of the protein. Nevertheless, motifs need not be associated with a distinctive secondary structure. "Noncoding" sequences are not translated into proteins, and nucleic acids with such motifs need not deviate from the typical shape (e.g. the "B-form" DNA double helix).

Nucleic acids are important for the manufacturing of DNA and RNA and transmitting of traits to offspring through genes. Carbonic acid is important for maintenance of pH equilibrium in the body. Human bodies contain a variety of organic and inorganic compounds, among those dicarboxylic acids play an essential role in many biological behaviors. Many of those acids are amino acids which mainly serve as materials for the synthesis of proteins.

148: 49–61. Ultraviolet irradiation can be used to excite nucleic acids and create photoreactions, which results in damaged bases in the DNA strand. Photoreactions can include: single strand breaks, interactions between or within DNA strands, reactions with solvents, or crosslinks with proteins. The workflow for this method has an additional step, once both your protected and unprotected DNA have been treated, there is subsequent primer extension of the cleaved products.

Cartoon diagram of a dimer of Escherichia coli galactose-1-phosphate uridylyltransferase (GALT) in complex with UDP-galactose (stick models). Potassium, zinc, and iron ions are visible as purple, gray, and bronze-colored spheres respectively. In biochemistry, a protein dimer is a macromolecular complex formed by two protein monomers, or single proteins, which are usually non-covalently bound. Many macromolecules, such as proteins or nucleic acids, form dimers.

Biomolecular engineering deals with the manipulation of many key biomolecules. These include, but are not limited to, proteins, carbohydrates, nucleic acids, and lipids. These molecules are the basic building blocks of life and by controlling, creating, and manipulating their form and function there are many new avenues and advantages available to society. Since every biomolecule is different, there are a number of techniques used to manipulate each one respectively.

Hubbard's research interests are in Bioinformatics, Computational biology and Genome Informatics. During his tenure at WTSI he supervised several successful PhD students to completion in these areas of research. Hubbard was appointed Professor of Bioinformatics at King's in October 2013. His research has been published in leading peer reviewed scientific journals including Nature, the Journal of Molecular Biology, Nucleic Acids Research, Genome Biology, Nature Methods, Nature Reviews Cancer and Bioinformatics.

RNA with its nucleobases to the left and DNA to the right. Nucleic acid analogues are compounds which are analogous (structurally similar) to naturally occurring RNA and DNA, used in medicine and in molecular biology research. Nucleic acids are chains of nucleotides, which are composed of three parts: a phosphate backbone, a pentose sugar, either ribose or deoxyribose, and one of four nucleobases. An analogue may have any of these altered.

Expression of TLR 7 and TLR 9 allows pDCs to interact with viral and host nucleic acids. TLR 7 and TLR 9 detect ssRNA and unmethylated CpG DNA sequences, respectively. ILT7 and BDCA-4 are also expressed on human pDC surfaces, although their signaling pathways are still obscure. However, there are speculations that the interaction between ILT7 and BST2 may have a negative regulatory effect on the cell’s interferon production.

Raman amplification is used in optical amplifiers. The Raman effect is also involved in producing the appearance of the blue sky (see Rayleigh Scattering: 'Rayleigh scattering of molecular nitrogen and oxygen in the atmosphere includes elastic scattering as well as the inelastic contribution from rotational Raman scattering in air'). Raman spectroscopy has been used to chemically image small molecules, such as nucleic acids, in biological systems by a vibrational tag.

Antibody mimetics are organic compounds, like antibodies, that can specifically bind antigens. They are usually artificial peptides or proteins with a molar mass of about 3 to 20 kDa. Nucleic acids and small molecules are sometimes considered antibody mimetics, but not artificial antibodies, antibody fragments, and fusion proteins are composed from these. Common advantages over antibodies are better solubility, tissue penetration, stability towards heat and enzymes, and comparatively low production costs.

Other than denaturation by heat, nucleic acids can undergo the denaturation process through various chemical agents such as formamide, guanidine, sodium salicylate, dimethyl sulfoxide (DMSO), propylene glycol, and urea. These chemical denaturing agents lower the melting temperature (Tm) by competing for hydrogen bond donors and acceptors with pre-existing nitrogenous base pairs. Some agents are even able to induce denaturation at room temperature. For example, alkaline agents (e.g.

TBE or Tris/Borate/EDTA, is a buffer solution containing a mixture of Tris base, boric acid and EDTA. In molecular biology, TBE and TAE buffers are often used in procedures involving nucleic acids, the most common being electrophoresis. Tris-acid solutions are effective buffers for slightly basic conditions, which keep DNA deprotonated and soluble in water. EDTA is a chelator of divalent cations, particularly of magnesium (Mg2+).

Uramustine (INN) or uracil mustard is a chemotherapy drug which belongs to the class of alkylating agents. It is used in lymphatic malignancies such as non- Hodgkin's lymphoma. It works by damaging DNA, primarily in cancer cells that preferentially take up the uracil due to their need to make nucleic acids during their rapid cycles of cell division. The DNA damage leads to apoptosis of the affected cells.

Satellite tobacco mosaic virus molecular graphics produced in VMD and rendered using Tachyon. The scene is shown with a combination molecular surfaces colored by a radial distance, and nucleic acids shown in ribbon representations. The Tachyon rendering uses both direct lighting and ambient occlusion lighting to improve the visibility of pockets and cavities. The VMD axes are shown as a simple example of rendering of non-molecular geometry.

PCR inhibitors are any factor which prevent the amplification of nucleic acids through the polymerase chain reaction (PCR). PCR inhibition is the most common cause of amplification failure when sufficient copies of DNA are present. PCR inhibitors usually affect PCR through interaction with DNA or interference with the DNA polymerase. Inhibitors can escape removal during the DNA purification procedure by binding directly to single or double-stranded DNA.

Maurice Stroun (born September 3, 1926) is a researcher and professor at the University of Geneva in the Department of Plant Biochemistry and Physiology. He is known for first hypothesizing and demonstrating the existence of disease-specific circulating nucleic acids as well as first developing techniques for the detection of tumor-related characteristics of circulating DNA and RNA in plasma and serum, or liquid biopsies as this field is now known.

In 1937 Bell arrived at the University of Leeds, where she joined Astbury's laboratory. During her graduate studies she used X-ray diffraction to characterise biomolecules, including nucleic acids. Her initial work was on the structure of protein multilayers, but after Leeds received samples of highly purified DNA, Astbury directed her to study DNA as the second part of her Ph.D. thesis. She received her Ph.D. in 1939.

WU virus was discovered by shotgun sequencing of the nucleic acids found in the respiratory secretions of a young patient diagnosed with pneumonia in whom other known respiratory viruses had not been detected. Sequence homology was detected among the sequences found in the clinical sample and the known genomes of other human polyomaviruses. WU virus was one of two new human polyomaviruses discovered in 2007; the other was KI virus.

Nitrogen is essential for algal growth. Within a cell, nitrogen is involved in synthesizing amino acids, nucleic acids, chlorophyll, and other nitrogen-containing organic compounds. In a study in which 30 different microalgal strains were screened, one Nannochloropsis strain was shown to obtain 60% lipid content after nitrogen deprivation, up from 30% under normal growth conditions. This strain was selected for further scale-up experiments in a photobioreactor under natural sunlight.

In molecular biology, exonuclease VII (, Escherichia coli exonuclease VII, E. coli exonuclease VII, endodeoxyribonuclease VII, Exodeoxyribonuclease VII) is a bacterial exonuclease enzyme. It is composed of two nonidentical subunits; one large subunit and 4 small ones. Exonuclease VII catalyses exonucleolytic cleavage in either 5'-3' or 3'-5' direction to yield 5'-phosphomononucleotides. The large subunit also contains an N-terminal OB- fold domain that binds to nucleic acids.

In 1883, Kossel left Strassburg to become Director of the Chemistry Division of the Physiological Institute at the University of Berlin. In this post, he succeeded Eugen Baumann and worked under the supervision of Emil du Bois-Reymond. Kossel continued his previous work on the nucleic acids. During the period 1885 to 1901, he was able to isolate and name its five constituent organic compounds: adenine, cytosine, guanine, thymine, and uracil.

Dynamics 2013, 242, no p.n. In Drosophila melanogaster (fly), Caenorhabditis elegans (worm), and other lower animals SoxC is made up of only one member, but humans, mice and most other vertebrates have three members of the SoxC group.Dy, P. et al. The three SoxC proteins–Sox4, Sox11 and Sox12–exhibit overlapping expression patterns and molecular properties. Nucleic Acids Research 2008, 36, 3101–3117 The three are Sox4, Sox11, and Sox12.

52(6): p. 1179. The nucleic interactions of cyclobuxine has been well-studied in one particular research. It was found that cyclobuxine has a biphasic effect on the stability of nucleic acids. This means that at low concentrations, cyclobuxine has a favourable effect of stabilization on the original conformation of DNA and other polydeoxynucleotides, it has an adverse effect of destabilization on the original structure at high concentrations.

The interaction between carbon nanotubes and biomolecules has been widely studied because of their potential to be used in biological applications. The modification of the carbon nanotubes with proteins, carbohydrates, and nucleic acids are built with the bottom-up technique. Proteins have high affinity to carbon nanotubes due to their diversity of amino acids being hydrophobic or hydrophilic. Polysaccharides have been successfully been used to modify carbon nanotubes forming stable hybrids.

This is associated with the accumulation of nucleic acids which is important for both dormancy and germination of the akinete. Despite being a resting cell, it is still capable of some metabolic activities such as photosynthesis, protein synthesis, and carbon fixation, albeit at significantly lower levels. Akinetes can remain dormant for extended periods of time. Studies have shown that some species could be cultured that were 18 and 64 years old.

The dyes bind to the minor groove of double- stranded DNA with a preference for sequences rich in adenine and thymine. Although the dyes can bind to all nucleic acids, AT-rich double-stranded DNA strands enhance fluorescence considerably. Hoechst dyes are cell-permeable and can bind to DNA in live or fixed cells. Thus, these stains are often called supravital, meaning that live cells survive a treatment with these compounds.

Nucleic acids have the property that two molecules will only bind to each other to form a double helix if the two sequences are complementary, meaning that they form matching sequences of base pairs, with A only binding to T, and C only to G.Background: Because the formation of correctly matched base pairs is energetically favorable, nucleic acid strands are expected in most cases to bind to each other in the conformation that maximizes the number of correctly paired bases. The sequences of bases in a system of strands thus determine the pattern of binding and the overall structure in an easily controllable way. In DNA nanotechnology, the base sequences of strands are rationally designed by researchers so that the base pairing interactions cause the strands to assemble in the desired conformation. While DNA is the dominant material used, structures incorporating other nucleic acids such as RNA and peptide nucleic acid (PNA) have also been constructed.

Early cover of the General Subjects section Biochimica et Biophysica Acta was published as a single title until 1962, when additional sections began to be published alongside the main journal: first Specialized Section on Nucleic Acids and Related Subjects and then, from 1963, Specialized Section on Enzymological Subjects and Specialized Section on Lipids and Related Subjects.OHSU Library: BBA Decoder (accessed 10 December 2008) In 1964, the main journal became Biochimica et Biophysica Acta (BBA) – General Subjects, and was published alongside the three established sections plus Specialized Section on Biophysical Subjects and Specialized Section on Mucoproteins and Mucopolysaccharides. In 1965, the specialist sections were renamed, becoming Biophysics including Photosynthesis, Nucleic Acids and Protein Synthesis, Enzymology and Biological Oxidation, Lipids and Lipid Metabolism and Mucoproteins and Mucopolysaccharides (ceased in 1965). In 1967, Biophysics including Photosynthesis split into Bioenergetics and Biomembranes, and Enzymology and Biological Oxidation split into Enzymology and Protein Structure; the latter pair rejoined in 1982 to become Protein Structure and Molecular Enzymology.

The diameter of TNTs ranges from 50 to 200 nm and they can reach lengths of several cell diameters. These structures may be involved in cell-to-cell communication, transfer of nucleic acids between cells in a tissue, and the spread of pathogens or toxins such as HIV and prions. TNTs have observed lifetimes ranging from a few minutes up to several hours, and several proteins have been implicated in their formation or inhibition.

Zinc-finger proteins bind nucleic acids and play important roles in various cellular functions, including cell proliferation, differentiation, and apoptosis. This protein and Grb10-interacting GYF protein 2 have been identified as a components of the mammalian 4EHP (m4EHP) complex. The complex is thought to function as a translation repressor in embryonic development. ZNF598 and its yeast homologue Hel2 are ubiquitin ligases that ubiquitinate the 40S ribosomal subunit during ribosome-associated protein quality control.

Rho is a member of the RecA/SF5 family of ATP-dependent hexameric helicases that function by wrapping nucleic acids around a single cleft extending around the entire hexamer. Rho functions as an ancillary factor for RNA polymerase. There are two types of transcriptional termination in prokaryotes, rho-dependent termination and intrinsic termination (also called Rho-independent termination). Rho-dependent terminators account for about half of the E. coli factor-dependent terminators.

Supported by the NCBI, The Online Mendelian Inheritance in Man (OMIM) is a database that catalogues all the known diseases with a genetic component, and predicts their relationship to relevant genes in the human genome and provides references for further research and tools for genomic analysis of a catalogued gene.A. Homosh, "Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders," Nucleic Acids Research, vol. 33, no. 1, pp.

High-resolution structures of two complexes between thrombin and thrombin-binding aptamer shed light on the role of cations in the aptamer inhibitory activity. Nucleic Acids Research 40, 8119-8128, doi:10.1093/nar/gks512 (2012). were provided, another topology with the TGT loop on the wide side and the TT loops on the narrow sites has been considered as a correct structure of TBA. In addition to protein-selectivity, TBA also shows ion preference.

Protein-ligand complexes can be found in almost any cellular process. Binding of a ligand causes a conformational change in the protein and often also in the ligand. This change initiates a sequence of events leading to different cellular functions. The complexes are formed by different molecules like macromolecules as in protein complexes, protein DNA or protein RNA complexes as well as by proteins that bind smaller molecules like peptides, lipids, carbohydrates, small nucleic acids.

The diagnosis by symptoms is not reliable enough so it’s better to do a molecular diagnosis based in test samples. Some of these methods (like Dot-blot hybridisation) allow the scientists to detect the viroid even six months before noticing the first symptoms. The first step is the purification to obtain the nucleic acids of the plant cells. The leaves of the plant located four or more below the spare leaf are cut.

IV. DNA sequence of the region from 89.2 to 92.8 minutes. Nucleic Acids Res. 1993 Nov 25;21(23):5408-17.y During his stay at UCSC Brosius met visiting professor Carl Woese, who incited his interest in evolutionary thought and the power of molecular phylogenetic analysis. His second postdoctoral fellowship (1980–1982), supported by the Deutsche Forschungsgesellschaft, took him to the laboratory of Walter Gilbert, Nobel prize laureate in Chemistry (1980), at Harvard University.

This allows the concentration of the QR-substance (could be a protein or nucleic acids) to be measured. This also indirectly allows the binding ability of QR to the substance to be measured. Using this technique gives an emission wavelength of 520/160 nm. QR's ability to bind to substrates and fluoresce can be further utilized to determine the location of a substrate with the use of Raman spectroscopy and the electronic absorption spectra.

By the early 1930s various firms manufactured ultraviolet fluorescent microscopes. The stage was set for cytometry to now go beyond the now established hemocytometer. At this time, Torbjörn Caspersson, working at the Karolinska Institute in Stockholm, developed a series of progressively more sophisticated instruments called cytophotometers. These instruments combined a fluorescent microscope with a spectrophotometer to quantify cellular nucleic acids and their relation to cell growth and function. Caspersson’s early apparatus now seems hopelessly primitive.

Molecular building blocks of life Primary metabolites as defined by Kossel are components of basic metabolic pathways that are required for life. They are associated with essential cellular functions such as nutrient assimilation, energy production, and growth/development. They have a wide species distribution that span many phyla and frequently more than one kingdom. Primary metabolites include carbohydrates, lipids, amino acids, and nucleic acids which are the basic building blocks of life.

The device to read such a plate is known as a phosphorimager (occasionally spelled phosphoimager, perhaps reflecting its common application in molecular biology for detecting radiolabeled phosphorylated proteins and nucleic acids). Projectional radiography using a photostimulable phosphor plate as an X-ray detector can be called "phosphor plate radiography" or "computed radiography" (not to be confused with computed tomography which uses computer processing to convert multiple projectional radiographies to a 3D image).

The two most common masses of individual acetylsalicylic acid molecules are and . The molecular masses of proteins, nucleic acids, and other large polymers are often expressed with the units kilodaltons (kDa), megadaltons (MDa), etc. Titin, one of the largest known proteins, has a molecular mass of between 3 and 3.7 megadaltons. The DNA of chromosome 1 in the human genome has about 249 million base pairs, each with an average mass of about , or total.

Examples of potentiometric biosensors include ion-sensitive field effect transistors (ISFET), Chemical field-effect transistors (chem-FET), and light-addressable potentiometric sensors (LAPS). In conductometric biosensors, changes in electrical impedance between two electrodes are measured as a result of a biomolecular reaction. Conductive measurements are simple and easy to use because there is no need for a specific reference electrode, and have been used to detect biochemicals, toxins, nucleic acids, and bacterial cells.

It can also be formed by the deamination of adenosine monophosphate by AMP deaminase. It can be hydrolysed to inosine. The enzyme deoxyribonucleoside triphosphate pyrophosphohydrolase, encoded by YJR069C in Saccharomyces cerevisiae and containing (d)ITPase and (d)XTPase activities, hydrolyzes inosine triphosphate (ITP) releasing pyrophosphate and IMP. Important derivatives of inosinic acid include the purine nucleotides found in nucleic acids and adenosine triphosphate, which is used to store chemical energy in muscle and other tissues.

PubMeth is a database that contains information about DNA hypermethylation in cancer. It can be queried either by searching a list of genes, or cancer (sub)types. It was created at the lab for bioinformatics and computational genomics in the Department of Molecular Biotechnology, Faculty of Bioscience Engineering at Ghent University, Belgium. It was published in Nucleic Acids Research Maté Ongenaert, Leander Van Neste, Tim De Meyer, Gerben Menschaert, Sofie Bekaert, and Wim Van Criekinge.

Genetic Code ChartBy the Cold Spring Harbor Symposium of 1966, between Nirenberg and Khorana the genetic code was almost completely decoded. Nirenberg was awarded the 1968 Nobel Prize in Physiology or Medicine. He shared the award with Har Gobind Khorana of the University of Wisconsin and Robert W. Holley of the Salk Institute. Working independently, Khorana had mastered the synthesis of nucleic acids, and Holley had discovered the exact chemical structure of transfer-RNA.

DEAE-Dextran (DEAE-D) is a positively charged dextran derivative that can be used for vaccine production, gene therapy, protein stabilization, dyslipidemia prevention, flocculating agents, and many other applications. DEAE-D is also used for transfecting animal cells with foreign DNA. It is added to solution containing DNA meant for transfection. It binds and interacts with negatively charged DNA molecules and via an unknown mechanism brings about the uptake of nucleic acids by the cell.

N-Nitroso-N-methylurea (NMU) is a highly reliable carcinogen, mutagen, and teratogen. NMU is an alkylating agent, and exhibits its toxicity by transferring its methyl group to nucleobases in nucleic acids, which can lead to AT:GC transition mutations. NMU is the traditional precursor in the synthesis of diazomethane. It has the potentially advantageous property that the stoichiometric byproducts formed are water, carbon dioxide, and ammonia, which are innocuous or easily removed.

Her research has been funded by the Medical Research Council and the Biotechnology and Biological Sciences Research Council (BBSRC). Orengo is co-editor with David Jones and Janet Thornton of the textbook Bioinformatics: Genes, Proteins and Computers. , according to Google Scholar and Scopus her most cited work has been published in Nature, Nucleic Acids Research, Structure and the Journal of Molecular Biology. Her former doctoral students include Sonja Lehtinen and Ian Sillitoe.

Brand, Fischer, Harter, Kohlbacher and Wanke (2013) Elucidating the evolutionary conserved DNA-binding specificities of WRKY transcription factors by molecular dynamics and in vitro binding assays. Nucleic Acids Research. 41(21). 9764-9778 The original WRKY protein domain has been proposed to have arisen from the GCM1 and FLYWCH zinc finger factors.Babu, Iyer, Balaji and Aravind (2006) The natural history of the WRKY–GCM1 zinc fingers and the relationship between transcription factors and transposons.

The replication of the agent would depend on how the particular strain interacted with the replication site and of what the site was composed. The fact that different strains of scrapie were known had suggested the agent was similar to conventional viruses in that it carried a genome composed of nucleic acids. Thus, variants could arise during incubation, giving rise to new strains. No host-encoded properties were found to determine scrapie agent strain differences.

Adenine Thymine Guanine Cytosine Uracil A nitrogenous base, or nitrogen- containing base, is an organic molecule with a nitrogen atom that has the chemical properties of a base. The main biological function of a nitrogenous base is to bond nucleic acids together. A nitrogenous base owes its basic properties to the lone pair of electrons of a nitrogen atom. Nitrogenous bases are typically classified as the derivatives of two parent compounds, pyrimidine and purine.

For example, transitions tend to occur more often than transversions in the evolution of nucleic acids. This assumption can be relaxed by assigning differential costs to specific character state changes, resulting in a weighted parsimony algorithm. # Rapid evolution. The upshot of the "minimum evolution" heuristic underlying such methods is that such methods assume that changes are rare, and thus are inappropriate in cases where change is the norm rather than the exception.

Metabolism-like reactions could have occurred naturally in early oceans, before the first organisms evolved. Metabolism may predate the origin of life, which may have evolved from the chemical conditions in the earliest oceans. Reconstructions in laboratories show that some of these reactions can produce RNA, and some others resemble two essential reaction cascades of metabolism: glycolysis and the pentose phosphate pathway, that provide essential precursors for nucleic acids, amino acids and lipids.

"Effect of viral infection on sinking rates of Heterosigma akashiwo and its implications for bloom termination." Aquatic microbial ecology37.1 (2004): 1-7. The biological pump has an important role at sequestering carbon to the benthic zone, thereby impacting global carbon cycles, budget, and even affecting temperature. Crucial nutrients, such as nitrogen, phosphorus, cellular components, such as amino acids and nucleic acids, would be sequestered through the biological pump in the event of cells sinking.

All constituents in a DCL are in equilibrium, and their distribution is determined by their thermodynamic stability within the DCL. The interconversion of these building blocks may involve covalent or non-covalent interactions. When a DCL is exposed to an external influence (such as proteins or nucleic acids), the equilibrium shifts and those components that interact with the external influence are stabilised and amplified, allowing more of the active compound to be formed.

Lipid bilayers are generally impermeable to ions and polar molecules. The arrangement of hydrophilic heads and hydrophobic tails of the lipid bilayer prevent polar solutes (ex. amino acids, nucleic acids, carbohydrates, proteins, and ions) from diffusing across the membrane, but generally allows for the passive diffusion of hydrophobic molecules. This affords the cell the ability to control the movement of these substances via transmembrane protein complexes such as pores, channels and gates.

A tetrapeptide, a hetero-oligomer of the amino acids valine (green), glycine (black), serine (black), and alanine (blue). The units were joined by condensation of the carboxylic acid group –C(=O)OH of one monomer with the amine group of the next one. Some biologically important oligomers consist of macromolecules like proteins or nucleic acids; for instance, hemoglobin is a protein tetramer. An oligomer of amino acids is called an oligopeptide or just a peptide.

C2C12 cells have been shown to effectively incorporate exogenous cDNA and nucleic acids by transfection. In the piloting research originally conducted by Yaffe and Saxel, C2C12 were obtained through serial passage of myoblasts cultured from the thigh muscle of C3H mice after crush injury. In their study, a set of C2C12 cells were cultured from mice homozygous recessive for the dy gene. These mice exhibited a syndrome similar to early-onset human muscular dystrophy.

He became an American citizen in 1940. During his time at Columbia, Chargaff published numerous scientific papers, dealing primarily with the study of nucleic acids such as DNA using chromatographic techniques. He became interested in DNA in 1944 after Oswald Avery identified the molecule as the basis of heredity. In 1950, he published that the amounts of adenine and thymine in DNA were roughly the same, as were the amounts of cytosine and guanine.

The amino acids are characterised by having a variety of side chains which vary from being hydrophilic to hydrophobic: their individual characters reside in the very different properties these side chains have. By contrast, a nucleic acid is composed of a string of nucleotides whose sequence presents a geometrically defined surface for hydrogen bonding. This makes nucleic acids good at recognising each other, but poor at distinguishing the varied side chains of amino acids.

Benner's approach opened new perspectives on how nucleic acids work, as well as tools for diagnostics and nanotechnology. The FDA has approved products that use AEGIS DNA in human diagnostics. These monitor the loads of virus in patients infected with hepatitis B, hepatitis C and HIV. AEGIS has been the basis of the development of tools for multiplexed detection of genetic markers such as cancer cells and single nucleotide polymorphisms in patient samples.

One of the important properties of lactoferrin is its ability to bind with nucleic acids. The fraction of protein extracted from milk, contains 3.3% RNA, but, the protein preferably binds to double-stranded DNA rather than single-stranded DNA. The ability of lactoferrin to bind DNA is used for its isolation and purification using affinity chromatography with columns containing immobilized DNA-containing sorbents, such as agarose with the immobilized single-stranded DNA.

This allows for the escape of many intracellular contents, such as ions and metabolites as well as the simultaneous uptake of drugs, molecular probes, and nucleic acids. For cells that are difficult to transfect electroporation is advantageous however cell death is more probable under this technique. This method has been used to deliver siRNA targeting VEGF into the xenografted tumors in nude mice, which resulted in a significant suppression of tumor growth.

Picture of an SDS-PAGE. The molecular markers (ladder) are in the left lane Polyacrylamide gel electrophoresis (PAGE) is a technique widely used in biochemistry, forensic chemistry, genetics, molecular biology and biotechnology to separate biological macromolecules, usually proteins or nucleic acids, according to their electrophoretic mobility. Electrophoretic mobility is a function of the length, conformation and charge of the molecule. Polyacrylamide gel electrophoresis is a powerful tool used to analyze RNA samples.

Amanda Cordelia Bryant-Friedrich is the Dean of the Graduate School and a professor in the College of Pharmacy and Health Sciences at Wayne State University. She was awarded the 2014 American Chemical Society Stanley C. Israel Regional Award for Advancing Diversity in the Chemical Sciences and is a Fellow of the American Association for the Advancement of Science and the American Chemical Society. Her research considers modified nucleic acids and biomarkers of disease.

However, this approach comes with several difficulties. For instance, GFP is a very large unit and can often affect the folding of the protein of interest. Moreover, by being expressed at either terminus, the GFP adduct can also affect the targeting and expression of the desired protein. Finally, using this method, GFP can only be attached to proteins, and not post-translationally, leaving other important biomolecular classes (nucleic acids, lipids, carbohydrates, etc.) out of reach.

Various kits are commercially available to help in food pathogen nucleic acids extraction,FOOD PATHOGEN DNA EXTRACTION filter paper card PCR detection, and differentiation. The detection of bacterial strands in food products is very important to everyone in the world, for it helps prevent the occurrence of food borne illness. Therefore, PCR is recognized as a DNA detector in order to amplify and trace the presence of pathogenic strands in different processed food.

In this way, marine viruses are thought to play an important role in nutrient cycles by increasing the efficiency of the biological pump. Viruses cause lysis of living cells, that is, they break the cell membranes down. This releases compounds such as amino acids and nucleic acids, which tend to be recycled near the surface. Viral activity also enhances the ability of the biological pump to sequester carbon in the deep ocean.

This could include bridging proteins, nucleic acids (DNA or RNA), or other molecules. Bimolecular fluorescence complementation (BiFC) is a new technique in observing the interactions of proteins. Combining with other new techniques, this method can be used to screen protein–protein interactions and their modulators, DERB. Affinity electrophoresis as used for estimation of binding constants, as for instance in lectin affinity electrophoresis or characterization of molecules with specific features like glycan content or ligand binding.

UV/Vis spectroscopy is widely used as a technique in chemistry to analyze chemical structure, the most notable one being conjugated systems. UV radiation is often used to excite a given sample where the fluorescent emission is measured with a spectrofluorometer. In biological research, UV radiation is used for quantification of nucleic acids or proteins. A collection of mineral samples brilliantly fluorescing at various wavelengths as seen while being irradiated by UV light.

Virome refers to the assemblage of viruses that is often investigated and described by metagenomic sequencing of viral nucleic acids that are found associated with a particular ecosystem, organism or holobiont. The word is frequently used to describe environmental viral shotgun metagenomes. Viruses, including bacteriophages, are found in all environments and studies of the virome have provided insights into nutrient cycling, development of immunity, and a major source of genes through lysogenic conversion.

"Nuclear Magnetic Resonance Fourier Transform Spectroscopy" Ernst's Nobel lecture. (Includes mention of Jeener's suggestion.) Multi- dimensional FT NMR experiments were then further developed into powerful methodologies for studying molecules in solution, in particular for the determination of the structure of biopolymers such as proteins or even small nucleic acids. In 2002 Kurt Wüthrich shared the Nobel Prize in Chemistry (with John Bennett Fenn and Koichi Tanaka) for his work with protein FT NMR in solution.

Bdellovibrio is a genus of Gram-negative, obligate aerobic bacteria. One of the more notable characteristics of this genus is that members can prey upon other Gram-negative bacteria and feed on the biopolymers, e.g. proteins and nucleic acids, of their hosts. They have two lifestyles: a host-dependent, highly mobile phase, the "attack phase", in which they form "bdelloplasts" in their host bacteria; and a slow-growing, irregularly shaped, host-independent form.

Nuclease MB is a specific DNA and RNA exo-endonuclease which will degrade single-stranded extensions from the ends of DNA and RNA molecules, leaving blunt, ligatable ends. Its higher single-strand specificity makes it the enzyme of choice for most applications requiring a single-strand-specific nuclease. Unlike S1 Nuclease, Mung Bean Nuclease will not cleave the intact strand of nicked duplex DNA. Its ability to recognise double-stranded nucleic acids depends on the base sequence.

Watson's version differs from Crick's because Watson describes a two-step (DNA → RNA and RNA → protein) process as the central dogma. While the dogma, as originally stated by Crick, remains valid today, Watson's version does not. The dogma is a framework for understanding the transfer of sequence information between information-carrying biopolymers, in the most common or general case, in living organisms. There are 3 major classes of such biopolymers: DNA and RNA (both nucleic acids), and protein.

In the context of biochemistry and drug development, a hybridization assay is a type of Ligand Binding Assay (LBA) used to quantify nucleic acids in biological matrices. Hybridization assays can be in solution or on a solid support such as 96-well plates or labelled beads. Hybridization assays involve labelled nucleic acid probes to identify related DNA or RNA molecules (i.e. with significantly high degree of sequence similarity) within a complex mixture of unlabelled nucleic acid molecules.

He spent his childhood in La Hulpe, Belgium. Very young, he was already fascinated by biology and published his first scientific article at the age of 13 years old. He continued his studies at the Royal Athenaeum of Ixelles (Brussels), and at the Université Libre de Bruxelles (ULB), where he studied chemistry. At ULB, Thomas attended lectures by Jean Brachet, who pioneered the field of nucleic acids (DNA and RNA) and their role in heredity and protein synthesis.

The Rat Genome Database (RGD) began as a collaborative effort between leading research institutions involved in rat genetic and genomic research. The rat continues to be extensively used by researchers as a model organism for investigating the biology and pathophysiology of disease. In the past several years, there has been a rapid increase in rat genetic and genomic data.M. Dwinell, E. Worthey and S. M, "The Rat genome Database 2009: variation, ontologies and pathways," Nucleic Acids Research, vol.

Daly developed methods for separating out the nuclei of tissues and measuring the base composition of purines and pyrimidines in desoxypentose nucleic acids. She concluded, among other things, that "no bases other than adenine, guanine, thymine, and cytosine were present in appreciable amounts." She investigated protein synthesis, including the role of cytoplasmic ribonucleoprotein in protein synthesis. Using radiolabeled amino acid glycine, she was able to measure how protein metabolism changed under feeding and fasting conditions in mice.

An insect uses its digestive system to extract nutrients and other substances from the food it consumes. Most of this food is ingested in the form of macromolecules and other complex substances like proteins, polysaccharides, fats and nucleic acids. These macromolecules must be broken down by catabolic reactions into smaller molecules like amino acids and simple sugars before being used by cells of the body for energy, growth, or reproduction. This break-down process is known as digestion.

Both 4NQO and its reduced metabolite 4-hydroxyaminoquinoline 1-oxide (4HAQO) bind covalently to cellular macromolecules such as nucleic acids and proteins. 4NQO has been shown to trap topoisomerase I cleavage complexes. It may also induce DNA damage through the production of reactive oxygen species thought to arise from enzymatic reduction of its nitro group, although its exact mechanism is unknown. 4NQO’s reactive oxygen species may serve as a byproduct of DNA damage or signaling molecule from damage.

Depurination is a chemical reaction of purine deoxyribonucleosides, deoxyadenosine and deoxyguanosine, and ribonucleosides, adenosine or guanosine, in which the β-N-glycosidic bond is hydrolytically cleaved releasing a nucleic base, adenine or guanine, respectively. The second product of depurination of deoxyribonucleosides and ribonucleosides is sugar, 2'-deoxyribose and ribose, respectively. More complex compounds containing nucleoside residues, nucleotides and nucleic acids, also suffer from depurination. Deoxyribonucleosides and their derivatives are substantially more prone to depurination than their corresponding ribonucleoside counterparts.

Like nitrogen, phosphorus is involved with many vital plant processes. Within a plant, it is present mainly as a structural component of the nucleic acids: deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), as well as a constituent of fatty phospholipids, that are important in membrane development and function. It is present in both organic and inorganic forms, both of which are readily translocated within the plant. All energy transfers in the cell are critically dependent on phosphorus.

Aminoallyl uridine (aa-UTP) Aminoallyl nucleotide is a nucleotide with a modified base containing an allylamine. They are used in post-labeling of nucleic acids by fluorescence detection in microarray. They are reactive with N-Hydroxysuccinimide ester group which helps attach a fluorescent dye to the primary amino group on the nucleotide. These nucleotides are known as 5-(3-aminoallyl)-nucleotides since the aminoallyl group is usually attached to carbon 5 of the pyrimidine ring of uracil or cytosine.

Merriam-Webster defines chemotaxonomy as the method of biological classification based on similarities and dissimilarity in the structure of certain compounds among the organisms being classified. Advocates argue that, as proteins are more closely controlled by genes and less subjected to natural selection than the anatomical features, they are more reliable indicators of genetic relationships. The compounds studied most are proteins, amino acids, nucleic acids, peptides etc. Physiology is the study of working of organs in a living being.

Under neutral conditions (pH 7-8), both DNA and RNA partition into the aqueous phase. In a last step, the nucleic acids are recovered from the aqueous phase by precipitation with 2-propanol. The 2-propanol is then washed with ethanol and the pellet briefly air-dried and dissolved in TE buffer or RNAse free water. Guanidinium thiocyanate denatures proteins, including RNases, and separates rRNA from ribosomal proteins, while phenol, isopropanol and water are solvents with poor solubility.

The Helicos Genetic Analysis System is capable of sequencing nucleic acids, from several nucleotides to several thousand nucleotides. However, the yield of sequences per unit mass is dependent on the number of 3’ end hydroxyl groups, and thus having relatively short templates for sequencing is more efficient than having long templates. Helicos recommends a length less than 1000nt (nucleotides), optimally about 100-200nt. Long fragments can be cleaved by shearing the DNA (the recommended approach), or restriction enzymes.

RuBisCO is thought to be the single most abundant protein on Earth. Phototrophs use the products of their photosynthesis as internal food sources and as raw material for the biosynthesis of more complex organic molecules, such as polysaccharides, nucleic acids and proteins. These are used for their own growth, and also as the basis of the food chains and webs that feed other organisms, including animals such as ourselves. Some important phototrophs, the coccolithophores synthesise hard calcium carbonate scales.

The International Journal of Biological Macromolecules is a peer-reviewed scientific journal covering research into chemical and biological aspects of all natural macromolecules. It publishes articles on the molecular structure of proteins, macromolecular carbohydrates, lignins, biological poly-acids, and nucleic acids. It also includes biological activities and interactions, molecular associations, chemical and biological modifications, and functional properties as well as development of related model systems, structural including conformational studies, new analytical techniques, and relevant theoretical developments.

UV rays can damage the DNA of living organisms by creating nucleic acid dimers. However, the damages are usually not important due to low penetration of UVs through living tissues. UV rays can be used, however, to inactivate viruses since virus particules are small and the UV rays can reach the genetic material, inducing the dimerisation of nucleic acids. Once the DNA dimerised, the virus particules cannot replicate their genetic material which prevent them from spreading.

He is considered a pioneer of many novel drug delivery technologies, especially in the fields of transdermal, oral and targeted systems. He invented the use of low-frequency ultrasound, pulsed microjet injector, high throughput skin experimentation, skin penetrating peptides and ionic liquids for transdermal delivery of proteins and nucleic acids. He also invented intestinal patches and ionic liquids for oral delivery of proteins. Mitragotri also developed nanoparticles of different shapes and stiffness and demonstrated that they improve drug targeting.

Nobel rules now prohibit posthumous nominations (though this statute was not formally in effect until 1974) or splitting of Prizes more than three ways. The award was for their body of work on nucleic acids and not exclusively for the discovery of the structure of DNA. By the time of the award Wilkins had been working on the structure of DNA for more than 10 years, and had done much to confirm the Watson–Crick model.Wilkins, p. 240.

When phosphorylated, nucleosides become nucleotides, which are the building blocks of nucleic acids (DNA and RNA). As such, they're needed for replication (copying of the genome before cells divide so that each gets a copy). Therefore, cells that replicate frequently, such as cancer cells and bacteria have a high demand for nucleosides. Recognizing this, teams of scientists, including a team at Burroughs Wellcome including Janet Rideout dedicated themselves to studying chemical analogs that could mimic natural nucleosides, inhibiting replication.

Ribonuclease T (RNase T, exonuclease T, exo T) is a ribonuclease enzyme involved in the maturation of transfer RNA and ribosomal RNA in bacteria, as well as in DNA repair pathways. It is a member of the DnaQ family of exonucleases and non-processively acts on the 3' end of single-stranded nucleic acids. RNase T is capable of cleaving both DNA and RNA, with extreme sequence specificity discriminating against cytosine at the 3' end of the substrate.

These failures largely rule out a virus as the infective agent. Experiments using electron beams designed to disrupt large molecules have been performed to investigate the size of the agent show that it is very small: much smaller than the smallest known virus. The virino also has the benefit of explaining the traits of TSEs which resemble nucleic acids: for example, their occurrence in strains, which positively indicates the TSE agent is information carrying, and not merely a toxin.

In the 1920s Lepeshinskaya discredited the work of her supervisor, Alexander Gurvitch, who investigated biophotons and mitogenic rays. She claimed that low doses of ultraviolet light were released by dying cells that had been treated with high doses of UV light. Later she claimed that cells could propagate by disintegration into granules which could generate new forms of cells, different from the parental cells. Also, crystals of inorganic matter could be converted into cells by adding nucleic acids.

SNPedia: a wiki supporting personal genome annotation, interpretation and analysis, Michael Cariaso and Greg Lennon, Nucleic Acids Research, 2011, 1–5 On 7 September 2019, MyHeritage announced that they acquired both SNPedia and Promethease. All non-European raw genetic data files previously uploaded to Promethease, and not deleted by users by 1 Nov 2019, are to be copied to MyHeritage and the users will receive a free MyHeritage account with paid level of services, including Cousin Matching and Ethnicities.

To separate nucleic acids by TGGE, the following steps must be performed: preparing and pouring the gels, electrophoresis, staining, and elution of DNA. Because a buffered system must be chosen, it is important that the system remain stable within the context of increasing temperature. Thus, urea is typically utilized for gel preparation; however, researchers need to be aware that the amount of urea used will affect the overall temperature required to separate the DNA.(Biometra, 2000).

This was one of the first examples of 'adaptive enzymes.' (This is now understood as the rapid transcriptional activation of the gene encoding the formate hydrogenlyase when the inducer molecule, formate, is added to the culture). Later in the 1930s Stephenson worked with Ernest Gale on enzyme adaptation and amino acid metabolism, and with Arthur Trim on metabolic studies of nucleic acids. During her time at the laboratory, Stephenson produced, as author or co-author, more than twenty papers.

Paul Berg (born June 30, 1926) is an American biochemist and professor emeritus at Stanford University. He was the recipient of the Nobel Prize in Chemistry in 1980, along with Walter Gilbert and Frederick Sanger.Curriculum vitae from the Nobel Prize websiteBerg autobiography from the Nobel Prize websiteBerg interview from the Nobel Prize website The award recognized their contributions to basic research involving nucleic acids. Berg received his undergraduate education at Penn State University, where he majored in biochemistry.

Buffered formalin solutions cross link proteins and nucleic acids when they are used for fix tissues. The DNA, RNA, and protein within the tissues are damaged in various levels during the fixation. Therefore, lots of scientific experimental results from formalin fixed tissues are not reliable. Since frozen tissue sections don’t go through any fixation procedures, and therefore, the DNA, RNA, and protein in frozen tissues retain their native characteristics much more than in paraffin embedded tissues.

A protein's lifespan is measured in terms of its half-life and covers a wide range. They can exist for minutes or years with an average lifespan of 1–2 days in mammalian cells. Abnormal or misfolded proteins are degraded more rapidly either due to being targeted for destruction or due to being unstable. Like other biological macromolecules such as polysaccharides and nucleic acids, proteins are essential parts of organisms and participate in virtually every process within cells.

Pyrimidine is an aromatic heterocyclic organic compound similar to pyridine. One of the three diazines (six-membered heterocyclics with two nitrogen atoms in the ring), it has the nitrogen atoms at positions 1 and 3 in the ring. The other diazines are pyrazine (nitrogen atoms at the 1 and 4 positions) and pyridazine (nitrogen atoms at the 1 and 2 positions). In nucleic acids, three types of nucleobases are pyrimidine derivatives: cytosine (C), thymine (T), and uracil (U).

Agarose gel can have high gel strength at low concentration, making it suitable as an anti-convection medium for gel electrophoresis. Agarose gels as dilute as 0.15% can form slabs for gel electrophoresis. The agarose polymer contains charged groups, in particular pyruvate and sulfate. These negatively charged groups can slow down the movement of DNA molecules in a process called electroendosmosis (EEO), and low EEO agarose is therefore generally preferred for use in agarose gel electrophoresis of nucleic acids.

Glycosaminoglycans vary greatly in molecular mass, disaccharide construction, and sulfation. This is because GAG synthesis is not template driven like proteins or nucleic acids, but constantly altered by processing enzymes. GAGs are classified into four groups based on core disaccharide structures. Heparin/heparan sulfate (HSGAGs) and chondroitin sulfate/dermatan sulfate (CSGAGs) are synthesized in the Golgi apparatus, where protein cores made in the rough endoplasmic reticulum are post-translationally modified with O-linked glycosylations by glycosyltransferases forming proteoglycans.

As these ions are necessary co-factors for many enzymes, including contaminant nucleases, the role of the EDTA is to protect the nucleic acids against enzymatic degradation. But since Mg2+ is also a co-factor for many useful DNA-modifying enzymes such as restriction enzymes and DNA polymerases, its concentration in TBE or TAE buffers is generally kept low (typically at around 1 mM). More recently discovered substitutes for TBE and TAE buffers for electrophoresis are available.

No evidence of nucleic acid has been found in any prion particle studied. Treatments that destroy protein, like denaturation, destroy prion infectivity, but treatments that destroy nucleic acids, like UV radiation, do not destroy prion infectivity. The prion protein is known as PrP and is a cell surface glycophosphatidylinositol(GPI)-anchored protein. Its normal function in the body is unknown, though presumably it serves, or served, some purpose because it is coded for by a host gene.

PAGE of rotavirus proteins stained with Coomassie blue The following chemicals and procedures are used for processing of the gel and the protein samples visualized in it. Tracking dye; as proteins and nucleic acids are mostly colorless, their progress through the gel during electrophoresis cannot be easily followed. Anionic dyes of a known electrophoretic mobility are therefore usually included in the PAGE sample buffer. A very common tracking dye is Bromophenol blue (BPB, 3',3",5',5" tetrabromophenolsulfonphthalein).

M. Oda, N. Kobayashi, A. Ito, Y. Kurusu, K. Taira, cis-acting regulatory sequences for antitermination in the transcript of the Bacillus subtilis hut operon and histidine-dependent binding of HutP to the transcript containing the regulatory sequences, Mol. Microbiol. 35 (2000) 1244-1254. 5\. T. S. Kumarevel, H. Mizuno, P. K. R. Kumar, Characterization of the metal ion binding site in the anti-terminator protein, HutP, of Bacillus subtilis, Nucleic Acids Res. 33 (2005) 5494-5502. 6\.

Furthermore, the organic chemicals produced by the introduced life would confuse sensitive searches for biosignatures of living or ancient native life. The same applies to other more complex biosignatures. Life on other planets could have a common origin with Earth life, since in the early Solar System there was much exchange of material between the planets which could have transferred life as well. If so, it might be based on nucleic acids too (RNA or DNA).

In 1937, Astbury became interested in DNA and directed Bell to work on the molecule. Bell came up with a method to stretch out the fibers to make dried films of purified DNA, with which she took x-ray diffraction photographs that were clearer than previous work. Her work confirmed it was a regular, ordered structure with periodicity of 3.3 - 3.4 Å along the axis. She studied the nucleic acids in yeast, pancreases, tobacco mosaic virus and calf thymus.

Chemical structure of RNA A series of codons in part of a mRNA molecule. Each codon consists of three nucleotides, usually representing a single amino acid. Nucleic acids consist of a chain of linked units called nucleotides. Each nucleotide consists of three subunits: a phosphate group and a sugar (ribose in the case of RNA, deoxyribose in DNA) make up the backbone of the nucleic acid strand, and attached to the sugar is one of a set of nucleobases.

Plants can absorb nitrate or ammonium from the soil by their root hairs. If nitrate is absorbed, it is first reduced to nitrite ions and then ammonium ions for incorporation into amino acids, nucleic acids, and chlorophyll. In plants that have a symbiotic relationship with rhizobia, some nitrogen is assimilated in the form of ammonium ions directly from the nodules. It is now known that there is a more complex cycling of amino acids between Rhizobia bacteroids and plants.

Z containing nucleosomes around transcription start sites has now been shown to affect the downstream gene expression.Bargaje R., Alam P., Patowary A., Sarkar M., Ali T., Gupta S., Garg M., Singh M., Purkanti R., Scaria V., Sivasubbu S., Brahmachari V., Pillai B. (2012) Proximity of H2A.Z containing nucleosome to the transcription start site influences gene expression levels in the mammalian liver and brain. Nucleic Acids Research (Epub ahead of print) Recent evidence also points to a role for H2A.

The three dimensional structure of biological macromolecules like proteins and nucleic acids play critical role in determining their functional role. This process of decoding function from the sequence is an experimentally and computationally challenging question addressed widely. RNA structures form complex secondary and tertiary structures compared to DNA which form duplexes with full complementarity between two strands. This is partially because the extra oxygen in RNA increases the propensity for hydrogen bonding in the nucleic acid backbone.

The unprocessed solution immediately after lysis but before any further extraction steps is often referred to as a crude lysate. For example, lysis is used in western and Southern blotting to analyze the composition of specific proteins, lipids, and nucleic acids individually or as complexes. Depending on the detergent used, either all or some membranes are lysed. For example, if only the cell membrane is lysed then gradient centrifugation can be used to collect certain organelles.

Bain, BJ et al. (2017). p. 37. More advanced analyzers use additional techniques to provide a five- to seven-part differential, such as light scattering or radiofrequency analysis, or using dyes to stain specific chemicals inside cells—for example, nucleic acids, which are found in higher concentrations in immature cellsArneth, BM; Menschikowki, M. (2015). p. 3. or myeloperoxidase, an enzyme found in cells of the myeloid lineage.Smock, KJ. Chapter 1 in Greer JP et al, ed.

Carbon is separated into four distinct pools based on whether it is organic/inorganic and whether it is dissolved/particulate. The processes associated with each arrow describe the transformation associated with the transfer of carbon from one reservoir to another. Carbon compounds can be distinguished as either organic or inorganic, and dissolved or particulate, depending on their composition. Organic carbon forms the backbone of key component of organic compounds such as – proteins, lipids, carbohydrates, and nucleic acids.

Radiolysis of intracellular water by ionizing radiation creates peroxides, which are relatively stable precursors to hydroxyl radicals. 60%- 70% of cellular DNA damage is caused by hydroxyl radicals, yet hydroxyl radicals are so reactive that they can only diffuse one or two molecular diameters before reacting with cellular components. Thus, hydroxyl radicals must be formed immediately adjacent to nucleic acids in order to react. Radiolysis of water creates peroxides that can act as diffusable, latent forms of hydroxyl radicals.

The core unit of the Reactome data model is the reaction. Entities (nucleic acids, proteins, complexes and small molecules) participating in reactions form a network of biological interactions and are grouped into pathways. Examples of biological pathways in Reactome include signaling, innate and acquired immune function, transcriptional regulation, translation, apoptosis and classical intermediary metabolism. The pathways represented in Reactome are species-specific, with each pathway step supported by literature citations that contain an experimental verification of the process represented.

Koshland defines "Program" as an "organized plan that describes both the ingredients themselves and the kinetics of the interactions among ingredients as the living system persists through time."Koshland D. E. Jr (2002). The Seven Pillars of Life. Science, 295: 2215-2216 In natural life as it is known on Earth, the program operates through the mechanisms of nucleic acids and amino acids, but the concept of program can apply to other imagined or undiscovered mechanisms.

An insect uses its digestive system to extract nutrients and other substances from the food it consumes. Most of this food is ingested in the form of macromolecules and other complex substances (such as proteins, polysaccharides, fats, and nucleic acids) which must be broken down by catabolic reactions into smaller molecules (i.e. amino acids, simple sugars, etc.) before being used by cells of the body for energy, growth, or reproduction. This break-down process is known as digestion.

Nuclear magnetic resonance is extremely useful for analyzing samples non-destructively. Radio-frequency magnetic fields easily penetrate many types of matter and anything that is not highly conductive or inherently ferromagnetic. For example, various expensive biological samples, such as nucleic acids, including RNA and DNA, or proteins, can be studied using nuclear magnetic resonance for weeks or months before using destructive biochemical experiments. This also makes nuclear magnetic resonance a good choice for analyzing dangerous samples.

Banerjea's research has been focusing on HIV/AIDS with special emphasis on the pathogenesis, host-gene interactions and the genetic as well as the functional characterization of HIV-1. He worked on developing catalytic nucleic acids for antiviral uses and later, at Colorado State University, his research was centered around conversion of Small interfering RNA (siRNA) into stem cells which was reported inn 2003 by New York Times; the approach was subsequently put on clinical trial in the US. He has also worked on the effect of lentiviral vectors, stem cells, catalytic nucleic acids and siRNA for developing gene therapy against HI/AIDS as well as the study of host or viral genes in understanding the HIV/AIDS pathogenesis. His studies have been documented by way of a number of articles and ResearchGate, an online repository of scientific articles, has listed 103 of them. He has delivered key note or invited speeches at seminars and conferences at places such as Albert Einstein College of Medicine, Duke University, University of California, Los Angeles, National Cancer Institute, Drexel University and National University of Singapore.

Efforts toward the goal of artificial genetic systems were first reported by Benner and coworkers in 1989, when they developed the first unnatural base pair. Benner and his colleagues have since developed a six-letter artificially expanded genetic information system called Artificially Expanded Genetic Information System (AEGIS) which includes two additional nonstandard nucleotides (Z and P) in addition to the four standard nucleotides (G, A, C, and T). AEGIS has its own supporting molecular biology. It enables the synthesis of proteins with more than the naturally-encoded 20 amino acids, and provides insight into how nucleic acids form duplex structures, how proteins interact with nucleic acids, and how alternative genetic systems might appear in non-terran life. Benner is one of a number of researchers, including Eric T. Kool, Floyd E. Romesberg, Ichiro Hirao, Mitsuhiko Shionoya and Andrew Ellington, who have created an extended alphabet of synthetic bases that can be incorporated into DNA (as well as RNA) using Watson-Crick bonding (as well as non-Watson-Crick bonding).

The phosphate-starved bacteria had an intracellular volume 1.5 times normal; the greater volume appeared to be associated with the appearance of large "vacuole-like regions". Scanning electron micrograph of GFAJ-1 cells grown in defined minimal medium supplemented with 1.5 mM phosphate When the researchers added isotope-labeled arsenate to the solution to track its distribution, they found that arsenic was present in the cellular fractions containing the bacteria's proteins, lipids and metabolites such as ATP, as well as its DNA and RNA. Nucleic acids from stationary phase cells starved of phosphorus were concentrated via five extractions (one with phenol, three with phenol-chloroform and one with chloroform extraction solvent), followed by ethanol precipitation. Although direct evidence of the incorporation of arsenic into biomolecules is still lacking, radioactivity measurements suggested that approximately one-tenth (11.0 ± 0.1%) of the arsenic absorbed by these bacteria ended up in the fraction that contained the nucleic acids (DNA and RNA) and all other co-precipitated compounds not extracted by the previous treatments.

The microbe-specific molecules that are recognized by a given PRR are called pathogen-associated molecular patterns (PAMPs) and include bacterial carbohydrates (such as lipopolysaccharide or LPS, mannose), nucleic acids (such as bacterial or viral DNA or RNA), bacterial peptides (flagellin, microtubule elongation factors), peptidoglycans and lipoteichoic acids (from Gram-positive bacteria), N-formylmethionine, lipoproteins and fungal glucans and chitin. Endogenous stress signals are called damage-associated molecular patterns (DAMPs) and include uric acid and extracellular ATP, among many other compounds.

Hydroxyl radicals can occasionally be produced as a byproduct of immune action. Macrophages and microglia most frequently generate this compound when exposed to very specific pathogens, such as certain bacteria. The destructive action of hydroxyl radicals has been implicated in several neurological autoimmune diseases such as HAND when immune cells become over-activated and toxic to neighboring healthy cells. The hydroxyl radical can damage virtually all types of macromolecules: carbohydrates, nucleic acids (mutations), lipids (lipid peroxidation), and amino acids (e.g.

A DNA microarray being printed by a robot at the University of Delaware Microarrays can be fabricated using a variety of technologies, including printing with fine-pointed pins onto glass slides, photolithography using pre-made masks, photolithography using dynamic micromirror devices, ink- jet printing,J Biochem Biophys Methods. 2000 Mar 16;42(3):105-10. DNA- printing: utilization of a standard inkjet printer for the transfer of nucleic acids to solid supports. Goldmann T, Gonzalez JS. or electrochemistry on microelectrode arrays.

The limitations with the hybridization-ligation assay also apply to the dual ligation assay, with the 5'-end in addition to the 3'-end requiring to have a free hydroxyl (or a phosphate group). Further, T4 DNA ligases are incompatible with ligation of RNA molecules as a donor (i.e. RNA at the 5' end of the ligation). Therefore, second generation antisense that comprise 2'-O-methyl RNA, 2'-O-methoxyethyl or locked nucleic acids may not be compatible with the dual ligation assay.

Francis Harry Compton Crick (8 June 1916 – 28 July 2004) was a British molecular biologist, biophysicist, and neuroscientist. In 1953, he co-authored with James Watson the academic paper proposing the double helix structure of the DNA molecule. Together with Watson and Maurice Wilkins, he was jointly awarded the 1962 Nobel Prize in Physiology or Medicine "for their discoveries concerning the molecular structure of nucleic acids and its significance for information transfer in living material".The Nobel Prize in Physiology or Medicine 1962.

Hubert Chantrenne (1918–2007) was a Belgian scientist, and one of the pioneers of molecular biology at the Université Libre de Bruxelles. He elucidated the messenger role played by the ribonucleic acid (RNA) in the synthesis of proteins in ribosome, organelles of the cellular cytoplasm.Chantrenne H, Devreux S., Effects of 8-azaguanine on the synthesis of protein and nucleic acids in Bacillus cereus, Nature. 1958 June 21;181(4625):1737-8Chantrenne H., The polyribosomes, agents of protein synthesis, Arch Biol (Liege).

This one of the largest resources available for all genomic and genetic studies, it provides a centralized resource for geneticists, molecular biologists and other researchers studying the genomes of our own species and other vertebrates and model disease organisms. Ensembl is one of several well-known genome browsers for the retrieval of genomic-disease information. Ensembl imports variation data from a variety of different sources, Ensembl predicts the effects of variants.P. Flicek and M. Ridwan, "Ensembl 2012," Nucleic Acids Research, vol.

33, no.8, August 1995, p. 2162-2165. Another laboratory separation tool is the affinity magnetic separation (AMS), which is more suitable for the isolation of prokaryotic cells.Affinity magnetic separation of Listeria spp and Escherichia coli O157 (Bacteria Capture Kit) Immunomagnetic separation (IMS) is a method that deals with the isolation of cells, proteins, and nucleic acids within a cell culture or body fluid through the specific capture of biomolecules through the attachment of small-magnetized particles, beads, containing antibodies and lectins.

Ionizing radiation can cause biological effects which are passed on to offspring through the epigenome. The effects of radiation on cells has been found to be dependent on the dosage of the radiation, the location of the cell in regards to tissue, and whether the cell is a somatic or germ line cell. Generally, ionizing radiation appears to reduce methylation of DNA in cells. Ionizing radiation has been known to cause damage to cellular components such as proteins, lipids, and nucleic acids.

One of the earliest methods of efficiently editing nucleic acids employs nucleobase modifying enzymes directed by nucleic acid guide sequences was first described in the 1990s and has seen resurgence more recently. This method has the advantage that is does require breaking the genomic DNA strands, and thus avoids the random insertion and deletions associated with DNA strand breakage. It is only appropriate for precise editing requiring single nucleotide changes and has found to be highly efficient for this type of editing.

Scanning electron micrograph of mixed-culture biofilm, demonstrating in detail a spatially heterogeneous arrangement of bacterial cells and extracellular polymeric substances. The EPS matrix consists of exopolysaccharides, proteins and nucleic acids. A large proportion of the EPS is more or less strongly hydrated, however, hydrophobic EPS also occur; one example is cellulose which is produced by a range of microorganisms. This matrix encases the cells within it and facilitates communication among them through biochemical signals as well as gene exchange.

Several isomers exist with the formula H−(C=O)−(CH2)−(CHOH)3−H, but in deoxyribose all the hydroxyl groups are on the same side in the Fischer projection. The term "2-deoxyribose" may refer to either of two enantiomers: the biologically important -2-deoxyribose and to the rarely encountered mirror image -2-deoxyribose.C Bernelot-Moens and B Demple (1989), Multiple DNA repair activities for 3′-deoxyribose fragments in Escherichia coli. Nucleic Acids Research, Volume 17, issue 2, p. 587–600.

It can be performed at 10 weeks of gestational age.Noninvasive Prenatal Diagnosis of Fetal Aneuploidy Using Cell-Free Fetal Nucleic Acids in Maternal Blood: Clinical Policy (Effective 05/01/2013) from Oxford Health Plans One study in the United States estimated a false positive rate of 0.3% and a positive predictive value of 80% when using cffDNA to detect Down syndrome.. A recent study in the New England Journal of Medicine demonstrated the feasibility of using NIPT in a low risk population.

Chemical structure of a polypeptide macromolecule A macromolecule is a very large molecule, such as protein, commonly composed of the polymerization of smaller subunits called monomers. They are typically composed of thousands of atoms or more. A substance that is composed of monomers is called a polymer. The most common macromolecules in biochemistry are biopolymers (nucleic acids, proteins, and carbohydrates) and large non-polymeric molecules (such as lipids and macrocycles), synthetic fibers as well as experimental materials such as carbon nanotubes.

John Masson Gulland (1933) John Masson Gulland (14 October 1898 – 26 October 1947) was a Scottish chemist and biochemist. His main work was on nucleic acids, morphine and aporphine alkaloids. His work at University College Nottingham on electrometric titration was important in leading to the discovery of the DNA double helix by James Watson and Francis Crick, and he was described as "a great nucleic acid chemist." The Path to the Double Helix: The Discovery of DNA, by Robert Olby Courier Corp.

Ishino has contributed to the development of enzymology and nucleic acids research in his life. The "iap" gene in gut microbe E. coli was sequenced by Ishino and his colleagues in 1987. As the DNA segment used was longer than the gene itself, they accidentally discovered a partial DNA sequence of then-unnamed CRISPR in the process, which would eventually become the basis of CRISPR gene editing. Yoshizumi Ishino was one of the first scientists to have detected CRISPRs in E. coli.

Daniela Rhodes has made many fundamental contributions to understanding the structure and function of nucleic acids and their biologically important interactions with many different proteins. Her work combines biochemical analyses with direct structural determination. She determined the structures of a number of important protein-DNA complexes involved in transcription, such as zinc-fingers and nuclear hormone receptors. She has provided some of the first structural information on telomeric proteins, such as yeast Rap1p and human TRF1 and TRF2 and their complexes with DNA.

Like other sulfonamides, sulfadimethoxine is a dihydropteroate synthase inhibitor. Bacteria and some protozoa are unable to obtain folic acid from the environment, and must instead synthesize it by converting PABA (para-aminobenzoate) to dihydropteroate using the enzyme dihydropteroate synthase. Sulfonamides act as a competitive inhibitor; being structurally similar to PABA, they are able to bind to the enzyme's active site and prevent the synthesis of folic acid from progressing. Folic acid is necessary for these organisms to produce nucleic acids (i.e.

FlexAID is a molecular docking software that can use small molecules and peptides as ligands and proteins and nucleic acids as docking targets. As the name suggests, FlexAID supports full ligand flexibility as well side-chain flexibility of the target. It does using a soft scoring function based on the complementarity of the two surfaces (ligand and target). FlexAID has been shown to outperform existing widely used software such as AutoDock Vina and FlexX in the prediction of binding poses.

Ruth Nussinov received her B.Sc in Microbiology from University of Washington in 1966, her M.Sc in Biochemistry from Rutgers University in 1967 and her Ph.D. in Biochemistry from Rutgers in 1977. Her thesis was titled Secondary structure analysis of nucleic acids. She was a fellow at the Weizmann Institute and worked as a visiting scientist at Berkeley and at Harvard. She took a position at Tel Aviv University in 1985 as Associate Professor and was promoted to Professor in 1990.

Using diagnostic chemical tests, carbohydrate chemists showed that the two nucleic acids contained different sugars, whereupon the common name for RNA became "ribose nucleic acid". Other early biochemical studies showed that RNA was readily broken down at high pH, while DNA was stable (although denatured) in alkali. Nucleoside composition analysis showed first that RNA contained similar nucleobases to DNA, with uracil instead of thymine, and that RNA contained a number of minor nucleobase components, e.g. small amounts of pseudouridine and dimethylguanine.

Although determining the sequence of proteins was becoming somewhat routine, methods for sequencing of nucleic acids were not available until the mid-1960s. In this seminal work, a specific tRNA was purified in substantial quantities, and then sliced into overlapping fragments using a variety of ribonucleases. Analysis of the detailed nucleotide composition of each fragment provided the information necessary to deduce the sequence of the tRNA. Today, the sequence analysis of much larger nucleic acid molecules is highly automated and enormously faster.

Xenobiological systems are designed to convey orthogonality to natural biological systems. A (still hypothetical) organism that uses XNA,Herdewijn, P. and Marlière, P. (2009) Toward safe genetically modified organisms through the chemical diversification of nucleic acids. Chem. Biodivers. 6, 791–808 different base pairs and polymerases and has an altered genetic code will hardly be able to interact with natural forms of life on the genetic level. Thus, these xenobiological organisms represent a genetic enclave that cannot exchange information with natural cells.

Like LTR retrotransposons, non-LTR retrotransposons contain genes for reverse transcriptase, RNA-binding protein, nuclease, and sometimes ribonuclease H domain but they lack the long terminal repeats. RNA-binding protein binds RNA- transposition intermediate. Nucleases are enzymes that break phosphodiester bonds between nucleotides in nucleic acids. Instead they have short repeats that can have an inverted order of bases next to each other aside from direct repeats found in LTR retrotransposons that is just one sequence of bases repeating itself.

The tertiary structure of a protein or any other macromolecule is its three-dimensional structure, as defined by the atomic coordinates. Proteins and nucleic acids fold into complex three-dimensional structures which result in the molecules' functions. While such structures are diverse and complex, they are often composed of recurring, recognizable tertiary structure motifs and domains that serve as molecular building blocks. Tertiary structure is considered to be largely determined by the biomolecule's primary structure (its sequence of amino acids or nucleotides).

In active helicases, V_{un} is approximately equal to V_{trans}. Another way to view the active helicase is its ability to directly destabilize the replication fork to promote unwinding. Active helicases show similar behavior when acting on both double-strand nucleic acids, dsNA, or ssNA, in regards to the rates of unwinding and rates of translocation, where in both systems V_{un} and V_{trans} are approximately equal. These two categories of helicases may also be modelled as mechanisms.

Time-resolved hydroxyl radical protein footprinting employing mass spectrometry analysis was developed in the late 1990s in synchrotron radiolysis studies. The same year, these authors reported on the use of an electrical discharge source to effect the oxidation of proteins on millisecond timescales as proteins pass from the electrosprayed solution into the mass spectrometer. These approaches have since been used to determine protein structures, protein folding, protein dynamics, and protein–protein interactions. Unlike nucleic acids, proteins oxidize rather than cleave on these timescales.

Many members of the RNA Tie Club achieved professional success, with six of them becoming Nobel laureates, namely Richard Feynman, Melvin Calvin, James Watson, Max Delbruck, Francis Crick and Sydney Brenner. However, the ultimate goal of understanding and deciphering the code link between nucleic acids and amino acids was achieved by Marshall Nirenberg, who was not a member of the RNA Tie Club.Everson, Ted: The gene: a historical perspective, pg 90-91. Nirenberg also received a Nobel prize for this achievement.

The two-site, non-competitive immunoassay consists of a biomolecule (in green) captured by an immobile antibody and "sandwiched" by a labeled antibody. When exposed to a laser beam, the fluorochrome label (in yellow) is excited and its fluorescent signal is measured. SOLID was designed for automatic in situ detection and identification of substances from liquid and crushed samples under the conditions of outer space. The system uses hundreds of carefully selected antibodies to detect lipids, proteins, polysaccharides, and nucleic acids.

He has served as president of the international Oligonucleotide Therapeutic Society (2011-12). In 2012, Hartmann was awarded the Gottfried Wilhelm Leibniz Prize by the DFG in recognition of his work on the detection of nucleic acids by the immune system. In 2016, he was appointed Vice Dean of Research for the Medical Faculty of the University of Bonn. Beginning in 2018, he is serving as the spokesperson for the Collaborative Research Center/Transregio grant “Nucleic Acid Immunity”, funded by the DFG.

Outside of gene exons, there exist regulatory sequence motifs and motifs within the "junk", such as satellite DNA. Some of these are believed to affect the shape of nucleic acids (see for example RNA self-splicing), but this is only sometimes the case. For example, many DNA binding proteins that have affinity for specific DNA binding sites bind DNA in only its double-helical form. They are able to recognize motifs through contact with the double helix's major or minor groove.

Conpoy or dried scallop is a type of Cantonese dried seafood product made from the adductor muscle of scallops. The smell of conpoy is marine, pungent, and reminiscent of certain salt-cured meats. Its taste is rich in umami due to its high content of various free amino acids, such as glycine, alanine, and glutamic acid. It is also rich in nucleic acids such as inosinic acid, amino acid byproducts such as taurine, and minerals, such as calcium and zinc.

The structure of deoxyribonucleic acid (DNA), the picture shows the monomers being put together. Nucleic acids, so-called because of their prevalence in cellular nuclei, is the generic name of the family of biopolymers. They are complex, high-molecular-weight biochemical macromolecules that can convey genetic information in all living cells and viruses. The monomers are called nucleotides, and each consists of three components: a nitrogenous heterocyclic base (either a purine or a pyrimidine), a pentose sugar, and a phosphate group.

An insect uses its digestive system for all steps in food processing: digestion, absorption, and feces delivery and elimination. Most of this food is ingested in the form of macromolecules and other complex substances like proteins, polysaccharides, fats, and nucleic acids. These macromolecules must be broken down by catabolic reactions into smaller molecules like amino acids and simple sugars before being used by cells of the body for energy, growth, or reproduction. This break-down process is known as digestion.

The trimethyl ammonium group of Ach binds to the aromatic residue of tryptophan (Trp). The indole site provides a much more intense region of negative electrostatic potential than benzene and phenol residue of Phe and Tyr. S-Adenosyl methionine (SAM) can act as a catalyst for the transfer of methyl group from the sulfonium compound to nucleophile. The nucleophile can be any of a broad range structures including nucleic acids, proteins, sugars or C=C bond of lipids or steroids.

As both experimentalist and theorist, his experiments and interpretations have led the way in understanding of energy states of products of molecular dissociations. He has been called the leading laser chemist in the world for good reason." # Günther Wilke 1991 # Harry B. Gray 1992 # Peter B. Dervan 1993 "For his outstanding contributions to the fields of physical organic chemistry and bio- organic chemistry. His work constitutes a breakthrough for modern organic chemistry directed toward studies of the noncovalent bond and nucleic acids.

The nucleobases are classified into two types: the purines, A and G, which are fused five- and six-membered heterocyclic compounds, and the pyrimidines, the six-membered rings C and T. A fifth pyrimidine nucleobase, uracil (U), usually takes the place of thymine in RNA and differs from thymine by lacking a methyl group on its ring. In addition to RNA and DNA, many artificial nucleic acid analogues have been created to study the properties of nucleic acids, or for use in biotechnology.

Nucleic acids, phospholipids, and amino acids are important cell building- blocks, which are greatly needed by highly proliferating cells, such as tumor cells. Due to the key position of pyruvate kinase within glycolysis, the tetramer:dimer ratio of PKM2 determines whether glucose carbons are converted to pyruvate and lactate under the production of energy (tetrameric form) or channelled into synthetic processes (dimeric form). In tumor cells, PKM2 is mainly in the dimeric form and has, therefore, been termed Tumor M2-PK.

X-ray crystallography is the primary method for determining the molecular conformations of biological macromolecules, particularly protein and nucleic acids such as DNA and RNA. In fact, the double-helical structure of DNA was deduced from crystallographic data. The first crystal structure of a macromolecule was solved in 1958, a three-dimensional model of the myoglobin molecule obtained by X-ray analysis. The Protein Data Bank (PDB) is a freely accessible repository for the structures of proteins and other biological macromolecules.

In general, the ideal buffer should have good conductivity, produce less heat and have a long life. There are a number of buffers used for agarose electrophoresis; common ones for nucleic acids include Tris/Acetate/EDTA (TAE) and Tris/Borate/EDTA (TBE). The buffers used contain EDTA to inactivate many nucleases which require divalent cation for their function. The borate in TBE buffer can be problematic as borate can polymerize, and/or interact with cis diols such as those found in RNA.

Denaturation is a process in which proteins or nucleic acids lose the quaternary structure, tertiary structure, and secondary structure which is present in their native state, by application of some external stress or compound such as a strong acid or base, a concentrated inorganic salt, an organic solvent (e.g., alcohol or chloroform), radiation or heat. If proteins in a living cell are denatured, this results in disruption of cell activity and possibly cell death. Protein denaturation is also a consequence of cell death.

There are numerous exceptions, however—some viruses have genomes made of double-stranded RNA and other viruses have single-stranded DNA genomes, and, in some circumstances, nucleic acid structures with three or four strands can form. Nucleic acids are linear polymers (chains) of nucleotides. Each nucleotide consists of three components: a purine or pyrimidine nucleobase (sometimes termed nitrogenous base or simply base), a pentose sugar, and a phosphate group. The substructure consisting of a nucleobase plus sugar is termed a nucleoside.

Voltage is, however, not the sole factor in determining electrophoresis of nucleic acids. The nucleic acid to be separated can be prepared in several ways before separation by electrophoresis. In the case of large DNA molecules, the DNA is frequently cut into smaller fragments using a DNA restriction endonuclease (or restriction enzyme). In other instances, such as PCR amplified samples, enzymes present in the sample that might affect the separation of the molecules are removed through various means before analysis.

The bulk of the data deposited at the BMRB consists of over 11,900 entries containing 1H, 13C, 15N and 31P assigned chemical shifts and coupling constants of peptides, proteins and nucleic acids. Other derived data like residual dipolar couplings (RDC), relaxation parameters, NOE values, order parameters and hydrogen exchange rates are also available. The database contains also a smaller amount of NMR data from carbohydrates, cofactors and ligands. These data are crossreferenced to 3D structures in the PDB when available.

There are some similarities and many differences inherent in the character of biopolymer backbones. The backbone of each of the three biological polymers; proteins, carbohydrates, and nucleic acids, is formed through a net condensation reaction. In a condensation reaction, monomers are covalently connected along with the loss of some small molecule, most commonly water. Because they are polymerized through complex enzymatic mechanisms, none of the biopolymers' backbones are formed through the elimination of water but through the elimination of other small biological molecules.

In the late 1970s, building on the discovery of circulating DNA in human blood by Mandel and Metais,Mandel P, Métais P: Les acides nucléiques du plasma sanguin chez l'Homme. CR Acad Sci Paris 142: 241–243, 1948. Leon and his collaborators developed a radioimmunoassay for measuring nanogram quantities of nucleic acids in serum. This technique enabled them to observe that cancer patients tended to possess a greater quantity of circulating DNA in serum (on average) than their healthy counterparts.

He was a chief biochemist and professor at Cornell University. Anderson researched dietary polyneuritis of poultry and the chemistry and genetics of grape pigments. He then focused his researched into nucleic acids of plants, but got carried away and left his focus onto the sterols present in the oils of plant seeds. In 1926 he was relocated to Yale University where he focused his research on isolating the sterols of the tubercle bacillus which resulted in the making of Tuberculosis vaccine.

A nucleic acid sequence is a succession of bases signified by a series of a set of five different letters that indicate the order of nucleotides forming alleles within a DNA (using GACT) or RNA (GACU) molecule. By convention, sequences are usually presented from the 5' end to the 3' end. For DNA, the sense strand is used. Because nucleic acids are normally linear (unbranched) polymers, specifying the sequence is equivalent to defining the covalent structure of the entire molecule.

During this period, he worked with several chemists, including Albrecht Kossel and Emil Fischer, who were the experts in proteins. In 1905, Levene was appointed as head of the biochemical laboratory at the Rockefeller Institute of Medical Research. He spent the rest of his career at this institute, and it was there that he identified the components of DNA. In 1909, Levene and Walter Jacobs in 1909 recognised -ribose as a natural product and an essential component of nucleic acids.

Ruthenium red, [(NH3)5Ru-O-Ru(NH3)4-O-Ru(NH3)5]6+, is a biological stain used to stain polyanionic molecules such as pectin and nucleic acids for light microscopy and electron microscopy. The beta-decaying isotope 106 of ruthenium is used in radiotherapy of eye tumors, mainly malignant melanomas of the uvea. Ruthenium- centered complexes are being researched for possible anticancer properties. Compared with platinum complexes, those of ruthenium show greater resistance to hydrolysis and more selective action on tumors.

Fungi in the genus Cercospora produce the plant toxin cercosporin, which causes the leaf spot appearance. Cercosporin is a photosensitizing perylenequione plant toxin that absorbs light energy and converts it into a highly activated state. This activated state then reacts with molecular oxygen to form activated oxygen, which in turn reacts with proteins, lipids, and nucleic acids causing damage or cell death. The fungal spores are not harmed by the production of this toxin because they produce pyridoxine which neutralizes the reaction.

The PEG–NaCl system has been shown to be effective at partitioning small molecules, such as peptides and nucleic acids. These compounds are often flavorants or odorants. The system could then be used by the food industry to isolate or eliminate particular flavors. Caffeine extraction used to be done using liquid–liquid extraction, specifically direct and indirect liquid–liquid extraction (Swiss Water Method), but has since moved towards super-critical CO2 as it is cheaper and can be done on a commercial scale.

Yan, C., Terribilini, M., Wu, F., Jernigan, R.L., Dobbs, D., and Honavar V. Predicting DNA-binding sites of proteins from amino acid sequence. BMC Bioinformatics, 2006, 7:262 DISPLAR makes a prediction based on properties of protein structure. Knowledge of the protein structure is required Tjong , H. and Zhou, H.-X. DISPLAR: an accurate method for predicting DNA-binding sites on protein surfaces. Nucleic Acids Research 35:1465-1477 (2007) BindN makes a prediction based on chemical properties of the input protein sequence.

One of his most important contributions was the prebiotic synthesis of the nucleobase adenine (a key component of nucleic acids) from hydrogen cyanide (HCN). He also showed that amino acids can be made from HCN plus ammonia in an aqueous solution.Michael Mark Woolfson, Time, Space, Stars & Man: The Story of the Big Bang, World Scientific, 2013, , p. 383. This was achieved during the period 1959–1962 and stands, together with the Miller-Urey experiment, as one of the fundamental results of prebiotic chemistry.

D. nigrospiracula exhibit sexual dimorphism through differing ratios of phosphorus concentration in adult males and females. Females have about 3 times as much phosphorus in their gonads as males. This inequality is due to the importance of phosphorus in the synthesis of nucleic acids during oogenesis. The cacti on which D. nigrospiracula breed and feed have low concentrations of phosphorus, but research has shown that the higher concentration in females comes from the phosphorus transferred from the male to the female during copulation.

STING mediates the type I interferon production in response to intracellular DNA and a variety of intracellular pathogens, including viruses, intracellular bacteria and intracellular parasites. Upon infection, STING from infected cells can sense the presence of nucleic acids from intracellular pathogens, and then induce interferon β and more than 10 forms of interferon α production. Type I interferon produced by infected cells can find and bind to Interferon-alpha/beta receptor of nearby cells to protect cells from local infection.

This possibility generated considerable excitement: Simon Conway Morris of the University of Cambridge stated that the discovery is "a very interesting surprise, and it poses lots and lots of questions." He noted the "most intriguing similarity to certain Ediacaran forms," but cautioned that "the similarities are exactly that. They are intriguing rather than compelling." Genetic identification was not possible with the original specimens, as they were preserved with formaldehyde and alcohol, a method that does not preserve nucleic acids suitably for most analyses.

Westheimer's 1987 paper in Science, "Why nature chose phosphates", discusses the importance of phosphates as signaling and building blocks for living organisms. Phosphates possess a value of pKa that allows them to be doubly ionized at physiological pH. The singly ionized form in the phosphodiester linkages of nucleic acids resists being hydrolyzed by water, but is not so stable that it won't undergo enzymatic hydrolysis. This work continues to challenge and inspire researchers studying biological chemistry and reactions in RNA, DNA, and ribozymes.

Magnet- assisted transfection is a relatively new and time-saving method to introduce nucleic acids into a target cell with increased efficiency. In particular, adherent mammalian cell lines and primary cell cultures show very high transfection rates. Suspension cells and cells from other organisms can also be successfully transfected. A major advantage of the method is the mild treatment of the cells in comparison to liposome-based transfection reagents (lipofection) and electroporation, which may result in the death of 20-50% of cells.

In addition, the transfection efficiency is increased in numerous cases by the directed transport in a magnetic field, especially for low amounts of nucleic acids. In contrast, methods like lipofection offer only statistical hits between cargo and cells, because of the three-dimensional motion of cells and transfection aggregates in a liquid suspension. Magnet-assisted transfection can also be performed in the presence of serum, which is a further benefit. Currently, there are over 150 cells known to be successfully transfected.

Artificial negatively charged substances that activate FXII include L-homocysteine, heparan sulfates, chondroitin sulfates, dermatan sulfate, uric acid crystals, lipoproteins, ferritin and porphyrins. However, the physiological substances or surfaces that activate FXII are still under debate. These may include proteins, such as gC1q-R, aggregated proteins, amyloid, collagen, nucleic acids, and polyphosphates. The ability of FXII to bind to negatively charged surfaces and activate coagulation forms the basis of the aPTT test, in which artificial materials act as a surface for contact activation.

On the day of her doctoral defense, Heemstra received a phone call from her proposed postdoctoral advisor who was concerned that she would become pregnant during her research position, which would result in her taking time out of the laboratory. Heemstra lost the postdoctoral position as a result, and instead spent two years working on medicinal chemistry in industry before starting a different postdoctoral position at Harvard University. Here she developed new approaches to template nucleic acids, working under the supervision of David Liu.

Nucleic acids are formed when nucleotides come together through phosphodiester linkages between the 5' and 3' carbon atoms. A nucleic acid sequence is the order of nucleotides within a DNA (GACT) or RNA (GACU) molecule that is determined by a series of letters. Sequences are presented from the 5' to 3' end and determine the covalent structure of the entire molecule. Sequences can be complementary to another sequence in that the base on each position is complementary as well as in the reverse order.

Spermine is associated with nucleic acids and is thought to stabilize helical structure, particularly in viruses. Crystals of spermine phosphate were first described in 1678, in human semen, by Antonie van Leeuwenhoek. The name spermin was first used by the German chemists Ladenburg and Abel in 1888, and the correct structure of spermine was not finally established until 1926, simultaneously in England (by Dudley, Rosenheim, and Starling) and Germany (by Wrede et al.). Spermine is the chemical primarily responsible for the characteristic odor of semen.

This virus contains an envelope that is made up of glycoproteins and nucleic acids. The virus is transmitted to people and horses by bites from infected mosquitoes (Culex tarsalis and Aedes taeniorhynchus) and birds during wet, summer months. According to the CDC, geographic occurrence for this virus is worldwide, and tends to be more prevalent in places in and around swampy areas where human populations tend to be limited. In the U.S., WEE is seen primarily in states and Canadian provinces west of the Mississippi River.

IFIT proteins are suggested to show anti viral activity in two ways; one, by binding specifically to viral nucleic acids and the other, by directly binding to eukaryotic initiation factor 3 (eIF3) and preventing eIF3 from initiating the translational process. Experimental data and the three dimensional structure of IFIT1 reveals that the proteins bind to viral PPP RNA in a sequence specific manner. Few viruses like Rift Valley fever virus (RVFV), vesicular stomatitis virus (VSV), and influenza A produce PPP RNA nucleic acid during their life cycle.

PCR product compared to a DNA ladder. In the case of nucleic acids, the direction of migration, from negative to positive electrodes, is due to the naturally occurring negative charge carried by their sugar-phosphate backbone. Double-stranded DNA fragments naturally behave as long rods, so their migration through the gel is relative to their size or, for cyclic fragments, their radius of gyration. Circular DNA such as plasmids, however, may show multiple bands, the speed of migration may depend on whether it is relaxed or supercoiled.

Basic Principle of CLIP CLIP begins with the in-vivo cross- linking of RNA-protein complexes using ultraviolet light (UV). Upon UV exposure, covalent bonds are formed between proteins and nucleic acids that are in close proximity. The cross-linked cells are then lysed, and the protein of interest is isolated via immunoprecipitation. In order to allow for sequence specific priming of reverse transcription, RNA adapters are ligated to the 3' ends, while radiolabeled phosphates are transferred to the 5' ends of the RNA fragments.

Guanosine is a purine nucleoside comprising guanine attached to a ribose (ribofuranose) ring via a β-N9-glycosidic bond. Guanosine can be phosphorylated to become guanosine monophosphate (GMP), cyclic guanosine monophosphate (cGMP), guanosine diphosphate (GDP), and guanosine triphosphate (GTP). These forms play important roles in various biochemical processes such as synthesis of nucleic acids and proteins, photosynthesis, muscle contraction, and intracellular signal transduction (cGMP). When guanine is attached by its N9 nitrogen to the C1 carbon of a deoxyribose ring it is known as deoxyguanosine.

Plasma Gelsolin is a sticky protein known to bind to a number of peptides and proteins: Actin (see also: Relationships with actin), Apo-H, Aβ, α-Synuclein, Integrin, Tcp-1, Fibronectin, Syntaxin-4, Tropomyosin, fatty acids and phospholipids (see also: Binding and inactivation of diverse inflammatory mediators): LPA, LPS (endotoxin), LTA, PAF, S1P, polyphosphoinositides including PIP2; and nucleic acids: Ap3A, ATP, ADP. PIP2, a phospholipid component of cell membranes, competes with ATP and actin for pGSN binding, and will dissociate F-Actin-capped pGSN.

Cold Spring Harbor Symposia on Quantitative Biology, vol. XXXVI (1972) That meeting led to the creation of the Protein Data Bank (PDB) at Brookhaven National Laboratory. In 1989, Berman moved to Rutgers and in 1992, along with other scientists, she co-founded the Nucleic Acid Database (NDB) to collect and disseminate information about nucleic acid structure.About the Nucleic Acid Database At Rutgers, she continued to study nucleic acids, their interactions with proteins, and also researched the structure of collagen in collaboration with Barbara Brodsky and Jordi Bella.

Chloroform converts slowly in air to phosgene (COCl2), releasing HCl in the process. :2 CHCl3 \+ O2 → 2 COCl2 \+ 2 HCl To prevent accidents, commercial chloroform is stabilized with ethanol or amylene, but samples that have been recovered or dried no longer contain any stabilizer. Amylene has been found ineffective, and the phosgene can affect analytes in samples, lipids, and nucleic acids dissolved in or extracted with chloroform. Phosgene and HCl can be removed from chloroform by washing with saturated aqueous carbonate solutions, such as sodium bicarbonate.

Some alkaloids can inhibit or activate enzymes, or alter carbohydrate and fat storage by inhibiting the formation phosphodiester bonds involved in their breakdown. Certain alkaloids bind to nucleic acids and can inhibit synthesis of proteins and affect DNA repair mechanisms. Alkaloids can also affect cell membrane and cytoskeletal structure causing the cells to weaken, collapse, or leak, and can affect nerve transmission. Although alkaloids act on a diversity of metabolic systems in humans and other animals, they almost uniformly invoke an aversively bitter taste.

These three methods were published independently over a short period of time, and their principles are identical. STORM was originally described using Cy5 and Cy3 dyes attached to nucleic acids or proteins, while PALM and FPALM were described using photoswitchable fluorescent proteins. In principle any photoswitchable fluorophore can be used, and STORM has been demonstrated with a variety of different probes and labeling strategies. Using stochastic photoswitching of single fluorophores, such as Cy5, STORM can be performed with a single red laser excitation source.

Evidence for common descent may be found in traits shared between all living organisms. In Darwin's day, the evidence of shared traits was based solely on visible observation of morphologic similarities, such as the fact that all birds have wings, even those that do not fly. There is strong evidence from genetics that all organisms have a common ancestor. For example, every living cell makes use of nucleic acids as its genetic material, and uses the same twenty amino acids as the building blocks for proteins.

The 1953 Cold Spring Harbor Symposium was the first opportunity for many to see the model of the DNA double helix. Watson's accomplishment is displayed on the monument at the American Museum of Natural History in New York City. Because the monument memorializes only American laureates, Francis Crick and Maurice Wilkins (who shared the 1962 Nobel Prize in Physiology or Medicine) are omitted. Watson, Crick, and Wilkins were awarded the Nobel Prize in Physiology or Medicine in 1962 for their research on the structure of nucleic acids.

A general overview of in vitro selection protocol. NA stands for Nucleic Acids (DNA, RNA, PNA) which start as a random pool, and are enriched through the selection process. Systematic evolution of ligands by exponential enrichment (SELEX), also referred to as in vitro selection or in vitro evolution, is a combinatorial chemistry technique in molecular biology for producing oligonucleotides of either single-stranded DNA or RNA that specifically bind to a target ligand or ligands. These single-stranded DNA or RNA are commonly referred to as aptamers.

Biosensors used for screening combinatorial DNA libraries In a biosensor, the bioreceptor is designed to interact with the specific analyte of interest to produce an effect measurable by the transducer. High selectivity for the analyte among a matrix of other chemical or biological components is a key requirement of the bioreceptor. While the type of biomolecule used can vary widely, biosensors can be classified according to common types of bioreceptor interactions involving: antibody/antigen, enzymes/ligands, nucleic acids/DNA, cellular structures/cells, or biomimetic materials.

Quantifying gene expression by traditional DNA detection methods is unreliable. Detection of mRNA on a northern blot or PCR products on a gel or Southern blot does not allow precise quantification. For example, over the 20–40 cycles of a typical PCR, the amount of DNA product reaches a plateau that is not directly correlated with the amount of target DNA in the initial PCR. Real-time PCR can be used to quantify nucleic acids by two common methods: relative quantification and absolute quantification.

The second is that phenol has a density of 1.07 g/cm3, which is higher than the density of water (1.00 g/cm3). Thus, when phenol is added to a cell sample solution the water and phenol remain separate. Two “phases” form when phenol is added to the solution and centrifuged. There is an aqueous, polar phase at the top of the solution containing nucleic acids and water, and an organic phase containing denatured proteins and other cell components at the bottom of the solution.

The short W repeat intron, rather than being spliced and rapidly degraded, persists after splicing and is the third most abundant EBV- produced small ncRNA in latency III. Nucleotides 4 to 26 of ebv-sisRNA-1 form a short hairpin loop that presents a Uridine-rich sequence motif (a possible platform for protein interactions) into the loop. The remainder of the sequence is unlikely to form stable RNA structure. This unstructured stretch of sequence may be exposed to allow for interactions with nucleic acids or other proteins.

Non-coding sequences important for gene regulation, such as the binding or recognition sites of ribosomes and transcription factors, may be conserved within a genome. For example, the promoter of a conserved gene or operon may also be conserved. As with proteins, nucleic acids that are important for the structure and function of non-coding RNA (ncRNA) can also be conserved. However, sequence conservation in ncRNAs is generally poor compared to protein-coding sequences, and base pairs that contribute to structure or function are often conserved instead.

There is an estimate of 80–100 active L1s in the reference genome of the Human Genome Project, and an even smaller number of L1s within those active L1s retrotranspose often. L1 insertions have been associated with tumorigenesis by activating cancer-related genes oncogenes and tumor suppressors. Each human LINE1 contains two regions from which gene products can be encoded. The first coding region contains a leucine zipper protein involved in protein-protein interactions and a protein that binds to the terminus of nucleic acids.

Assembly process involves putting together and modifying newly made viral nucleic acids and structural proteins to form the virus's nucleocapsid. Release of viruses could be done by two different mechanisms depending on the type of virus. Lytic viruses burst the cell's membrane or wall through a process called lysis in order to release themselves. On the other hand, enveloped viruses become released by a process called budding in which a virus obtain its lipid membrane as it buds out of the cell through membrane or intracellular vesicle.

Coxiella burnetii, the causative agent of Q fever, thrives and replicates in the acidic phagolysosomes of its host cell. The acidity of the phagolysosome is essential for C.burnetii to transport glucose, glutamate, and proline, as well as for its synthesis of nucleic acids and proteins. Similarly, when in its amastigote stage, Leishmania obtains all its purine sources, various vitamins, and a number of its essential amino acids from the phagolysosome of its host. Leishmania also obtain heme from the proteolysis of proteins in the host phagolysosome .

Duan MR, Nan J, Liang YH, Mao P, Lu L, Li L, Wei C, Lai L, Li Y and Su XD (2007) DNA binding mechanism revealed by high resolution crystal structure of Arabidopsis thaliana WRKY1 protein. Nucleic Acids Res. 35:1145-1154 From these two studies it appears that the conserved WRKYGQK signature amino acid sequence enters the major groove of the DNA to bind to the W-Box. Recently, the first structural determination of the WRKY domain complexed with a W-Box was reported.

SELEX, another system commonly used to identify the target nucleic acids for DNA-binding proteins, requires multiple rounds of selection. In contrast, the bacterial one-hybrid system requires just one round of in vitro selection and also offers a low-tech alternative to microarray-based technologies. Antibodies are not required for studying the interactions of DNA-binding proteins in the B1H system. A further advantage is that the B1H system works not only for monomeric proteins but also for proteins that bind DNA as complexes.

In 1925, Treat Baldwin Johnson and Coghill were detected a minor amount of a methylated cytosine derivative as a product of hydrolysis of tuberculinic acid, from avian tubercle bacilli, with sulfuric acid. This report was seriously challenged because they failed to reproduce the result after a series of tests. But Johnson and Coghill were in fact proved correct. In 1948, Hotchkiss separated the nucleic acids of DNA from calf thymus using paper chromatography, by which he detected a unique methylated cytosine, quite distinct from cytosine and uracil.

Carbon compounds can be distinguished as either organic or inorganic, and as dissolved or particulate, depending on their composition. Organic carbon forms the backbone of key component of organic compounds such as – proteins, lipids, carbohydrates, and nucleic acids. Inorganic carbon is found primarily in simple compounds such as carbon dioxide, carbonic acid, bicarbonate, and carbonate (CO2, H2CO3, HCO3−, CO32− respectively). Dissolved inorganic carbon (DIC) includes three major aqueous species, CO2, HCO3− ,CO32−, and to a lesser extent their complexes in solution with metal ions.

During electroporation, the lipid molecules in the membrane shift position, opening up a pore (hole) that acts as a conductive pathway through which hydrophobic molecules like nucleic acids can pass the lipid bilayer. A similar transfer of content across protocells and with the surrounding solution can be caused by freezing and subsequent thawing. This could, for instance, occur in an environment in which day and night cycles cause recurrent freezing. Laboratory experiments have shown that such conditions allow an exchange of genetic information between populations of protocells.

According to Melvin Calvin, certain reactions of condensation-dehydration of amino acids and nucleotides in individual blocks of peptides and nucleic acids can take place in the primary hydrosphere with pH 9–11 at a later evolutionary stage. Some of these compounds like hydrocyanic acid (HCN) have been proven in the experiments of Miller. This is the environment in which the stromatolites have been created. David Ward of Montana State University described the formation of stromatolites in hot mineral water at the Yellowstone National Park.

16, 424-430. degenerate primer studies,Omar J. Jabado, Gustavo Palacios, Vishal Kapoor, Jeffrey Hui, Neil Renwick, Zhai Junhui, Thomas Briese, and W. Ian Lipkin (2006) Greene SCPrimer: a Rapid Comprehensive Tool for Designing Degenerate Primers from Multiple Sequence Alignments; Nucleic Acids Research. 34, 6605-6611. microsatellite analysis,Alberto Arias, Ruth Freire, Josefina Méndez, and Ana Insua (2010) Isolation and characterization of microsatellite markers in the queen scallop Aequipecten opercularis and their application to a population genetic study; Aquatic Living Resources 23, 199 - 207.

Singer has made important contributions to the fields of biochemistry and molecular biology. Her research with Leon Heppel on the role of enzymes that regulate synthesis of nucleic acids played a part in helping Marshall Nirenberg and Heinrick Matthaei in deciphering the genetic code. They studied polynucleotide phosphorylase, an enzyme that can put together individual nucleotides into random RNA sequences. They investigated the base compositions of these polynucleotides using electrophoresis and paper chromatography, which enabled them to understand how the enzyme catalyzed their synthesis.

The translation machinery works relatively slowly compared to the enzyme systems that catalyze DNA replication. Proteins in bacteria are synthesized at a rate of only 18 amino acid residues per second, whereas bacterial replisomes synthesize DNA at a rate of 1000 nucleotides per second. This difference in rate reflects, in part, the difference between polymerizing four types of nucleotides to make nucleic acids and polymerizing 20 types of amino acids to make proteins. Testing and rejecting incorrect aminoacyl-tRNA molecules takes time and slows protein synthesis.

Antibody mimetics are organic compounds that, like antibodies, can specifically bind antigens, but that are not structurally related to antibodies. They are usually artificial peptides or proteins with a molar mass of about 3 to 20 kDa. (Antibodies are ~150 kDa.) Nucleic acids and small molecules are sometimes considered antibody mimetics as well, but not artificial antibodies, antibody fragments and fusion proteins composed from these. Common advantages over antibodies are better solubility, tissue penetration, stability towards heat and enzymes, and comparatively low production costs.

To perform in vitro analysis, a protein must be purified away from other cellular components. This process usually begins with cell lysis, in which a cell's membrane is disrupted and its internal contents released into a solution known as a crude lysate. The resulting mixture can be purified using ultracentrifugation, which fractionates the various cellular components into fractions containing soluble proteins; membrane lipids and proteins; cellular organelles, and nucleic acids. Precipitation by a method known as salting out can concentrate the proteins from this lysate.

The phosphodiester backbone of DNA and RNA consists of pairs of deoxyribose or ribose sugars linked by phosphates at the respective 3' and 5' positions. The backbone is negatively charged and hydrophilic, which allows strong interactions with water. Sugar-phosphate backbone forms the structural framework of nucleic acids, including DNA and RNA. Sugar phosphates are defined as carbohydrates to which a phosphate group is bound by an ester or an either linkage, depending on whether it involves an alcoholic or a hemiacetalic hydroxyl, respectively.

Repeated sequences (also known as repetitive elements, repeating units or repeats) are patterns of nucleic acids (DNA or RNA) that occur in multiple copies throughout the genome. Repetitive DNA was first detected because of its rapid re-association kinetics. In many organisms, a significant fraction of the genomic DNA is highly repetitive, with over two-thirds of the sequence consisting of repetitive elements in humans. Repetitive elements found in genomes fall into different classes, depending on their structure and/or the mode of multiplication.

Although some more ATP is generated in the citric acid cycle, the most important product is NADH, which is made from NAD+ as the acetyl-CoA is oxidized. This oxidation releases carbon dioxide as a waste product. In anaerobic conditions, glycolysis produces lactate, through the enzyme lactate dehydrogenase re- oxidizing NADH to NAD+ for re-use in glycolysis. An alternative route for glucose breakdown is the pentose phosphate pathway, which reduces the coenzyme NADPH and produces pentose sugars such as ribose, the sugar component of nucleic acids.

Anabolism is the set of constructive metabolic processes where the energy released by catabolism is used to synthesize complex molecules. In general, the complex molecules that make up cellular structures are constructed step-by-step from small and simple precursors. Anabolism involves three basic stages. First, the production of precursors such as amino acids, monosaccharides, isoprenoids and nucleotides, secondly, their activation into reactive forms using energy from ATP, and thirdly, the assembly of these precursors into complex molecules such as proteins, polysaccharides, lipids and nucleic acids.

In contrast to catabolic pathways, anabolic pathways require an energy input to construct macromolecules such as polypeptides, nucleic acids, proteins, polysaccharides, and lipids. The isolated reaction of anabolism is unfavorable in a cell due to a positive Gibbs Free Energy (+ΔG). Thus, an input of chemical energy through a coupling with an exergonic reaction is necessary. The coupled reaction of the catabolic pathway affects the thermodynamics of the reaction by lowering the overall activation energy of an anabolic pathway and allowing the reaction to take place.

Dinitrogen forms about 78% of Earth's atmosphere, making it the most abundant uncombined element. Nitrogen occurs in all organisms, primarily in amino acids (and thus proteins), in the nucleic acids (DNA and RNA) and in the energy transfer molecule adenosine triphosphate. The human body contains about 3% nitrogen by mass, the fourth most abundant element in the body after oxygen, carbon, and hydrogen. The nitrogen cycle describes movement of the element from the air, into the biosphere and organic compounds, then back into the atmosphere.

The structure of the DNA double helix. The atoms in the structure are colour- coded by element and the detailed structures of two base pairs are shown in the bottom right. The structure of part of a DNA double helix Deoxyribonucleic acid (; DNA) is a molecule composed of two polynucleotide chains that coil around each other to form a double helix carrying genetic instructions for the development, functioning, growth and reproduction of all known organisms and many viruses. DNA and ribonucleic acid (RNA) are nucleic acids.

Ijeoma Uchegbu is a Professor of Pharmacy at University College London where she also holds the position of Pro-Vice Provost for Africa and the Middle East. She is the Chief Scientific Officer of Nanomerics, a pharmaceutical nanotechnology company specialising in drug delivery solutions for poorly water-soluble drugs, nucleic acids and peptides. Apart from her highly cited scientific research in Pharmaceutical Nanoscience, Uchegbu is also known for her work in science public engagement and equality and diversity in Science, Technology, Engineering and Mathematics (STEM).

Small molecules, proteins, and nucleic acids have been found to stimulate levels of frameshifting. For example, the mechanism of a negative feedback loop in the polyamine synthesis pathway is based on polyamine levels stimulating an increase in +1 frameshifts, which results in production of an inhibitory enzyme. Certain proteins which are needed for codon recognition or which bind directly to the mRNA sequence have also been shown to modulate frameshifting levels. MicroRNA (miRNA) molecules may hybridize to a RNA secondary structure and affect its strength.

Ascorbic acid is special because it can transfer a single electron, owing to the resonance-stabilized nature of its own radical ion, called semidehydroascorbate. The net reaction is: :RO• \+ → RO− \+ C6H7O → ROH + C6H6O6 On exposure to oxygen, ascorbic acid will undergo further oxidative decomposition to various products including diketogulonic acid, xylonic acid, threonic acid and oxalic acid. Reactive oxygen species are damaging to animals and plants at the molecular level due to their possible interaction with nucleic acids, proteins, and lipids. Sometimes these radicals initiate chain reactions.

Nitrogen fixation is a process by which molecular nitrogen in the air is converted into ammonia () or related nitrogenous compounds in soil. Atmospheric nitrogen is molecular dinitrogen, a relatively nonreactive molecule that is metabolically useless to all but a few microorganisms. Biological nitrogen fixation converts into ammonia, which is metabolized by most organisms. Nitrogen fixation is essential to life because fixed inorganic nitrogen compounds are required for the biosynthesis of all nitrogen- containing organic compounds, such as amino acids and proteins, nucleoside triphosphates and nucleic acids.

Reduction of a typical disulfide bond by DTT via two sequential thiol-disulfide exchange reactions. The sample to analyze is optionally mixed with a chemical denaturant if so desired, usually SDS for proteins or urea for nucleic acids. SDS is an anionic detergent that denatures secondary and non–disulfide–linked tertiary structures, and additionally applies a negative charge to each protein in proportion to its mass. Urea breaks the hydrogen bonds between the base pairs of the nucleic acid, causing the constituent strands to anneal.

Each of these biopolymers can be characterized as either a heteropolymer, meaning it consists of more than one monomer ordered in the backbone chain, or a homopolymer, which consists of just one repeating monomer. Polypeptides and nucleic acids are very commonly heteropolymers whereas common carbohydrate macromolecules such as glycogen can be homopolymers. This is because the chemical differences of peptide and nucleotide monomers determines the biological function of their polymers whereas common carbohydrate monomers have one general function such as for energy storage and delivery.

The virus-induced expression of IFNA/IFNB genes is primarily controlled at the gene transcription level, by the interferon regulatory factors (IRFs) and IFN- stimulated genes. Viruses and immune complexes (ICs) containing nucleic acids can access intracellular TLRs (TLR3, TLR7/8 and TLR9) after binding to Fc receptors and induce IFN-α production by activation of the IRFs. Signaling through TLRs can broadly be categorized into two pathways the MyD88 and the Trip-dependent pathway. All TLRs except TLR3 signal through the MyD88-dependent pathway.

In microarray experiments DNA or RNA is labeled with either Cy3 or Cy5 that has been synthesized to carry an N-hydroxysuccinimidyl ester (NHS-ester) reactive group. Since NHS-esters react readily only with aliphatic amine groups, which nucleic acids lack, nucleotides have to be modified with aminoallyl groups. This is done through incorporating aminoallyl-modified nucleotides during synthesis reactions. A good ratio is a label every 60 bases such that the labels are not too close to each other, which would result in quenching effects.

The human body contains chemical compounds such as water, carbohydrates, amino acids (found in proteins), fatty acids (found in lipids), and nucleic acids (DNA and RNA). These compounds are composed of elements such as carbon, hydrogen, oxygen, nitrogen, and phosphorus. Any study done to determine nutritional status must take into account the state of the body before and after experiments, as well as the chemical composition of the whole diet and of all the materials excreted and eliminated from the body (including urine and feces).

More recently, it has been demonstrated that the most important factor contributing to the thermal stability of double-stranded nucleic acids is actually due to the base stackings of adjacent bases rather than the number of hydrogen bonds between the bases. There is more favorable stacking energy for GC pairs than for AT or AU pairs because of the relative positions of exocyclic groups. Additionally, there is a correlation between the order in which the bases stack and the thermal stability of the molecule as a whole.

A chaotropic agent is a molecule in water solution that can disrupt the hydrogen bonding network between water molecules (i.e. exerts chaotropic activity). This has an effect on the stability of the native state of other molecules in the solution, mainly macromolecules (proteins, nucleic acids) by weakening the hydrophobic effect. For example, a chaotropic agent reduces the amount of order in the structure of a protein formed by water molecules, both in the bulk and the hydration shells around hydrophobic amino acids, and may cause its denaturation.

Hence, peptides fall under the broad chemical classes of biological polymers and oligomers, alongside nucleic acids, oligosaccharides, polysaccharides, and others. A polypeptide that contains more than approximately fifty amino acids is known as a protein. Proteins consist of one or more polypeptides arranged in a biologically functional way, often bound to ligands such as coenzymes and cofactors, or to another protein or other macromolecule such as DNA or RNA, or to complex macromolecular assemblies. Amino acids that have been incorporated into peptides are termed residues.

Khorana was excited by the prospect of starting his own lab, a colleague later recalled. His mentor later said that the Council had few facilities at the time but gave the researcher "all the freedom in the world". His work in British Columbia was on "nucleic acids and synthesis of many important biomolecules" according to the American Chemical Society. In 1960 Khorana accepted a position as co-director of the Institute for Enzyme research at the Institute for Enzyme Research at the University of Wisconsin at Madison.

Important examples of self-assembly in materials science include the formation of molecular crystals, colloids, lipid bilayers, phase-separated polymers, and self-assembled monolayers. The folding of polypeptide chains into proteins and the folding of nucleic acids into their functional forms are examples of self-assembled biological structures. Recently, the three-dimensional macroporous structure was prepared via self- assembly of diphenylalanine derivative under cryoconditions, the obtained material can find the application in the field of regenerative medicine or drug delivery system. P. Chen et al.

Figure 4. Nucleic acids arranged in a spherical geometry offer a fundamentally new path toward gene regulation. Benefits to this approach include the ability to enter cells without precomplexation with transfection agents, nuclease resistance, and minimal immune response. SNAs are being utilized as therapeutic materials. Despite their high negative charge, they are taken up by cells (also negatively charged) in high quantities without the need for positively charged co-carriers, and they are effective as gene regulation agents in both antisense and RNAi pathways (Fig. 4).

Nucleic acids became the sole and universal means of encoding genetic information, requiring DNA repair mechanisms that in their basic form have been inherited by all extant life forms from their common ancestor. The emergence of Earth's oxygen-rich atmosphere (known as the "oxygen catastrophe") due to photosynthetic organisms, as well as the presence of potentially damaging free radicals in the cell due to oxidative phosphorylation, necessitated the evolution of DNA repair mechanisms that act specifically to counter the types of damage induced by oxidative stress.

He begins by stating the coincidence that all amino acids are left handed molecules and all nucleic acids are right handed molecules. He argues that life could have been created by any combinations of the amino-acids found on earth, but life settled on the 21 acids by chance. Cline mentions a meteor found in Australia, referencing the Murchison meteorite. He explains that because the meteor had a large volume, the core of the meteor was left unharmed from the radiation that had damaged the outer layers.

Models with three pseudo-atoms per base pair, representing the two backbone sugars and the helix axis, have been reported to have a sufficient level of detail to predict experimental results. However, models with five pseudo-atoms per base pair, explicitly including the backbone phosphates, are also used. Software for geometrical modeling of nucleic acids includes GIDEON, Tiamat, Nanoengineer-1, and UNIQUIMER 3D. Geometrical concerns are especially of interest in the design of DNA origami, because the sequence is predetermined by the choice of scaffold strand.

Biotech is mostly about exploiting living systems in anyway possible. Molecular Biology and related disciplines compare the mechanism of function of proteins in particular - and nucleic acids to a lesser extent - as like "molecular machines". In order for engineers to mimic these nanoscale machines in a way that they could be produced with some efficiency, they must look into bottom- up manufacturing. Bottom-up manufacturing deals with manipulating individual atoms during the manufacturing process, so that there is absolute control of their placement and interactions.

Circulating nucleic acids were first discovered by Mandel and Metais in 1948. It was later discovered that the level of cfDNA is significantly increased in the plasma of diseased patients. This discovery was first made in lupus patients and later it was determined that the levels of cfDNA are elevated in over half of cancer patients. Molecular analysis of cfDNA resulted in an important discovery that blood plasma DNA from cancer patients contains tumor-associated mutations and it can be used for cancer diagnostics and follow up.

Nucleic acids Res. 37, e14 In 2013, they applied the Ds-Px pair to DNA aptamer generation by in vitro selection (SELEX) and demonstrated the genetic alphabet expansion significantly augment DNA aptamer affinities to target proteins. In 2012, a group of American scientists led by Floyd Romesberg, a chemical biologist at the Scripps Research Institute in San Diego, California, published that his team designed an unnatural base pair (UBP). The two new artificial nucleotides or Unnatural Base Pair (UBP) were named d5SICS and dNaM.

Once oxygen was released into the environment, sulfates made metals more soluble and released those metals into the environment; especially into the water. Incorporation of metals perhaps combatted oxidative stress. The central chemistry of all these cells has to be reductive in order that the synthesis of the required chemicals, especially biopolymers, is possible. The different anaerobic, autocatalysed, reductive, metabolic pathways seen in the earliest known cells developed in separate energised vesicles, protocells, where they were produced cooperatively with certain bases of the nucleic acids.

VCD can be regarded as a relatively recent technique. Although Vibrational Optical Activity and in particular Vibrational Circular Dichroism, has been known for a long time, the first VCD instrument was developed in 1973L. A. Nafie, T. A. Keiderling, P. J. Stephens, JACS 1973, 98, 2715 and commercial instruments were available only since 1997.BioTools Catalog, page 4 For biopolymers such as proteins and nucleic acids, the difference in absorbance between the levo- and dextro- configurations is five orders of magnitude smaller than the corresponding (unpolarized) absorbance.

She uses fluorescence force-measuring optical tweezers to link molecular deformation (strain) and resistive forces (stress). She has also shown it is possible to use optical tweezers to transport microspheres through composite networks, measuring the forces that polymers use to resist the strain, and fluorescence microscopy to understand macromolecular mobility. She develops analysis algorithms, microfluidics and macromolecular synthesis techniques to determine the dynamics of nucleic acids. Her platform, Spatiotemporal Light-sheet Assisted Multiscale Macromolecular Transport Analysis Probe (SLAMMTAP), can be used to characterise DNA and cytoskeleton environments.

Patel's research focuses on structural biology of nucleic acids and has been particularly impactful in the study of RNA structure and protein-RNA interaction mechanisms. Patel's research group has studied riboswitches and ribozymes, as well as nuclease proteins involved in RNA interference processes. More recently his group has focused on the structural biology of epigenetic regulation, examining the mechanisms through which chemical modifications of DNA and histone proteins exert regulatory effects. The group also uses structural techniques to study innate immunity and lipid binding proteins.

Having the full spectroscopic information available in every measurement spot has the advantage that several components can be mapped at the same time, including chemically similar and even polymorphic forms, which cannot be distinguished by detecting only one single wavenumber. Furthermore, material properties such as stress and strain, crystal orientation, crystallinity and incorporation of foreign ions into crystal lattices (e.g., doping, solid solution series) can be determined from hyperspectral maps. Taking the cell culture example, a hyperspectral image could show the distribution of cholesterol, as well as proteins, nucleic acids, and fatty acids.

A number of PRRs do not remain associated with the cell that produces them. Complement receptors, collectins, ficolins, pentraxins such as serum amyloid and C-reactive protein, lipid transferases, peptidoglycan recognition proteins (PGRs) and the LRR, XA21D are all secreted proteins. One very important collectin is mannan- binding lectin (MBL), a major PRR of the innate immune system that binds to a wide range of bacteria, viruses, fungi and protozoa. MBL predominantly recognizes certain sugar groups on the surface of microorganisms but also binds phospholipids, nucleic acids and non-glycosylated proteins.

Bateman has also been involved in promoting the use of Wikipedia within the science community and in particular, community-based annotation of biological databases through Wikipedia, for example, annotation of the Rfam database through WikiProject RNA. Bateman served as Executive Editor of the journal Bioinformatics from 2004 to 2012 and has also served as Editor of Nucleic Acids Research, Genome Biology and Current Protocols in Bioinformatics. In 2014, he was appointed one of the first Honorary Editors of Bioinformatics. As of 2015, Bateman also serves on the ISCB Board of Directors.

The most common bioconjugations are coupling of a small molecule (such as biotin or a fluorescent dye) to a protein, or protein-protein conjugations, such as the coupling of an antibody to an enzyme. Other less common molecules used in bioconjugation are oligosaccharides, nucleic acids, synthetic polymers such as polyethylene glycol, and carbon nanotubes. Antibody-drug conjugates such as Brentuximab vedotin and Gemtuzumab ozogamicin are also examples of bioconjugation, and are an active area of research in the pharmaceutical industry. Recently, bioconjugation has also gained importance in nanotechnology applications such as bioconjugated quantum dots.

RBPs interact with RNA through various structural motifs. Aromatic amino acid residues in RNA-binding proteins result in stacking interactions with RNA. Lysine residues in the helical portion of RNA binding proteins help to stabilize interactions with other nucleic acids as a result of the force of attraction between the positively-charged lysine side chains and the negatively-charged phosphate "backbone" of RNA. It is hypothesized that RNA sequences in the 3'-untranslated region determine the binding of RBPs, and that these RBPs determine the post-transcriptional fate of mRNAs.

A biopharmaceutical, also known as a biologic(al) medical product, or biologic, is any pharmaceutical drug product manufactured in, extracted from, or semisynthesized from biological sources. Different from totally synthesized pharmaceuticals, they include vaccines, whole blood, blood components, allergenics, somatic cells, gene therapies, tissues, recombinant therapeutic protein, and living medicines used in cell therapy. Biologics can be composed of sugars, proteins, nucleic acids, or complex combinations of these substances, or may be living cells or tissues. They (or their precursors or components) are isolated from living sources—human, animal, plant, fungal, or microbial.

In other words, the final step in the flow of information from nucleic acids to proteins is irreversible. During the remainder of his career, he held the post of J.W. Kieckhefer Distinguished Research Professor at the Salk Institute for Biological Studies in La Jolla, California. His later research centered on theoretical neurobiology and attempts to advance the scientific study of human consciousness. He remained in this post until his death; "he was editing a manuscript on his death bed, a scientist until the bitter end" according to Christof Koch.

"Nucleic acid NMR" is the use of NMR spectroscopy to obtain information about the structure and dynamics of polynucleic acids, such as DNA or RNA. , nearly half of all known RNA structures had been determined by NMR spectroscopy. Nucleic acid and protein NMR spectroscopy are similar but differences exist. Nucleic acids have a smaller percentage of hydrogen atoms, which are the atoms usually observed in NMR spectroscopy, and because nucleic acid double helices are stiff and roughly linear, they do not fold back on themselves to give "long-range" correlations.

Biological sequence analysis: probabilistic models of proteins and nucleic acids, Cambridge University Press, 1998. SAM has been used as a source of alignments for protein structure prediction to participate in the CASP structure prediction experiment and to develop a database of predicted proteins in the yeast species S. cerevisiae. HHsearch is a software package for the detection of remotely related protein sequences based on the pairwise comparison of HMMs. A server running HHsearch (HHpred) was by far the fastest of the 10 best automatic structure prediction servers in the CASP7 and CASP8 structure prediction competitions.

SCP-ISM, or screened Coulomb potentials implicit solvent model, is a continuum approximation of solvent effects for use in computer simulations of biological macromolecules, such as proteins and nucleic acids, usually within the framework of molecular dynamics. It is based on the classic theory of polar liquids, as developed by Peter Debye and corrected by Lars Onsager to incorporate reaction field effects. The model can be combined with quantum chemical calculations to formally derive a continuum model of solvent effects suitable for computer simulations of small and large molecular systems.

They could be screened easily by using a specific strain of E. coli, known as K12 (λ), that was susceptible to wild type T4 but not to r mutants.Jayaraman, p. 903 Benzer's concept was quite controversial within classical genetic thought, in which each gene is treated as a singular point along a chromosome, not a divisible stretch of nucleic acids (as implied by the work of Watson and Crick). Initially, Max Delbrück--a respected phage geneticist and leader of the so-called phage group of which Benzer was a part--found Benzer's idea outrageous.

284x284pxQuiet breathing produces few droplets, but forced exhalations such as sneezing, coughing, shouting and singing can produce many thousands or even millions of small droplets. Droplets from healthy people consist of saliva from the mouth and/or the mucus that lines the respiratory tract. Saliva is >99% water, with small amounts of salts, proteins and other molecules. Respiratory mucus is more complex, 95% water with large amounts of mucin proteins and varying amounts of other proteins, especially antibodies, as well as lipids and nucleic acids, both secreted and derived from dead airway cells.

Deoxyribonucleic acid is a molecule that carries most of the genetic instructions used in the growth, development, functioning and reproduction of all known living organisms and many viruses. DNA and RNA are nucleic acids; alongside proteins and complex carbohydrates, they are one of the three major types of macromolecule that are essential for all known forms of life. Most DNA molecules consist of two biopolymer strands coiled around each other to form a double helix. The two DNA strands are known as polynucleotides since they are composed of simpler units called nucleotides.

This systematic position of Limulus was controversial for a long time, but has been found to show that human serum is more closely related to arachnids than to crustaceans. The field of biochemistry has greatly developed since Darwin's time, and this serological study is one of the most recent pieces of evidence of evolution. A number of biochemical products like nucleic acids, enzymes, hormones and phosphagens clearly show the relationship of all life forms. The composition of body fluid has shown that the first life originated in the oceans.

In the presence of chloroform or BCP (bromochloropropane), these solvents separate entirely into two phases that are recognized by their color: a clear, upper aqueous phase (containing the nucleic acids) and a lower phase (containing the proteins dissolved in phenol and the lipids dissolved in chloroform). Other denaturing chemicals such as 2-mercaptoethanol and sarcosine may also be used. The major downside is that phenol and chloroform are both hazardous and inconvenient materials, and the extraction is often laborious, so in recent years many companies now offer alternative ways to isolate RNA.

One downside, however, is that complexes may not separate cleanly or predictably, as it is difficult to predict how the molecule's shape and size will affect its mobility. Addressing and solving this problem is a major aim of quantitative native PAGE. Unlike denaturing methods, native gel electrophoresis does not use a charged denaturing agent. The molecules being separated (usually proteins or nucleic acids) therefore differ not only in molecular mass and intrinsic charge, but also the cross- sectional area, and thus experience different electrophoretic forces dependent on the shape of the overall structure.

In chemistry, a molecular knot is a mechanically interlocked molecular architecture that is analogous to a macroscopic knot. Naturally forming molecular knots are found in organic molecules like DNA, RNA, and proteins. It is not certain that naturally occurring knots are evolutionarily advantageous to nucleic acids or proteins, though knotting is thought to play a role in the structure, stability, and function of knotted biological molecules. The mechanism by which knots naturally form in molecules, and the mechanism by which a molecule is stabilized or improved by knotting, is ambiguous.

Organic molecules containing knots may fall into the categories of slipknots or pseudo-knots. They are not considered mathematical knots because they are not a closed curve, but rather a knot that exists within an otherwise linear chain, with termini at each end. Knotted proteins are thought to form molecular knots during their tertiary structure folding process, and knotted nucleic acids generally form molecular knots during genomic replication and transcription, though details of knotting mechanism continue to be disputed and ambiguous. Molecular simulations are fundamental to the research on molecular knotting mechanisms.

The development of various hypotheses and theories about XNAs have altered a key factor in our current understanding of nucleic acids: that heredity and evolution are not limited to DNA and RNA as once thought, but are simply processes that have developed from polymers capable of storing information. Investigations into XNAs will allow for researchers to assess whether DNA and RNA are the most efficient and desirable building blocks of life, or if these two molecules were chosen randomly after evolving from a larger class of chemical ancestors.

From 1998 to 2011, he served as editor- in-chief of the Collection of the Czechoslovak Chemical Communications, and from 2011, he has served on the Editorial Advisory Board of the journals ChemPlusChem and ChemBioChem. In 2013, he was named an F1000 faculty member for chemical biology. He is a currently a member of the Czech Chemical Society, the American Chemical Society, and the International Society for Nucleosides, Nucleotides, and Nucleic Acids. In September 2016, Hocek was featured on Hyde Park Civilizace, a Czech television show featuring prominent Czech and international scientists.

Gel electrophoresis methods, such as this formation assay on a DX complex, are used to ascertain whether the desired structures are forming properly. Each vertical lane contains a series of bands, where each band is characteristic of a particular reaction intermediate. The sequences of the DNA strands making up a target structure are designed computationally, using molecular modeling and thermodynamic modeling software. The nucleic acids themselves are then synthesized using standard oligonucleotide synthesis methods, usually automated in an oligonucleotide synthesizer, and strands of custom sequences are commercially available.

In interactions of proteins with nucleic acids, arginine residues are important hydrogen bond donors for the phosphate backbone — many arginine- methylated proteins have been found to interact with DNA or RNA. Enzymes that facilitate histone acetylation as well as histones themselves can be arginine methylated. Arginine methylation affects the interactions between proteins and has been implicated in a variety of cellular processes, including protein trafficking, signal transduction and transcriptional regulation. In epigenetics, arginine methylation of histones H3 and H4 is associated with a more accessible chromatin structure and thus higher levels of transcription.

Lysosomes contain a variety of enzymes, enabling the cell to break down various biomolecules it engulfs, including peptides, nucleic acids, carbohydrates, and lipids (lysosomal lipase). The enzymes responsible for this hydrolysis require an acidic environment for optimal activity. In addition to being able to break down polymers, lysosomes are capable of fusing with other organelles & digesting large structures or cellular debris; through cooperation with phagosomes, they are able to conduct autophagy, clearing out damaged structures. Similarly, they are able to break- down virus particles or bacteria in phagocytosis of macrophages.

Cooperative binding of proteins onto nucleic acids has also been shown. A classical example is the binding of the lambda phage repressor to its operators, which occurs cooperatively. Other examples of transcription factors exhibit positive cooperativity when binding their target, such as the repressor of the TtgABC pumps (n=1.6), as well as conditional cooperativity exhibited by the transcription factors HOXA11 and FOXO1. Conversely, examples of negative cooperativity for the binding of transcription factors were also documented, as for the homodimeric repressor of the Pseudomonas putida cytochrome P450cam hydroxylase operon (n=0.56).

Bombykol is known to be derived from acetyl-CoA via the C-16 fatty acyl palmitoyl-CoA.Caspi et al, Nucleic Acids Research 42:D459-D471 2014. Palmitoyl-CoA is converted to bombykol in steps that involve desaturation and reductive modification of the carbonyl carbon. Compared to other Type I pheromones, bombykol biosynthesis does not need chain-shortening or any other kind of modification of the terminal hydroxyl group. A desaturase enzyme encoded by the gene Bmpgdesat1 (Desat1), produces the monoene (11Z)-hexadecenoyl-CoA as well as the diene (10E,12Z)-10,12-hexadecadienoyl-CoA.

Watson then went to Copenhagen University in September 1950 for a year of postdoctoral research, first heading to the laboratory of biochemist Herman Kalckar. Kalckar was interested in the enzymatic synthesis of nucleic acids, and he wanted to use phages as an experimental system. Watson wanted to explore the structure of DNA, and his interests did not coincide with Kalckar's. After working part of the year with Kalckar, Watson spent the remainder of his time in Copenhagen conducting experiments with microbial physiologist Ole Maaløe, then a member of the Phage Group.

Petermann was the first person to isolate animal ribosomes, the sites of protein synthesis. In earlier work using cell fractionation to investigate the content of animal cells, Albert Claude found a pool of particles containing nucleic acids and proteins he termed "microsomes." Petermann found that these particles contained roughly equal amounts of RNA and protein but varied greatly in size. To purify the components further, she used a technique called analytical ultracentrifugation to separate components of mouse spleen and liver homogenates based on their relative sedimentation velocity (related to their size).

Each class of polymeric biomolecule has a different set of subunit types. For example, a protein is a polymer whose subunits are selected from a set of twenty or more amino acids, carbohydrates are formed from sugars known as monosaccharides, oligosaccharides, and polysaccharides, lipids are formed from fatty acids and glycerols, and nucleic acids are formed from nucleotides. Biochemistry studies the chemical properties of important biological molecules, like proteins, and in particular the chemistry of enzyme-catalyzed reactions. The biochemistry of cell metabolism and the endocrine system has been extensively described.

In addition to killing their target cells, granzymes can target and kill intracellular pathogens. Granzymes A and B induce lethal oxidative damage in bacteria by cleaving components of the electron transport chain, while granzyme B cleaves viral proteins to inhibit viral activation and replication. The granzymes bind directly to the nucleic acids DNA and RNA; this enhances their cleavage of nucleic acid binding proteins. More recently, in addition to T lymphocytes, granzymes have been shown to be expressed in other types of immune cells such as dendritic cells, B cells and mast cells.

Optical transfection is the process of introducing nucleic acids into cells using light. Typically, a laser is focussed to a diffraction limited spot (~1 µm diameter) using a high numerical aperture microscope objective. The plasma membrane of a cell is then exposed to this highly focussed light for a small amount of time (typically tens of milliseconds to seconds), generating a transient pore on the membrane. The generation of a photopore allows exogenous plasmid DNA, RNA, organic fluorophores, or larger objects such as semiconductor quantum nanodots to enter the cell.

An ideal chain (or freely-jointed chain) is the simplest model to describe polymers, such as nucleic acids and proteins. It only assumes a polymer as a random walk and neglects any kind of interactions among monomers. Although it is simple, its generality gives insight about the physics of polymers. In this model, monomers are rigid rods of a fixed length l, and their orientation is completely independent of the orientations and positions of neighbouring monomers, to the extent that two monomers can co-exist at the same place.

Nucleic acid NMR is the use of NMR spectroscopy to obtain information about the structure and dynamics of nucleic acid molecules, such as DNA or RNA. As of 2003, nearly half of all known RNA structures had been determined by NMR spectroscopy. Nucleic acid NMR uses similar techniques as protein NMR, but has several differences. Nucleic acids have a smaller percentage of hydrogen atoms, which are the atoms usually observed in NMR, and because nucleic acid double helices are stiff and roughly linear, they do not fold back on themselves to give "long-range" correlations.

In biochemistry it involves adding a class-specific (DNA, proteins, lipids, carbohydrates) dye to a substrate to qualify or quantify the presence of a specific compound. Staining and fluorescent tagging can serve similar purposes. Biological staining is also used to mark cells in flow cytometry, and to flag proteins or nucleic acids in gel electrophoresis. Staining is not limited to biological materials, it can also be used to study the structure of other materials for example the lamellar structures of semi- crystalline polymers or the domain structures of block copolymers.

This receptor is often composed of leucine-rich repeats (LRRs). LRRs have a wide range of bacterial (proteins), fungal (carbohydrates) and virulent (nucleic acids) recognition, this means that LRRs recognizes many different molecules but each LRRs usually has a very specific molecule it detects. The ability of PRRs to recognize various pathogenic components relies on a regulatory protein called brassinosteroid insensitive 1 –associated receptor kinase (BAK1). Once the pathogen has been recognized by PRRs the release of a kinase into the nucleus has been transduced triggering a transcriptional reprogramming.

While TERRA currently represents the primary subject of study for RNA transcripts originating from telomeres, a wide variety of alternative transcripts have also been identified as part of the yeast telomeric transcriptome: a transcript complementary to the 5' subtelomeric sequence known as ARRET; a subtelomeric transcript complementary to ARRET known as αARRET; and a C-rich telomeric repeat-containing transcript known as ARIA.Greenwood J, Cooper JP. Non-coding telomeric and subtelomeric transcripts are differentially regulated by telomeric and heterochromatin assembly factors in fission yeast. Nucleic Acids Res 2012, 40:2956–2963.

Many protein-containing solutions have the highest absorption at 280 nm in the spectrophotometer, the UV range. This requires spectrophotometers capable of measuring in the UV range, which many cannot. Additionally, the absorption maxima at 280 nm requires that proteins contain aromatic amino acids such as tyrosine (Y), phenylalanine (F) and/or tryptophan (W). Not all proteins contain these amino acids, a fact which will skew the concentration measurements. If nucleic acids are present in the sample, they would also absorb light at 280 nm, skewing the results further.

The primary biological importance of phosphates is as a component of nucleotides, which serve as energy storage within cells (ATP) or when linked together, form the nucleic acids DNA and RNA. The double helix of our DNA is only possible because of the phosphate ester bridge that binds the helix. Besides making biomolecules, phosphorus is also found in bone and the enamel of mammalian teeth, whose strength is derived from calcium phosphate in the form of hydroxyapatite. It is also found in the exoskeleton of insects, and phospholipids (found in all biological membranes).

HMG-box containing proteins only bind non-B-type DNA conformations (kinked or unwound) with high affinity. HMG-box domains are found in high mobility group proteins, which are involved in the regulation of DNA-dependent processes such as transcription, replication, and DNA repair, all of which require changing the conformation of chromatin. The single and the double box HMG proteins alter DNA architecture by inducing bends upon binding.D. Murugesapillai et al, DNA bridging and looping by HMO1 provides a mechanism for stabilizing nucleosome-free chromatin, Nucleic Acids Res (2014) 42 (14): 8996-9004D.

Autophagy-related protein 101 also known as ATG101 is a protein that in humans is encoded by the C12orf44 gene (chromosome 12 open reading frame 44). Autophagy is the process of forming a vacuole around proteins and nucleic acids that are to be broken down in lysosomes. The transcribed mRNA sequence of C12orf44 is 1287 base pairs, and following translation the sequence is 218 amino acids in length. The ATG101 protein is localized in the cytoplasm, but can possibly also be found bound to a structure known as a phagophore, involved in autophagy.

TIGAR can promote development or inhibition of several cancers depending on the cellular context. TIGAR can have some effect on three characteristics of cancer; the ability to evade apoptosis, uncontrolled cell division, and altered metabolism. Many cancer cells have altered metabolism where the rate of glycolysis and anaerobic respiration are very high whilst oxidative respiration is low, which is called the Warburg Effect (or aerobic glycolysis). This allows cancer cells to survive under low oxygen conditions, and use molecules from respiratory pathways to synthesise amino acids and nucleic acids to maintain rapid growth.

Micrococcal nuclease (, S7 Nuclease, MNase, spleen endonuclease, thermonuclease, nuclease T, micrococcal endonuclease, nuclease T', staphylococcal nuclease, spleen phosphodiesterase, Staphylococcus aureus nuclease, Staphylococcus aureus nuclease B, ribonucleate (deoxynucleate) 3'-nucleotidohydrolase) is an endo-exonuclease that preferentially digests single-stranded nucleic acids. The rate of cleavage is 30 times greater at the 5' side of A or T than at G or C and results in the production of mononucleotides and oligonucleotides with terminal 3'-phosphates. The enzyme is also active against double-stranded DNA and RNA and all sequences will be ultimately cleaved.

This budding process involves multiple signaling pathways including the elevation of intracellular calcium and reorganization of the cell's structural scaffolding. The formation and release of microvesicles involve contractile machinery that draws opposing membranes together before pinching off the membrane connection and launching the vesicle into the extracellular space. Microvesicle budding takes place at unique locations on the cell membrane that are enriched with specific lipids and proteins reflecting their cellular origin. At these locations, proteins, lipids, and nucleic acids are selectively incorporated into microvesicles and released into the surrounding environment.

EDTA is a chelator of divalent cations, particularly of magnesium (Mg2+). As these ions are necessary co-factors for many enzymes, including contaminant nucleases, the role of the EDTA is to protect the nucleic acids against enzymatic degradation. But since Mg2+ is also a co-factor for many useful DNA- modifying enzymes such as restriction enzymes and DNA polymerases, its concentration in TSE buffers is generally kept low (typically at around 2.5 mM). The sodium chloride is generally kept at a concentration of 0.05 M.Ivan Lefkovits: Immunological Methods.

The size of the activation barrier to overcome by the helicase contributes to its classification as an active or passive helicase. In passive helicases, a significant activation barrier exists (defined as B> k_{B}T, where k_{B} is Boltzmann's constant and T is temperature of the system). Because of this significant activation barrier, its unwinding progression is affected largely by the sequence of nucleic acids within the molecule to unwind, and the presence of destabilization forces acting on the replication fork. Certain nucleic acid combinations will decrease unwinding rates (i.e.

Leulliot N, Bohnsack MT, Graille M, Tollervey D, Van Tilbeurgh H.(2008). The yeast ribosome synthesis factor Emg1 is a novel member of the superfamily of alpha/beta knot fold methyltransferases. Nucleic Acids Res 36(2):629-39 In many cases the trefoil knot is part of the active site or a ligand-binding site and is critical to the activity of the enzyme in which it appears. Before the discovery of the first knotted protein, it was believed that the process of protein folding could not efficiently produce deep knots in protein backbones.

It was hypothesized that gluten, as occurs in celiac disease, is the cause of NCGS. In addition to its ability to elicit abnormal responses of the immune system, in vitro studies on cell cultures showed that gluten is cytotoxic and causes direct intestinal damage. Gluten and gliadin promote cell apoptosis (a form of programmed cell death) and reduce the synthesis of nucleic acids (DNA and RNA) and proteins, leading to a reduction in the viability of cells. Gluten alters cellular morphology and motility, cytoskeleton organization, oxidative balance and intercellular contact (tight junction proteins).

Pyrimidine nucleobases are simple ring molecules. Nucleobases, also known as nitrogenous bases or often simply bases, are nitrogen-containing biological compounds that form nucleosides, which, in turn, are components of nucleotides, with all of these monomers constituting the basic building blocks of nucleic acids. The ability of nucleobases to form base pairs and to stack one upon another leads directly to long-chain helical structures such as ribonucleic acid (RNA) and deoxyribonucleic acid (DNA). Five nucleobases—adenine (A), cytosine (C), guanine (G), thymine (T), and uracil (U)—are called primary or canonical.

Nucleosides can be produced from nucleotides de novo, particularly in the liver, but they are more abundantly supplied via ingestion and digestion of nucleic acids in the diet, whereby nucleotidases break down nucleotides (such as the thymidine monophosphate) into nucleosides (such as thymidine) and phosphate. The nucleosides, in turn, are subsequently broken down in the lumen of the digestive system by nucleosidases into nucleobases and ribose or deoxyribose. In addition, nucleotides can be broken down inside the cell into nitrogenous bases, and ribose-1-phosphate or deoxyribose-1-phosphate.

Uridine is a glycosylated pyrimidine-analog containing uracil attached to a ribose ring (or more specifically, a ribofuranose) via a β-N1-glycosidic bond. It is one of the five standard nucleosides which make up nucleic acids, the others being adenosine, thymidine, cytidine and guanosine. The five nucleosides are commonly abbreviated to their one-letter codes U, A, T, C and G respectively. However, thymidine is more commonly written as 'dT' ('d' represents 'deoxy') as it contains a 2'-deoxyribofuranose moiety rather than the ribofuranose ring found in uridine.

The genetic material of a virus is stored within a viral protein structure called the capsid. The capsid is a "shield" that protects the viral nucleic acids from getting degraded by host enzymes or other types of pesticides or pestilences. It also functions to attach the virion to its host, and enable the virion to penetrate the host cell membrane. Many copies of a single viral protein or a number of different viral proteins make up the capsid, and each of these viral proteins are coded for by one gene from the viral genome.

Within the fields of molecular biology and pharmacology, a small molecule is a low molecular weight (< 900 daltons) organic compound that may regulate a biological process, with a size on the order of 1 nm. Many drugs are small molecules. Larger structures such as nucleic acids and proteins, and many polysaccharides are not small molecules, although their constituent monomers (ribo- or deoxyribonucleotides, amino acids, and monosaccharides, respectively) are often considered small molecules. Small molecules may be used as research tools to probe biological function as well as leads in the development of new therapeutic agents.

As heat is added, this disrupts the intramolecular bonds found in tertiary structure of proteins, causing the protein to unfold and become inactive. Most life-forms on Earth live at temperatures of less than 50 °C, commonly from 15 to 50 °C. Within these organisms are macromolecules (proteins and nucleic acids) which form the three-dimensional structures essential to their enzymatic activity. Above the native temperature of the organism, thermal energy may cause the unfolding and denaturation, as the heat can disrupt the intramolecular bonds in the tertiary and quaternary structure.

Transfection is the process of deliberately introducing naked or purified nucleic acids into eukaryotic cells. It may also refer to other methods and cell types, although other terms are often preferred: "transformation" is typically used to describe non-viral DNA transfer in bacteria and non-animal eukaryotic cells, including plant cells. In animal cells, transfection is the preferred term as transformation is also used to refer to progression to a cancerous state (carcinogenesis) in these cells. Transduction is often used to describe virus-mediated gene transfer into eukaryotic cells.

As it slowly decomposes, it supplies nutrients, particularly potassium, phosphorus, and nitrogen, that are necessary for the production of cellular components such as carbohydrates, nucleic acids, and proteins; these nutrients are often a limiting factor in growth and maturation. This provides for the growth of the trees, ferns, and smaller ground plants. When earthworms are introduced into areas where they previously did not reside, the earthworms break up the organic layer. They often mix the nutrients into the soil, out of the reach of all but the deeper tree roots.

Wojciech Rychlik, William J. Spencer, and Robert E. Rhoads (1990) Optimization of the Annealing Temperature for DNA Amplification in Vitro; Nucleic Acids Res. 18, 6409-6412. and consecutive upgrades in the 1990s and 2000s, all have been cited together over 600 times in scientific journals and over 500 times in patents (according to Scopus). The program is a comprehensive real time PCR primer and probe search and analysis tool, and also does other tasks such as siRNA and molecular beacon searches, open reading frame and restriction enzyme analysis etc.

Born in Prague, Czechoslovakia, Antonín Holý studied organic chemistry from 1954 to 1959 at the Faculty of Science of Charles University in Prague. From 1960 he trained at the Institute of Organic Chemistry and Biochemistry (IOCB) of the Czechoslovak Academy of Sciences in Prague and had been a researcher there since 1963. He became the Institute's lead scientist in 1967, and from 1983 headed its working group for nucleic acids. In 1987 he became chief of the Department of Nucleic Acid Chemistry and from 1994 to 2002 he was head of the IOCB.

Plants are capable of detecting invaders through the recognition of non-self signals despite the lack of a circulatory or immune system like those found in animals. Often a plant's first line of defense against microbes occurs at the plant cell surface and involves the detection of microorganism-associated molecular patterns (MAMPs). MAMPs include nucleic acids common to viruses and endotoxins on bacterial cell membranes which can be detected by specialized pattern-recognition receptors. Another method of detection involves the use of plant immune receptors to detect effector molecules released into plant cells by pathogens.

Non-viral methods involve complexing therapeutic DNA to various macromolecules including cationic lipids and liposomes, polymers, polyamines and polyethylenimine, and nanoparticles. FuGene 6 and modified cationic liposomes are two non-viral gene delivery methods that have so far been utilized for gene delivery to cartilage. FuGene 6 is a non-liposomal lipid formulation, which has proved to be successful in transfecting a variety of cell lines. Liposomes have shown to be an appropriate candidate for gene delivery, where cationic liposomes are made to facilitate the interaction with the cell membranes and nucleic acids.

Depending upon the sequence and other conditions, nucleic acids can form a variety of structural motifs which is thought to have biological significance. ;Stem-loop: Stem-loop intramolecular base pairing is a pattern that can occur in single-stranded DNA or, more commonly, in RNA. The structure is also known as a hairpin or hairpin loop. It occurs when two regions of the same strand, usually complementary in nucleotide sequence when read in opposite directions, base-pair to form a double helix that ends in an unpaired loop.

The resulting structure is a key building block of many RNA secondary structures. ;Cruciform DNA: Cruciform DNA is a form of non-B DNA that requires at least a 6 nucleotide sequence of inverted repeats to form a structure consisting of a stem, branch point and loop in the shape of a cruciform, stabilized by negative DNA supercoiling. Two classes of cruciform DNA have been described; folded and unfolded. ;G-quadruplex: G-quadruplex secondary structures (G4) are formed in nucleic acids by sequences that are rich in guanine.

Maturation of the GI tract is mediated by pattern recognition receptors (PRRs), which recognize non-self pathogen associated molecular patterns (PAMPs) including bacterial cell wall components and nucleic acids. These data suggest that commensal microbes aid in intestinal homeostasis and immune system development. To prevent constant activation of immune cells and resulting inflammation, hosts and bacteria have evolved to maintain intestinal homeostasis and immune system development. For example, the human symbiont Bacteroides fragilis produces polysaccharide A (PSA), which binds to toll-like receptor 2 (TLR-2) on CD4+ T cells.

By using Raman microspectroscopy, in vivo time- and space-resolved Raman spectra of microscopic regions of samples can be measured. Sampling is non-destructive and water, media, and buffers typically do not interfere with the analysis. Consequently, in vivo time- and space- resolved Raman spectroscopy is suitable to examine proteins, cells and organs. In the field of microbiology, confocal Raman microspectroscopy has been used to map intracellular distributions of macromolecules, such as proteins, polysaccharides, and nucleic acids and polymeric inclusions, such as poly-β- hydroxybutyric acid and polyphosphates in bacteria and sterols in microalgae.

Due to the binding of metal ions being essential for various enzymes to maintain their enzymatic activity, thiomers are potent reversible enzyme inhibitors. Many non-invasively administered drugs such as therapeutic peptides or nucleic acids are degraded on the mucosa by membrane bound enzymes strongly reducing their bioavailability. In case of oral administration this ‘enzymatic barrier’ is even more pronounced as an additional degradation caused by luminally secreted enzymes takes place. Because of their capability to bind zinc ions via thiol groups, thiomers are potent inhibitors of most membrane bound and secreted zinc-dependent enzymes.

This exacerbates the dysfunction caused by the metabolic effects of hyperglycemia. Metabolic factors include the formation of advanced glycation end products (AGEs), which have a central role in the pathophysiology of many of the complications of diabetes mellitus, including cardiovascular complications. AGEs are chemical groups that form when a reducing sugar (glucose in this case) reacts non-enzymatically with an amine group, predominantly lysine and arginine, which are attached on proteins, lipids and nucleic acids. These glycosylation products accumulate on the proteins of vessel wall collagen, forming an irreversible complex of cross-linked AGEs.

With additional information from research reports of Wilkins and Franklin, obtained via Max Perutz, Watson and Crick correctly described the double-helix structure of DNA in 1953. Wilkins continued to test, verify, and make significant corrections to the Watson–Crick DNA model and to study the structure of RNA. Wilkins, Crick, and Watson were awarded the 1962 Nobel Prize for Physiology or Medicine, "for their discoveries concerning the molecular structure of nucleic acids and its significance for information transfer in living material."The Nobel Prize in Physiology or Medicine 1962.

The carbon atom has the unique ability to make four strong chemical bonds with other atoms, including other carbon atoms. These covalent bonds have a direction in space, so that carbon atoms can form the skeletons of complex 3-dimensional structures with definite architectures such as nucleic acids and proteins. Carbon forms more compounds than all other elements combined. The great versatility of the carbon atom, and its abundance in the visible universe, makes it the element most likely to provide the bases—even exotic ones—for the chemical composition of life on other planets.

Vander Meulen K.A., Butcher S.E., Characterization of the kinetic and thermodynamic landscape of RNA folding using a novel application of isothermal titration calorimetry. Nucleic Acids Res. 40(2011)2140-51 In short, kinITC allows obtaining with a single technique both the information obtained with classical ITC and with a technique like Surface Plasmon Resonance (SPR). In situations where a chemical reaction proceeds clearly through two successive kinetic steps, the major interest of kinITC is of being potentially more informative alone than ITC and SPR used jointly, but in a classical way.

The order of assembly of the amino acids is then determined by a specific recognition between the adaptor and the nucleic acid which is serving as the informational template. In this way the amino acids could be lined up by the template in a specific order. Coupling between adjacent amino acids would then lead to the synthesis of a polypeptide whose sequence is determined by the template nucleic acid. ;Basis Crick’s thinking behind this proposal was based on a general consideration of the chemical properties of the two classes of molecule — nucleic acids and proteins.

GROMACS is a molecular dynamics package mainly designed for simulations of proteins, lipids, and nucleic acids. It was originally developed in the Biophysical Chemistry department of University of Groningen, and is now maintained by contributors in universities and research centers worldwide. GROMACS is one of the fastest and most popular software packages available, and can run on central processing units (CPUs) and graphics processing units (GPUs). It is free, open-source software released under the GNU General Public License (GPL), and starting with version 4.6, the GNU Lesser General Public License (LGPL).

However, the idea of RNA catalysis is motivated in part by the old question regarding the origin of life: Which comes first, enzymes that do the work of the cell or nucleic acids that carry the information required to produce the enzymes? The concept of "ribonucleic acids as catalysts" circumvents this problem. RNA, in essence, can be both the chicken and the egg. In the 1980s Thomas Cech, at the University of Colorado at Boulder, was studying the excision of introns in a ribosomal RNA gene in Tetrahymena thermophila.

Colloidal gold and various derivatives have long been among the most widely used labels for antigens in biological electron microscopy. Colloidal gold particles can be attached to many traditional biological probes such as antibodies, lectins, superantigens, glycans, nucleic acids, and receptors. Particles of different sizes are easily distinguishable in electron micrographs, allowing simultaneous multiple-labelling experiments. In addition to biological probes, gold nanoparticles can be transferred to various mineral substrates, such as mica, single crystal silicon, and atomically flat gold(III), to be observed under atomic force microscopy (AFM).

Peat deposits are an indication of originating from the epicuticular wax of higher plants. Life processes may produce a range of biosignatures such as nucleic acids, lipids, proteins, amino acids, kerogen-like material and various morphological features that are detectable in rocks and sediments. Microbes often interact with geochemical processes, leaving features in the rock record indicative of biosignatures. For example, bacterial micrometer-sized pores in carbonate rocks resemble inclusions under transmitted light, but have distinct size, shapes and patterns (swirling or dendritic) and are distributed differently from common fluid inclusions.

Non-nucleoside phosphoramidites for 5'-modification of synthetic oligonucleotides Fluorescein amidites, abbreviated as FAM, are important synthetic equivalents of fluorescein dye used in oligonucleotide synthesis and molecular biology. FAM is used in the preparation of fluorescein-labeled oligonucleotide probes for the detection of the presence of the complementary nucleic acids or primers for polymerase chain reaction. Oligonucleotides labeled with fluorescein at one of the termini and with a quencher at the other can serve as molecular beacons. The commercially available 6-FAM version is shown in the figure.

Mutations in four genes can cause this syndrome:Ren R, Hardikar S, Horton JR, Lu Y, Zeng Y, Singh AK, Lin K, Coletta LD, Shen J, Lin Kong CS, Hashimoto H, Zhang X, Chen T, Cheng X (2019) Structural basis of specific DNA binding by the transcription factor ZBTB24. Nucleic Acids Res Cell division cycle associated protein 7 (CDCA7), DNA-methyltransferase 3b (DNMT3B), Lymphoid specific helicase (HELLS) and Zinc finger- and BTB domain containing protein 24 (ZBTB24). The CDCA7 gene is located on chromosome 2 (2q31.1). The DNMT3B gene is located on chromosome 20 (20q11.2)).

Death from elapid bites usually results from asphyxiation because the diaphragm can no longer contract. However, this rule does not always apply; some elapid bites include proteolytic symptoms typical of viperid bites, while some viperid bites produce neurotoxic symptoms. Proteolytic venom is also dual-purpose: first, it is used for defense and to immobilize prey, as with neurotoxic venoms; secondly, many of the venom's enzymes have a digestive function, breaking down molecules in prey items, such as lipids, nucleic acids, and proteins. This is an important adaptation, as many vipers have inefficient digestive systems.

Nucleic acids were first discovered in 1868 by Friedrich Miescher and by 1939 RNA had been implicated in protein synthesis. Two decades later, Francis Crick predicted a functional RNA component which mediated translation; he reasoned that RNA is better suited to base-pair with an mRNA transcript than a pure polypeptide. The cloverleaf structure of Yeast tRNAPhe (inset) and the 3D structure determined by X-ray analysis. The first non-coding RNA to be characterised was an alanine tRNA found in baker's yeast, its structure was published in 1965.

Nucleic acids may not be the only biomolecules in the Universe capable of coding for life processes. Astrobiology, formerly known as exobiology, is an interdisciplinary scientific field concerned with the origins, early evolution, distribution, and future of life in the universe. Astrobiology considers the question of whether extraterrestrial life exists, and if it does, how humans can detect it. Astrobiology makes use of molecular biology, biophysics, biochemistry, chemistry, astronomy, physical cosmology, exoplanetology and geology to investigate the possibility of life on other worlds and help recognize biospheres that might be different from that on Earth.

SILVA provides comprehensive, quality checked and regularly updated datasets of aligned small (16S/18S, SSU) and large subunit (23S/28S, LSU) ribosomal RNA (rRNA) sequences for all three domains of life as well as a suite of search, primer-design and alignment tools (Bacteria, Archaea and Eukarya).Elmar Pruesse, Christian Quast, Katrin Knittel, Bernhard M. Fuchs, Wolfgang Ludwig, Jörg Peplies, Frank Oliver Glöckner (2007) Nucleic Acids Res. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. December; 35(21): 7188–7196.

Propidium iodide (or PI) is a fluorescent intercalating agent that can be used to stain cells and nucleic acids. PI binds to DNA by intercalating between the bases with little or no sequence preference. When in an aqueous solution, PI has a fluorescent excitation maximum of 493 nm (blue-green), and an emission maximum of 636 nm (red). After binding DNA, the quantum yield of PI is enhanced 20-30 fold, and the excitation/emission maximum of PI is shifted to 535 nm (green) / 617 nm (orange-red).

Probes for northern blotting are composed of nucleic acids with a complementary sequence to all or part of the RNA of interest, they can be DNA, RNA, or oligonucleotides with a minimum of 25 complementary bases to the target sequence. RNA probes (riboprobes) that are transcribed in vitro are able to withstand more rigorous washing steps preventing some of the background noise. Commonly cDNA is created with labelled primers for the RNA sequence of interest to act as the probe in the northern blot.Liang, P. Pardee, A. B. (1995) Recent advances in differential display.

The Protein Data Bank (PDB) is a database for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids. The data, typically obtained by X-ray crystallography, NMR spectroscopy, or, increasingly, cryo-electron microscopy, and submitted by biologists and biochemists from around the world, are freely accessible on the Internet via the websites of its member organisations (PDBe, PDBj, RCSB, and BMRB). The PDB is overseen by an organization called the Worldwide Protein Data Bank, wwPDB. The PDB is a key in areas of structural biology, such as structural genomics.

Natural compounds refer to those that are produced by plants or animals. Many of these are still extracted from natural sources because they would be more expensive to produce artificially. Examples include most sugars, some alkaloids and terpenoids, certain nutrients such as vitamin B12, and, in general, those natural products with large or stereoisometrically complicated molecules present in reasonable concentrations in living organisms. Further compounds of prime importance in biochemistry are antigens, carbohydrates, enzymes, hormones, lipids and fatty acids, neurotransmitters, nucleic acids, proteins, peptides and amino acids, lectins, vitamins, and fats and oils.

Macromolecular crowding in the cytosol of cells alters the properties of macromolecules such as proteins and nucleic acids. The phenomenon of macromolecular crowding alters the properties of molecules in a solution when high concentrations of macromolecules such as proteins are present. Such conditions occur routinely in living cells; for instance, the cytosol of Escherichia coli contains about 300– of macromolecules. Crowding occurs since these high concentrations of macromolecules reduce the volume of solvent available for other molecules in the solution, which has the result of increasing their effective concentrations.

She recognised that the "beginnings of life are clearly associated with the interaction of proteins and nucleic acids". Bell and Astbury published an X-ray study on DNA in 1938, describing the nucleotides as a "Pile of Pennies". Astbury presented their work at the Cold Spring Harbor Laboratory. At the time, they were unaware that DNA can change conformation from A to B-form with humidity, and as a result their photographs are more blurry than the later Photo 51 x-ray image taken by Gosling in 1952.

A tandem mass tag (TMT) is a chemical label used for mass spectrometry (MS)-based quantification and identification of biological macromolecules such as proteins, peptides and nucleic acids. TMT belongs to a family of reagents referred to as isobaric mass tags. They provide an alternative to gel- or antibody-based quantification but may also be used in combination with these and other methods. In addition to aiding in protein quantification, TMT tags can also increase the detection sensitivity of certain highly hydrophilic analytes, such as phosphopeptides, in RPLC-MS analyses.

The natural bases of nucleic acids form a great variety of base pairs with at least two hydrogen bonds between them. These hydrogen bonds can occur between atoms belonging to any of the three edges of the nucleic acid edges. The possible combinations lead to a classification in twelve main families, with the Watson-Crick family being one of them. In a given family, some of the base pairs are isosteric between them, meaning that the positions and the distances between the C1’ carbon atoms are very similar.

Attaching proteins, nucleic acids, or small molecules to the VLP surface, such as for targeting a specific cell type or for raising an immune response is useful. In some cases a protein of interest can be genetically fused to the viral coat protein. However, this approach sometimes leads to impaired VLP assembly and has limited utility if the targeting agent is not protein-based. An alternative is to assemble the VLP and then use chemical crosslinkers, reactive unnatural amino acids or SpyTag/SpyCatcher reaction in order to covalently attach the molecule of interest.

Carl Woese first demonstrated that the sequence of the 16S ribosomal RNA molecule could be used to analyze phylogenetic relationships. Norm Pace took this seminal idea and applied it to analyze ‘who’s there’ in natural environments. The procedure involves (a) isolation of nucleic acids directly from a natural environment, (b) PCR amplification of small subunit rRNA gene sequences, (c) sequencing the amplicons, and (d) comparison of the those sequences to a database of sequences from pure cultures and environmental DNA. This has provided tremendous insights into the diversity present within microbial habitats.

Methods from modern molecular biology allow the extraction of nucleic acids, lipids and proteins from cells, DNA sequencing, and the physical and chemical analysis of molecules using mass spectrometry and flow cytometry. A lot can be learned about the microbial communities using these methods even when the individuals cannot be cultivated. For example, at the Richmond Mine in California, scientists used shotgun sequencing to identify four new species of bacteria, three new species of archaea (known as the Archaeal Richmond Mine acidophilic nanoorganisms), and 572 proteins unique to the bacteria.

Stoichiometric equation representing the metabolism of an aldehyde substrate by ALDH3A1 using NADP+ as a cofactor Electronic excitations of alkene and aromatic functional groups allow certain nucleic acids, proteins, fatty acids and organic molecules to absorb ultraviolet radiation (UVR). Moderate UVR exposure oxidizes specific proteins that eventually serve as signaling agents for an array of metabolic and inflammatory pathways. Overexposure to UVR, on the other hand, can be detrimental to the tissue. In the presence of molecular oxygen, UVR leads to the formation of reactive oxygen species (ROS) that are implicated in many degradation pathways.

She studies the mechanisms by which small molecules interact with nucleic acid. Her research involves the synthesis of modified nucleosides and nucleotides, monitoring the intercalation of small aromatic systems into DNA via the design of novel chromophores and the creation of probes that contain nucleic acids to study events that occur around DNA. She has studied the protection of small nuclear RNA (snRNAs) from oxidative damage, which typically damages cells. As snRNA is essential for the function of spliceosome, this type of damage can impact the structure and function of the spliceosome.

At the University of Washington in the 1990s, Hood, Alan Blanchard, and others developed ink-jet DNA synthesis technology for creating DNA microarrays. By 2004, their ink-jet DNA synthesizer supported high-throughput identification and quantification of nucleic acids through the creation of one of the first DNA array chips, with expression levels numbering tens of thousands of genes. Array analysis has become a standard technique for molecular biologists who wish to monitor gene expression. DNA ink-jet printer technology has had a significant impact on genomics, biology, and medicine.

Methylglyoxal. The principal physiological function of glyoxalase I is the detoxification of methylglyoxal, a reactive 2-oxoaldehyde that is cytostatic at low concentrations and cytotoxic at millimolar concentrations. Methylglyoxal is a by-product of normal biochemistry that is a carcinogen, a mutagen and can chemically damage several components of the cell, such as proteins and nucleic acids. Methylglyoxal is formed spontaneously from dihydroxyacetone phosphate, enzymatically by triosephosphate isomerase and methylglyoxal synthase, as also in the catabolism of threonine. To minimize the amount of toxic methylglyoxal and other reactive 2-oxoaldehydes, the glyoxalase system has evolved.

Non- covalent interactions are critical in maintaining the three-dimensional structure of large molecules, such as proteins and nucleic acids. In addition, they are also involved in many biological processes in which large molecules bind specifically but transiently to one another (see the properties section of the DNA page). These interactions also heavily influence drug design, crystallinity and design of materials, particularly for self-assembly, and, in general, the synthesis of many organic molecules. Intermolecular forces are non-covalent interactions that occur between different molecules, rather than between different atoms of the same molecule.

Some of the most common stable isotopes are 2H, 13C, and 15N, which can further be produced into NMR solvents, amino acids, nucleic acids, lipids, common metabolites and cell growth media. The compounds produced using stable isotopes are either specified by the percentage of labeled isotopes (i.e. 30% uniformly labeled 13C glucose contains a mixture that is 30% labeled with 13 carbon isotope and 70% naturally labeled carbon) or by the specifically labeled carbon positions on the compound (i.e. 1-13C glucose which is labeled at the first carbon position of glucose).

Others implicate the arginine residues of nuclear histones as the substrate of nuclear staining by haemalum. Structures that stain with aluminium-hematein (haemalum) are often said to be basophilic, but the staining mechanism is not as simple as for basic (cationic) dyes with smaller molecules. Truly basophilic structures are ones containing nucleic acids or other polyanions such as glycosaminoglycans of extracellular matrix or acidic glycoproteins in many types of mucus. As usually used, aluminium- hematein stains only nuclear chromatin and a few other materials such as keratohyalin granules and calcified deposits.

A chaotropic agent is a substance which disrupts the structure of, and denatures, macromolecules such as proteins and nucleic acids (e.g. DNA and RNA). Chaotropic solutes increase the entropy of the system by interfering with intermolecular interactions mediated by non-covalent forces such as hydrogen bonds, van der Waals forces, and hydrophobic effects. Macromolecular structure and function is dependent on the net effect of these forces (see protein folding), therefore it follows that an increase in chaotropic solutes in a biological system will denature macromolecules, reduce enzymatic activity and induce stress on a cell (i.e.

Alkaline and acid treatments can be effective companions with an SDS treatment due to their ability to degrade nucleic acids and solubilize cytoplasmic inclusions. The most well known non-ionic detergent is Triton X-100, which is popular because of its ability to disrupt the interactions between lipids and between lipids and proteins. Triton X-100 does not disrupt protein-protein interactions, which is beneficial to keeping the ECM intact. EDTA is a chelating agent that binds calcium, which is a necessary component for proteins to interact with one another.

Using TopFIND, terminal modifications can be identified and visualized across proteins thanks to all available in silico, in vitro, and in vivo findings. Using TopFINDer and Path FINDer software, research findings can be mathematically modelled into a network of pathways regulated by proteases,Fortelny N., Yang S., Pavlidis P., Lange P.F., Overall C.M.. Proteome TopFIND 3.0 with TopFINDer and PathFINDer: database and analysis tools for the association of protein termini to pre- and post- translational events. Nucleic Acids Res. 43(Database issue):D290-7 (2015). further contributing to the “protease web”.

Since that success, over 130,000 X-ray crystal structures of proteins, nucleic acids and other biological molecules have been determined. The nearest competing method in number of structures analyzed is nuclear magnetic resonance (NMR) spectroscopy, which has resolved less than one tenth as many. Crystallography can solve structures of arbitrarily large molecules, whereas solution-state NMR is restricted to relatively small ones (less than 70 kDa). X-ray crystallography is used routinely to determine how a pharmaceutical drug interacts with its protein target and what changes might improve it.

Cavalier-Smith argues that the most plausible location for obcells to survive and grow in number on Earth was by the land-water interface, not by oceanic seafloor vents. Due to their likely dependence on polyP and pyrophosphate for energy overAdenosine triphosphate ATP, obcells would likely congregate in areas where these minerals were formed in high concentrations. Polyphosphate could easily be formed by the seashore in "small salty pools, porous sediments, or protosoils." At lower temperatures, nucleic acids are more stable and shorter chain lipids can form membranes easier.

Nucleic acids are generally basophilic because they have a very high density of negative charge due to the sugar phosphate backbone. However, in contrast to other basic i.e. cationic dyes, Alcian blue usually (given the right pH and salt concentrations, and normal temperature and duration in minutes, not hours) preferably stains acidic glycosaminoglycans but not the chromatin and nissel substance, the mechanism of which had been a mystery for a long time and various theories were proposed. Though the presumed basis of the staining is its positive charge attracted to negative structures (e.g.

However, those covalent linking methods are limited by the concern that the synthetic covalent bond between CPP and nucleic acid may alter the biological activity of the latter. Thus, a new non-covalent strategy requiring no chemical modification with short amphipathic CPPs, like MPG and Pep-1 as carriers has been successfully applied for delivery of cargoes. These non-covalent conjugates are formed through either electrostatic or hydrophobic interactions. With this method, cargoes such as nucleic acids and proteins could be efficiently delivered while maintaining full biological activity.

An alternative method to assess DNA and RNA concentration is to tag the sample with a Fluorescent tag, which is a fluorescent dye used to measure the intensity of the dyes that bind to nucleic acids and selectively fluoresce when bound (e.g. Ethidium bromide). This method is useful for cases where concentration is too low to accurately assess with spectrophotometry and in cases where contaminants absorbing at 260 nm make accurate quantitation by that method impossible. The benefit of fluorescence quantitation of DNA and RNA is the improved sensitivity over spectrophotometric analysis.

Membrane proteins may be identified by a shift in mobility induced by a charged detergent. Nucleic acids or nucleic acid fragments may be characterized by their affinity to other molecules. The methods have been used for estimation of binding constants, as for instance in lectin affinity electrophoresis or characterization of molecules with specific features like glycan content or ligand binding. For enzymes and other ligand- binding proteins, one-dimensional electrophoresis similar to counter electrophoresis or to "rocket immunoelectrophoresis", affinity electrophoresis may be used as an alternative quantification of the protein.

Millions of potential interactions in several organisms have been screened in the latest decade using high-throughput screening systems (often using robots) and over thousands of interactions have been detected and categorized in databases as BioGRID. This system often utilizes a genetically engineered strain of yeast in which the biosynthesis of certain nutrients (usually amino acids or nucleic acids) is lacking. When grown on media that lacks these nutrients, the yeast fail to survive. This mutant yeast strain can be made to incorporate foreign DNA in the form of plasmids.

Diseases of abnormal polymerization are said the undergo “replication”, or rather that the number of proteins that are polymerized is shown to generally increase much like in a natural course of infection. Since the functional “pathogens” of DAPs are protein units the diseases are almost entirely independent from the use of nucleic acids. Multiple models illustrating this recruitment function exist, including the PrP protein in prion disease. The PrP protein is the major agent in spongiform encephalopathies and undergoes a clear process of polymerization based upon the natural balancing of thermodynamic states and kinetic summation.

Albrecht Kossel is considered one of the great scientists of biochemistry and genetics. By isolating and defining nucleic acid and the nucleobases, he provided the necessary precursors that led to the double-helix model of DNA, devised by James D. Watson and Francis Crick in 1953. " … his elucidation of the chemical nature of some building blocks that make up nucleic acids and chromatine has secured immortality for this exeedingly modest and almost shy man." The Albrecht Kossel Institute for Neuroregeneration at the University of Rostock is named in his honor.

Phenotype may also be determined by the number of RNA molecules, as more RNA transcripts lead to a greater expression of protein. Short tails of repetitive nucleic acids are often added to the ends of RNA molecules in order to prevent degradation, effectively increasing the number of RNA strands able to be translated into protein. During mammalian liver regeneration RNA molecules of growth factors increase in number due to the addition of signaling tails. With more transcripts present the growth factors are produced at a higher rate, aiding the rebuilding process of the organ.

A biological target is anything within a living organism to which some other entity (like an endogenous ligand or a drug) is directed and/or binds, resulting in a change in its behavior or function. Examples of common classes of biological targets are proteins and nucleic acids. The definition is context-dependent, and can refer to the biological target of a pharmacologically active drug compound, the receptor target of a hormone (like insulin), or some other target of an external stimulus. Biological targets are most commonly proteins such as enzymes, ion channels, and receptors.

Consequently, it would be better to use the original terms (bacterial, archaeal, or fungal community). In contrast to the microbiota, which can be studied separately, the microbiome is always composed by all members, which interact with each other, live in the same habitat, and form their ecological niche together. The well-established term virome is derived from virus and genome and is used to describe viral shotgun metagenomes consisting of a collection of nucleic acids associated with a particular ecosystem or holobiont.McDaniel, L., Breitbart, M., Mobberley, J., Long, A., Haynes, M., Rohwer, F. and Paul, J.H., 2008.

In chemistry, orthochromasia is the property of a dye or stain to not change color on binding to a target, as opposed to metachromatic stains, which change color. The word is derived from the Greek orthos (correct, upright), and chromatic (color). Toluidine blue is an example of a partially orthochromatic dye, as it stains nucleic acids by its orthochromatic color (blue), but stains mast cell granules in its metachromatic color (red). In spectral terms, orthochromasia refers to maintaining the position of spectral peaks, while metachromasia refers to a shift in wavelength, becoming either shorter or longer.

Superparamagnetic microbeads: the monosized Dynabeads (scanning electron microscope image) Microbeads, also called Ugelstad particles after the Norwegian chemist, professor dr.philos. John Ugelstad, who invented them in 1977 and patented the method in 1978,Rangnes 1997:4–5 are uniform polymer particles, typically 0.5 to 500 micrometres in diameter. Bio-reactive molecules can be absorbed or coupled to their surface, and used to separate biological materials such as cells, proteins, or nucleic acids. Microbeads have been used for isolation and handling of specific material or molecules, as well as for analyzing sensitive molecules, or those that are in low abundance, e.g.

PPT DB website home page The Protein Property Prediction and Testing Database (PPT-DB) is a collection of protein property databases for over 20 different protein properties including secondary structure, trans-membrane helices and beta barrels, accessible surface area, signal peptides, and more. PPT-DB is published in 2008. Its protocol is available via PPT-DB website David S. Wishart, David Arndt, Mark Berjanskii, An Chi Guo, Yi Shi, Savita Shrivastava, Jianjun Zhou, You Zhou and Guohui Lin: PPT-DB: the protein property prediction and testing database. Nucleic Acids Research 2008 36(Database issue):D222-D229.

A predictive database is one based on statistical inference. One particular approach to such inference is known as predictive inference, but the prediction can be undertaken within any of the several approaches to statistical inference. Indeed, one description of biostatistics is that it provides a means of transferring knowledge about a sample of a genetic population to the whole population (genomics), and to other related genes or genomes, which the same as prediction over time is not necessarily.S. Hunter and P. Jones, "InterPro in 2011: new developments in the family and domain prediction database," Nucleic Acids Research, vol.

These chemicals are stored in environmentally controlled conditions in small or large containers, often labeled with codes that pass back into a database. Each chemical in the storage bank must be monitored for shelf life, quantity, purity and other parameters, and its banked location. In some companies, the compounds can also include biological compounds, such as purified proteins or nucleic acids. The management of these chemical libraries, including renewal of outdated chemicals, databases containing the information, robotics often involved in fetching chemicals, and quality control of the storage environment is called Compound Management or Compound Control.

The Europe PMC project was originally launched in 2007 as the first 'mirror' site to PMC, which aims to provide international preservation of the open and free-access biomedical and life sciences literature. It forms part of a network of PMC International (PMCI) repositories that includes PubMed Central Canada. Europe PMC is not an exact "mirror" of the PMC database but has developed some different features."UKPMC: a full text article resource for the life sciences", Nucleic Acids Research, 2011 January; 39 (Database issue): D58–D65 On 15 February 2013 CiteXplore was subsumed under Europe PubMed Central.

Cisplatin Cisplatin is one of the most frequently used chemotherapy medications for many forms of cancer. It was discovered in the 1960s by Barnett Rosenberg, but its mechanism of action was not understood. Early work in Lippard's lab on the interaction of metal complexes with nucleic acids led to the discovery of the first metallo- intercalators and eventually to the understanding of the mechanisms of cisplatin. Lippard and his students examined sequences of DNA and RNA and incorporated sulfur atoms into the sugar-phosphate backbone, where they selectively bound mercury or platinum complexes to specific positions.

In 1950, Chase began working as a research assistant at Cold Spring Harbor Laboratory in the laboratory of bacteriologist and geneticist Alfred Hershey. In 1952, she and Hershey performed the Hershey–Chase experiment, which helped to confirm that genetic information is held and transmitted by DNA, not by protein. The experiment involved radioactively labeling either protein or nucleic acid of the bacteriophage T2 (a virus that infects bacteria) and seeing which component entered E coli upon infection. They found that nucleic acids but not protein were transferred, helping resolve controversy over the composition of hereditary information.

Protoplasm is composed of a mixture of small molecules such as ions, amino acids, monosaccharides and water, and macromolecules such as nucleic acids, proteins, lipids and polysaccharides. In eukaryotes the protoplasm surrounding the cell nucleus is known as the cytoplasm and that inside the nucleus as the nucleoplasm. In prokaryotes the material inside the plasma membrane is the bacterial cytoplasm, while in Gram-negative bacteria the region outside the plasma membrane but inside the outer membrane is the periplasm. Protoplasm was said to exist in two forms: a liquid-like sol state or a jelly-like gel state.

Figure 1. During meiosis, homologous recombination can produce new combinations of genes as shown here between similar but not identical copies of human chromosome 1. Homologous recombination is a type of genetic recombination in which nucleotide sequences are exchanged between two similar or identical molecules of double-stranded or single-stranded nucleic acids (usually DNA as in cellular organisms but may be also RNA in viruses). It is most widely used by cells to accurately repair harmful breaks that occur on both strands of DNA, known as double-strand breaks (DSB), in a process called homologous recombinational repair (HRR).

Cytosine was discovered and named by Albrecht Kossel and Albert Neumann in 1894 when it was hydrolyzed from calf thymus tissues.A. Kossel and Albert Neumann (1894) "Darstellung und Spaltungsprodukte der Nucleïnsäure (Adenylsäure)" (Preparation and cleavage products of nucleic acids (adenic acid)), Berichte der Deutschen Chemischen Gesellschaft zu Berlin, 27 : 2215–2222. The name "cytosine" is coined on page 2219: " … ein Produkt von basischen Eigenschaften, für welches wir den Namen "Cytosin" vorschlagen." ( … a product with basic properties, for which we suggest the name "cytosine".) A structure was proposed in 1903, and was synthesized (and thus confirmed) in the laboratory in the same year.

Hocek and his group have contributed significantly to organic chemistry and medicinal chemistry by developing methods to synthesize modified nucleobases, nucleosides, nucleotides, and nucleic acids through cross-coupling reactions and C-H activation. They discovered several novel classes of cytostatic agents with nanomolar antitumor activities based on substituted or fused deazapurine nucleosides. In the field of chemical biology, Hocek and his laboratories have developed a simple two-step synthesis of base-modified DNA through cross- coupling reactions of 2'-deoxyribonucleoside triphosphates (dNTPs) followed by polymerase incorporation. They have discovered some modified dNTPs that are better substrates for polymerases than natural nucleotides.

This type of bond can occur in inorganic molecules such as water and in organic molecules like DNA and proteins. The hydrogen bond is responsible for many of the anomalous physical and chemical properties of compounds of N, O, and F. In particular, intermolecular hydrogen bonding is responsible for the high boiling point of water (100 °C) compared to the other group 16 hydrides that have much weaker hydrogen bonds. Intramolecular hydrogen bonding is partly responsible for the secondary and tertiary structures of proteins and nucleic acids. It also plays an important role in the structure of polymers, both synthetic and natural.

Thiamine serves several indispensable roles in the brain that affect cognitive function either directly or indirectly. It is a functional component of neuronal and microglial cell membranes, and serves as a modulator of the acetylcholine neurotransmitter system. Thiamine indirectly drives cognitive processes as a necessary cofactor in the pathways needed to synthesise fatty acids, steroid hormones, nucleic acids and precursory molecules for various compounds involved in brain function. It has been shown that cats suffer irreversible brain damage when deprived of thiamine that hinders memory and learning even after thiamine has been reintroduced to the diet.

Three years later he was appointed assistant professor in the Department of Chemistry and Pharmacology, and in 1946 Jorpes was named the professor of medical chemistry. Jorpes retired in 1963 and continued as a professor emeritus until his death in 1973. In 1949–1951, Jorpes and his predecessor, the professor Einar Hammarsten had a major influence on the architectural design of the building of chemistry of the Karolinska Institute Campus in Solna. The drawings were originally made in 1937 by the architect Tore Rydberg but the construction was postponed due to the World War II. His first research involved pancreatic nucleic acids.

These protein cages are nanoparticles that have one or more cavities present in their structure. The size of the cavity contributes to the size of the particle that the cavity can enclose, for example inorganic nanoparticles, nucleic acids, and even other proteins. The interior or chamber portion of the protein cage is usually accessible through a pore which is located in between protein subunits. The RNA exosome has nuclease active sites that are present in a cavity where 3' RNA degradation takes place; access to this cavity is controlled by a pore and this serves to prevent uncontrollable RNA decay.

This difference in density is why phenol, which only has a slightly higher density than water, must be mixed with chloroform to form a mixture with a much higher density than water. The hydrophobic lipids will partition into the lower organic phase, and the proteins will remain at the interphase between the two phases, while the nucleic acids (as well as other contaminants such as salts, sugars, etc.) remain in the upper aqueous phase. The upper aqueous phase can then be pipetted off. Care must be taken to avoid pipetting any of the organic phase or material at the interface.

The schematic presentation how the nucleic acid templated chemistry works within cells Schematic presentation of chemical reaction within cells to combine two precursors into an active drug Nucleic acid templated chemistry (NATC), or DNA-templated chemistry, is a tool used in the controlled synthesis of chemical compounds. The main advantage of NAT-chemistry (NATC) is that it allows one to perform the chemical reaction as an intramolecular reaction. Two oligonucleotides or their analogues are linked via chemical groups to precursors of chemical compounds. The oligonucleotides recognize specific nucleic acids and are hybridized sterically close to each other.

Surface amine residues on PAMAM dendrimers bind to the phosphate backbone of nucleic acids through charged interactions (right, inset). Typically, G6-7 PAMAM dendrimers are used for gene transfection; these dendrimers are typically 6-10nm in length (spanning ~20-30 base pairs) and have a molecular mass of 30-50kDa. The discovery that mediating positive charge on PAMAM dendrimer surfaces decreases their cytotoxicity has interesting implications for DNA transfection applications. Because the cell membrane has a negatively charged exterior, and the DNA phosphate backbone is also negatively charged, the transfection of free DNA is not very efficient simply due to charge repulsion.

BLAST and its derivatives are probably the most widely used algorithms for this purpose. The emergence of the phrase "computational genomics" coincides with the availability of complete sequenced genomes in the mid-to-late 1990s. The first meeting of the Annual Conference on Computational Genomics was organized by scientists from The Institute for Genomic Research (TIGR) in 1998, providing a forum for this speciality and effectively distinguishing this area of science from the more general fields of Genomics or Computational Biology. The first use of this term in scientific literature, according to MEDLINE abstracts, was just one year earlier in Nucleic Acids Research.

Enzymes are used to indicate the extent of hybridization but are not used to manipulate the nucleic acids. Thus, small amounts of a nucleic acid can be detected and quantified without a reverse transcription step (in the case of RNA) and/or PCR. The assay can be run as a high throughput assay, unlike quantitative Northern-blotting or the RNAse-protection assay, which are labor-intensive and thus difficult to perform on a large number of samples. The other major high throughput technique employed in the quantification of specific RNA molecules is quantitative PCR, after reverse transcription of the RNA to cDNA.

In xenobiology, the aim is to design and construct biological systems that differ from their natural counterparts on one or more fundamental levels. Ideally these new-to-nature organisms would be different in every possible biochemical aspect exhibiting a very different genetic code. The long-term goal is to construct a cell that would store its genetic information not in DNA but in an alternative informational polymer consisting of xeno nucleic acids (XNA), different base pairs, using non-canonical amino acids and an altered genetic code. So far cells have been constructed that incorporate only one or two of these features.

The sequence hypothesis was first formally proposed in the review "On Protein Synthesis" by Francis Crick in 1958. It states that the sequence of bases in the genetic material (DNA or RNA) determines the sequence of amino acids for which that segment of nucleic acid codes, and this amino acid sequence determines the three-dimensional structure into which the protein folds. The three-dimensional structure of a protein is required for a protein to be functional. This hypothesis then lays the essential link between information stored and inherited in nucleic acids to the chemical processes which enable life to exist.

In 1995, after working at Burroughs Wellcome for over 26 years, and rising to the rank of associate division director, Rideout joined Inspire Pharmaceuticals (acquired by Merck in 2011) as Director of Chemistry. She subsequently had a number of promotions within the company: to Senior Director of Discovery in June 1996, Vice President in January 1998, and Senior Vice President of Discovery in February 2000. At Inspire Pharmaceuticals, she continued researching nucelosides but now as activators (agonists) instead of inhibitors. In addition to their role in the biosynthesis of nucleic acids, nucleotides can serve as important signaling molecules including through activating purinergic receptors.

In nucleic acids, the secondary structure is defined by the hydrogen bonding between the nitrogenous bases. For proteins, however, the hydrogen bonding is correlated with other structural features, which has given rise to less formal definitions of secondary structure. For example, helices can adopt backbone dihedral angles in some regions of the Ramachandran plot; thus, a segment of residues with such dihedral angles is often called a helix, regardless of whether it has the correct hydrogen bonds. Many other less formal definitions have been proposed, often applying concepts from the differential geometry of curves, such as curvature and torsion.

It is more challenging to perform single cell sequencing in comparison with sequencing from cells in bulk. The minimal amount of starting materials from a single cell make degradation, sample loss and contamination exert pronounced effects on quality of sequencing data. In addition, due to the picogram level of the amount of nucleic acids used, heavy amplification is often needed during sample preparation of single cell sequencing, resulting in the uneven coverage, noise and inaccurate quantification of sequencing data. Recent technical improvements make single cell sequencing a promising tool for approaching a set of seemingly inaccessible problems.

It is used to sequence all the microbial genomes in a sample by using the Shotgun approach. Its aim is to identify the nucleic acid diversity present in the sample (either DNA, RNA or both, depending on the sequencing method), in order to provide information about features of the viruses within the samples such as drug resistance, viral genotypes and virus epidemiology. The sensitivity of this method is affected by the presence of contaminating nucleic acids from the host and other microorganisms. This method has been used for the sequencing of viruses like Epstein-Barr virus (EBV) and HCV.

Acetone is also used and has been shown to produce better histological preservation than frozen sections when employed in the Acetone Methylbenzoate Xylene (AMEX) technique. Protein-denaturing methanol, ethanol and acetone are rarely used alone for fixing blocks unless studying nucleic acids. Acetic acid is a denaturant that is sometimes used in combination with the other precipitating fixatives, such as Davidson's AFA. The alcohols, by themselves, are known to cause considerable shrinkage and hardening of tissue during fixation while acetic acid alone is associated with tissue swelling; combining the two may result in better preservation of tissue morphology.

There are several principles and hypotheses for abiogenesis could have occurred. The study of abiogenesis aims to determine how pre-life chemical reactions gave rise to life under conditions strikingly different from those on Earth today. It primarily uses tools from biology, chemistry, and geophysics, with more recent approaches attempting a synthesis of all three: more specifically, astrobiology, biochemistry, biophysics, geochemistry, molecular biology, oceanography and paleontology. Life functions through the specialized chemistry of carbon and water and builds largely upon four key families of chemicals: lipids (cell membranes), carbohydrates (sugars, cellulose), amino acids (protein metabolism), and nucleic acids (DNA and RNA).

Fox observed in the 1960s that the proteinoids that he had synthesized could form cell-like structures that have been named "proteinoid microspheres". The amino acids had combined to form proteinoids, and the proteinoids had combined to form small globules that Fox called "microspheres". His proteinoids were not cells, although they formed clumps and chains reminiscent of cyanobacteria, but they contained no functional nucleic acids or any encoded information. Based upon such experiments, Colin Pittendrigh stated in 1967 that "laboratories will be creating a living cell within ten years," a remark that reflected the typical contemporary naivety about the complexity of cell structures.

OUP as Oxford Journals has also been a major publisher of academic journals, both in the sciences and the humanities; it publishes over 200 journals on behalf of learned societies around the world. It has been noted as one of the first university presses to publish an open access journal (Nucleic Acids Research), and probably the first to introduce Hybrid open access journals, offering "optional open access" to authors to allow all readers online access to their paper without charge. The "Oxford Open" model applies to the majority of their journals. The OUP is a member of the Open Access Scholarly Publishers Association.

Subsequent research established that XMRV was in fact a laboratory contaminant, rather than a novel pathogen. XMRV was generated unintentionally in the laboratory, through genetic recombination between two mouse retroviruses during propagation of a prostate-cancer cell line in the mid-1990s. via EBSCO login False-positive detection of XMRV may also occur because of contamination of clinical specimens and laboratory reagents with other mouse retroviruses or related nucleic acids. Most scientific publications claiming an association of XMRV with CFS or prostate cancer have been retracted, and allegations of research misconduct were leveled against at least one CFS investigator.

Viral vectors work efficiently and are mostly safe but present with some complications, contributing to the stringency of regulation on gene therapy. Despite partial inactivation of viral vectors in gene therapy research, they can still be immunogenic and elicit an immune response. This can impede viral delivery of the gene of interest, as well as cause complications for the patient themselves when used clinically, especially in those already suffering from a serious genetic illness. Another difficulty is the possibility that some viruses will randomly integrate their nucleic acids into the genome, which can interrupt gene function and generate new mutations.

Mutations within the CBS subdomain or a complete deletion of the domains do not impair the in vitro catalytic activity of IMPDH. An in vivo deletion of the CBS subdomain in E. coli suggests that the domain can act as a negative transregulator of adenine nucleotide synthesis. IMPDH has also been shown to bind nucleic acids, and this function can be impaired by mutations that are located in the subdomain. The CBS subdomain has also been implicated in mediating IMPDH association with polyribosomes, which suggests a potential moonlighting role for IMPDH as a translational regulatory protein.

One of the key developments within the field of DCC is the use of proteins (or other biological macromolecules, such as nucleic acids) to influence the evolution and generation of components within a DCL.Greaney, M. F.; Bhat, V. T. Protein- directed dynamic combinatorial chemistry. In Dynamic combinatorial chemistry: in drug discovery, bioinorganic chemistry, and materials sciences; Miller, B. L., Ed.; John Wiley & Sons: New Jersey, 2010; Chapter 2, pp 43–82. Protein- directed DCC provides a way to generate, identify and rank novel protein ligands, and therefore have huge potential in the areas of enzyme inhibition and drug discovery.

TLRs may also depend on other co- receptors for full ligand sensitivity, such as in the case of TLR4's recognition of LPS, which requires MD-2. CD14 and LPS-Binding Protein (LBP) are known to facilitate the presentation of LPS to MD-2. A set of endosomal TLRs comprising TLR3, TLR7, TLR8 and TLR9 recognize nucleic acid derived from viruses as well as endogenous nucleic acids in context of pathogenic events. Activation of these receptor leads to production of inflammatory cytokines as well as type I interferons (interferon type I) to help fight viral infection.

More generally, algorithms such as NUPACK, ViennaRNA, Ribosome Binding Site Calculator, Cello, and Non- Repetitive Parts Calculator enables the design of new genetic systems. Many technologies have been developed for incorporating unnatural nucleotides and amino acids into nucleic acids and proteins, both in vitro and in vivo. For example, in May 2014, researchers announced that they had successfully introduced two new artificial nucleotides into bacterial DNA. By including individual artificial nucleotides in the culture media, they were able to exchange the bacteria 24 times; they did not generate mRNA or proteins able to use the artificial nucleotides.

Nucleic acids attain their native state through base pairing and, to a lesser extent, other interactions such as coaxial stacking. Biological DNA usually exists as long linear double helices bound to proteins in chromatin, and biological RNA such as tRNA often form complex native configurations approaching the complexity of folded proteins. Additionally, artificial nucleic acid structures used in DNA nanotechnology are designed to have specific native configurations in which multiple nucleic acid strands are assembled into a single complex. In some cases native state of biological DNA performs their functions without being controlled by any other regulatory units.

Ribose is a constituent of RNA, and the related molecule, deoxyribose, is a constituent of DNA. Phosphorylated pentoses are important products of the pentose phosphate pathway, most importantly ribose 5-phosphate (R5P), which is used in the synthesis of nucleotides and nucleic acids, and erythrose 4-phosphate (E4P), which is used in the synthesis of aromatic amino acids. Like some other monosaccharides, pentoses exist in two forms, open-chain (linear) or closed- chain (cyclic), that easily convert into each other in water solutions. The linear form of a pentose, which usually exists only in solutions, has an open- chain backbone of five carbons.

The most commonly used and commercially available fluorescent base analogue, 2-aminopurine (2-AP), has a high-fluorescence quantum yield free in solution (0.68) that is considerably reduced (appr. 100 times but highly dependent on base sequence) when incorporated into nucleic acids. The emission sensitivity of 2-AP to immediate surroundings is shared by other promising and useful fluorescent base analogues like 3-MI, 6-MI, 6-MAP, pyrrolo-dC (also commercially available), modified and improved derivatives of pyrrolo-dC, furan-modified bases and many other ones (see recent reviews). This sensitivity to the microenvironment has been utilized in studies of e.g.

Oligonucleotides are short DNA or RNA molecules, oligomers, that have a wide range of applications in genetic testing, research, and forensics. Commonly made in the laboratory by solid-phase chemical synthesis, these small bits of nucleic acids can be manufactured as single-stranded molecules with any user- specified sequence, and so are vital for artificial gene synthesis, polymerase chain reaction (PCR), DNA sequencing, molecular cloning and as molecular probes. In nature, oligonucleotides are usually found as small RNA molecules that function in the regulation of gene expression (e.g. microRNA), or are degradation intermediates derived from the breakdown of larger nucleic acid molecules.

Molecular interactions can occur between molecules belonging to different biochemical families (proteins, nucleic acids, lipids, carbohydrates, etc.) and also within a given family. Whenever such molecules are connected by physical interactions, they form molecular interaction networks that are generally classified by the nature of the compounds involved. Most commonly, interactome refers to protein–protein interaction (PPI) network (PIN) or subsets thereof. For instance, the Sirt-1 protein interactome and Sirt family second order interactome is the network involving Sirt-1 and its directly interacting proteins where as second order interactome illustrates interactions up to second order of neighbors (Neighbors of neighbors).

Ribbon diagrams of α-helices are a prominent element in the laser-etched crystal sculptures of protein structures created by artist Bathsheba Grossman, such as those of insulin, hemoglobin, and DNA polymerase. Byron Rubin is a former protein crystallographer now professional sculptor in metal of proteins, nucleic acids, and drug molecules many of which featuring α-helices, such as subtilisin, human growth hormone, and phospholipase A2. Mike Tyka is a computational biochemist at the University of Washington working with David Baker. Tyka has been making sculptures of protein molecules since 2010 from copper and steel, including ubiquitin and a potassium channel tetramer.

This may be offset by other factors: for example, amides are not basic because the lone pair is delocalised into a double bond (though they may act as acids at very low pH, being protonated at the oxygen), and pyrrole is not acidic because the lone pair is delocalised as part of an aromatic ring. The amount of nitrogen in a chemical substance can be determined by the Kjeldahl method. In particular, nitrogen is an essential component of nucleic acids, amino acids and thus proteins, and the energy-carrying molecule adenosine triphosphate and is thus vital to all life on Earth.

UV light on a UV Transilluminator. Agarose is a preferred matrix for work with proteins and nucleic acids as it has a broad range of physical, chemical and thermal stability, and its lower degree of chemical complexity also makes it less likely to interact with biomolecules. Agarose is most commonly used as the medium for analytical scale electrophoretic separation in agarose gel electrophoresis. Gels made from purified agarose have a relatively large pore size, making them useful for separation of large molecules, such as proteins and protein complexes >200 kilodaltons, as well as DNA fragments >100 basepairs.

A particularly vexing question in the study of the chemical origins of life is the selection of ribose, which forms the backbone of the nucleic acids found in modern biological systems. Eschenmoser’s work on a variant of the formose reaction that produces phosphorylated ribose in relatively significant concentrations has provided significant insight. Eschenmoser and colleagues demonstrated that phosphorylated glycoaldehyde when condensed with glyceraldehyde (a product of successive formaldehyde condensations) produces phosphorylated ribose differentially, providing a plausible explanation for the origin of both the sugar ribose, and the phosphate group required to polymerize monomeric nucleotides, in modern biochemistry.

Gels of plasmid preparations usually show a major band of supercoiled DNA with other fainter bands in the same lane. Note that by convention DNA gel is displayed with smaller DNA fragments nearer to the bottom of the gel. This is because historically DNA gels were run vertically and the smaller DNA fragments move downwards faster. A number of factors can affect the migration of nucleic acids: the dimension of the gel pores (gel concentration), size of DNA being electrophoresed, the voltage used, the ionic strength of the buffer, and the concentration of intercalating dye such as ethidium bromide if used during electrophoresis.

Nucleic acids (including RNA and DNA) are nucleotide polymers synthesized by polymerase enzymes during either transcription or DNA replication. Following 5'-3' synthesis of the backbone, individual nitrogenous bases are capable of interacting with one another via hydrogen bonding, thus allowing for the formation of higher-order structures. Nucleic acid denaturation occurs when hydrogen bonding between nucleotides is disrupted, and results in the separation of previously annealed strands. For example, denaturation of DNA due to high temperatures results in the disruption of Watson and Crick base pairs and the separation of the double stranded helix into two single strands.

With all three joined, a nucleotide is also termed a "nucleo _side_ monophosphate", "nucleoside diphosphate" or "nucleoside triphosphate", depending on how many phosphates make up the phosphate group. In nucleic acids, nucleotides contain either a purine or a pyrimidine base—i.e., the nitrogenous base molecule, also known as a nucleobase—and are termed ribonucleotides if the sugar is ribose, or deoxyribonucleotides if the sugar is deoxyribose. Individual phosphate molecules repetitively connect the sugar-ring molecules in two adjacent nucleotide monomers, thereby connecting the nucleotide monomers of a nucleic acid end-to-end into a long chain.

If the sugar is a compound ribose, the polymer is RNA (ribonucleic acid); if the sugar is derived from ribose as deoxyribose, the polymer is DNA (deoxyribonucleic acid). Nucleic acids are the most important of all biomolecules. These are found in abundance in all living things, where they function to create and encode and then store information of every living cell of every life-form organism on Earth. In turn, they function to transmit and express that information inside and outside the cell nucleus—to the interior operations of the cell and ultimately to the next generation of each living organism.

This gives nucleic acids directionality, and the ends of nucleic acid molecules are referred to as 5'-end and 3'-end. The nucleobases are joined to the sugars via an N-glycosidic linkage involving a nucleobase ring nitrogen (N-1 for pyrimidines and N-9 for purines) and the 1' carbon of the pentose sugar ring. Non-standard nucleosides are also found in both RNA and DNA and usually arise from modification of the standard nucleosides within the DNA molecule or the primary (initial) RNA transcript. Transfer RNA (tRNA) molecules contain a particularly large number of modified nucleosides.

Associated with hyperoxia is an increased level of reactive oxygen species (ROS), which are chemically reactive molecules containing oxygen. These oxygen containing molecules can damage lipids, proteins, and nucleic acids, and react with surrounding biological tissues. The human body has naturally occurring antioxidants to combat reactive molecules, but the protective antioxidant defenses can become depleted by abundant reactive oxygen species, resulting in oxidation of the tissues and organs. The symptoms produced from breathing high concentrations of oxygen for extended periods have been studied in a variety of animals, such as frogs, turtles, pigeons, mice, rats, guinea pigs, cats, dogs and monkeys.

WHAT IF provides a flexible environment to display, manipulate, and analyze small molecules, proteins, nucleic acids, and their interactions. One notable use was detecting many millions of errors (often small, but sometimes catastrophic) in Protein Data Bank (PDB) files. WHAT IF also provides an environment for: homology modeling of protein tertiary structures and quaternary structures; validating protein structures, notably those deposited in the PDB; correcting protein structures; visualising macromolecules and their interaction partners (for example, lipids, drugs, ions, and water), and manipulating macromolecules interactively. WHAT IF is compatible with several other bioinformatics software packages, including YASARA and Jmol.

The Biological Magnetic Resonance Data Bank (BioMagResBank or BMRB) is an open access repository of nuclear magnetic resonance (NMR) spectroscopic data from peptides, proteins, nucleic acids and other biologically relevant molecules. The database is operated by the University of Wisconsin-Madison and is supported by the National Library of Medicine. The BMRB is part of the Research Collaboratory for Structural Bioinformatics and, since 2006, it is a partner in the Worldwide Protein Data Bank (wwPDB). The repository accepts NMR spectral data from laboratories around the world and, once the data is validated, it is available online at the BMRB website.

Capillary blotting system setup for the transfer of RNA from an electrophoresis gel to a blotting membrane. A nylon membrane with a positive charge is the most effective for use in northern blotting since the negatively charged nucleic acids have a high affinity for them. The transfer buffer used for the blotting usually contains formamide because it lowers the annealing temperature of the probe- RNA interaction, thus eliminating the need for high temperatures, which could cause RNA degradation. Once the RNA has been transferred to the membrane, it is immobilized through covalent linkage to the membrane by UV light or heat.

When subjected to an electric field in PAGE, the negatively charged polypeptide chains travel toward the anode with different mobility. Their mobility, or the distance traveled by molecules, is inversely proportional to the logarithm of their molecular weight. By comparing the relative ratio of the distance traveled by each protein to the length of the gel (Rf) one can make conclusions about the relative molecular weight of the proteins, where the length of the gel is determined by the distance traveled by a small molecule like a tracking dye. For nucleic acids, urea is the most commonly used denaturant.

Two SDS-PAGE-gels after a completed run Following electrophoresis, the gel may be stained (for proteins, most commonly with Coomassie Brilliant Blue R-250 or autoradiography; for nucleic acids, ethidium bromide; or for either, silver stain), allowing visualization of the separated proteins, or processed further (e.g. Western blot). After staining, different species biomolecules appear as distinct bands within the gel. It is common to run molecular weight size markers of known molecular weight in a separate lane in the gel to calibrate the gel and determine the approximate molecular mass of unknown biomolecules by comparing the distance traveled relative to the marker.

Though an unmodified PNA cannot readily cross the cell membrane to enter the cytosol, covalent coupling of a cell penetrating peptide to a PNA can improve cytosolic delivery. PNA is not known to occur naturally but N-(2-aminoethyl)-glycine (AEG), the backbone of PNA, has been hypothesized to be an early form of genetic molecule for life on earth and is produced by cyanobacteria.Cyanobacteria Produce N-(2-Aminoethyl)Glycine, a Backbone for Peptide Nucleic Acids Which May Have Been the First Genetic Molecules for Life on Earth PNA was invented by Peter E. Nielsen (Univ. Copenhagen), Michael Egholm (Univ.

Chromosome conformation capture techniques (often abbreviated to 3C technologies or 3C-based methods) are a set of molecular biology methods used to analyze the spatial organization of chromatin in a cell. These methods quantify the number of interactions between genomic loci that are nearby in three dimensional space, even if the loci are separated by many kilobases in the linear genome. Currently, 3C methods start with a similar set of steps, performed on a sample of cells. First, the cells are cross-linked, which introduces bonds between proteins, and between proteins and nucleic acids, that effectively "freeze" interactions between genomic loci.

In his 1977 paper "Unconventional Viruses and the Origin and Disappearance of Kuru," Gajdusek postulated that the cause of kuru, scrapie and Creutzfeldt–Jakob disease were caused by what he termed an unconventional virus. In comparison to normal viruses, unconventional viruses had a long incubation period and did not cause an immune system response in the host. Although Gajdusek noted that there were no demonstrable nucleic acids in unconventional viruses, he did not rule out the possibility that unconventional viruses contained RNA in a smaller amount despite radiation resistance These infectious agents were later discovered to be misfolded proteins, or prions.

Nucleofection is a method to transfer substrates into mammalian cells so far considered difficult or even impossible to transfect. Examples for such substrates are nucleic acids, like the DNA of an isolated gene cloned into a plasmid, or small interfering RNA (siRNA) for knocking down expression of a specific endogenous gene. Primary cells, for example stem cells, especially fall into this category, although many other cell lines are also difficult to transfect. Primary cells are freshly isolated from body tissue and thus cells are unchanged, closely resembling the in-vivo situation, and are therefore of particular relevance for medical research purposes.

Schematical diagram Catabolism () is the set of metabolic pathways that breaks down molecules into smaller units that are either oxidized to release energy or used in other anabolic reactions. Catabolism breaks down large molecules (such as polysaccharides, lipids, nucleic acids, and proteins) into smaller units (such as monosaccharides, fatty acids, nucleotides, and amino acids, respectively). Catabolism is the breaking-down aspect of metabolism, whereas anabolism is the building-up aspect. Cells use the monomers released from breaking down polymers to either construct new polymer molecules or degrade the monomers further to simple waste products, releasing energy.

Sequence alignment of TCTP sequences from more than 30 different species reveals a high degree of conservation over a long period of evolution. The solution structure of TCTP from yeast, Schizosaccharomyces pombe has been determined by NMR spectroscopy which indicated that this protein is structurally similar to two small guanine nucleotide-free chaperones, namely Mss4 and Dss4. TCTP and Mss4/Dss4 are now therefore structurally grouped into one protein superfamily. Translationally Controlled Tumor Protein (TCTP) is involved in a wide range of molecular interactions with biological and nonbiological partners of various chemical compositions such as proteins, peptides, nucleic acids, carbohydrates, or small molecules.

Notable Tübingen residents and scholars included the poets Friedrich Hölderlin, Eduard Mörike and Ludwig Uhland, the neurologist Alois Alzheimer from whom Alzheimer's disease takes its name, and Friedrich Miescher who was the first to discover nucleic acids. Wilhelm Schickard who was the main precursor to the mechanical calculator, was born in nearby Herrenberg. Georg Wilhelm Friedrich Hegel, Friedrich Schelling, David Friedrich Strauss, and Johannes Kepler studied in Tübingen at the Tübinger Stift, and Joseph Alois Ratzinger (Pope Benedict XVI) held a chair in dogmatic theology at the University. Hermann Hesse worked in Tübingen as a bookseller trainee from 1895 to 1899.

All of these elements are nonmetals. Sulfur is contained in the amino acids cysteine and methionine. Phosphorus is contained in phospholipids, a class of lipids that are a major component of all cell membranes, as they can form lipid bilayers, which keep ions, proteins, and other molecules where they are needed for cell function, and prevent them from diffusing into areas where they should not be. Phosphate groups are also an essential component of the backbone of nucleic acids (general name for DNA & RNA) and are required to form ATP – the main molecule used as energy powering the cell in all living creatures.

Along with lipids, proteins, and carbohydrates, nucleic acids constitute one of the four major macromolecules essential for all known forms of life. Like DNA, RNA is assembled as a chain of nucleotides, but unlike DNA, RNA is found in nature as a single strand folded onto itself, rather than a paired double strand. Cellular organisms use messenger RNA (mRNA) to convey genetic information (using the nitrogenous bases of guanine, uracil, adenine, and cytosine, denoted by the letters G, U, A, and C) that directs synthesis of specific proteins. Many viruses encode their genetic information using an RNA genome.

This depiction shows the location of the two predicted protein domains. Result of local sequence alignment- the amino acids found in the zinc finger domain are highlighted in different color The three amino acids which are coordinated to the zinc ion. Two domains were predicted by the program BLIMPSJorja Henikoff, Fred Hutchinson Cancer Research Center, 1100 Fairview AV N, A1-162, PO Box 19024 Seattle, WA 98109-1024 FAX: 206-667-5889 to exist in the protein of which one of the domains contains a zinc finger domain. Zinc finger domains assist the binding of the protein to nucleic acids.

In molecular biology, enzymes in the DNA/RNA non-specific endonuclease family of bacterial and eukaryotic endonucleases share the following characteristics: they act on both DNA and RNA, cleave double-stranded and single-stranded nucleic acids and require a divalent ion such as magnesium for their activity. A histidine has been shown to be essential for the activity of the Serratia marcescens nuclease. This residue is located in a conserved region which also contains an aspartic acid residue that could be implicated in the binding of the divalent ion. Notable members of the family include Serratia marcescens NucA and human Exonuclease G.

Har Gobind Khorana (9 January 1922 – 9 November 2011) was an Indian American biochemist. While on the faculty of the University of Wisconsin–Madison, he shared the 1968 Nobel Prize for Physiology or Medicine with Marshall W. Nirenberg and Robert W. Holley for research that showed the order of nucleotides in nucleic acids, which carry the genetic code of the cell and control the cell's synthesis of proteins. Khorana and Nirenberg were also awarded the Louisa Gross Horwitz Prize from Columbia University in the same year. Born in British India, Khorana served on the faculties of three universities in North America.

Villeponteau was born in the United States on December 19, 1944 and obtained a B.A. in Economics, a M.S. in Public Health Biostatistics, and a Ph.D. in Biology from UCLA in Los Angeles. Villeponteau was awarded a Molecular Biology Postdoctoral Fellowship in the UCLA Department of Chemistry and Biochemistry from 1978 to 1980, where he carried out genomic cloning of the B-globin gene cluster in Chickens....Villeponteau, B., and Martinson, H.G. (1981). Isolation and characterization of the complete chicken beta-globin gene region: frequent deletion of the adult beta-globin genes in lambda. Nucleic Acids Research 9, 3731-3746.

In collaboration with AstraZeneca, they invented Scorpion Primers system, a fluorescence-based real-time PCR method that can identify mutations and Single-nucleotide polymorphism in human genome. Most recently, his group is focusing on the Click chemistry based chemical modification of DNA and its application in bionanotechnology sector. As of January 2016, Brown has published more than 300 articles in peer-reviewed journals, with many of his papers appearing in highly selective journals like Nature, Nature Biotechnology, Cell, Nucleic Acids Research, JACS, and PNAS. His papers have been cited over 18,000 times and he has an h-index 68.

The alternating twists model was initially presented with the helicity changing every half turn, but later long stretches of each helical direction were later proposed. However, these models suffered from a lack of experimental support. Under torsional stress, a Z-DNA structure can form with opposite twist to B-form DNA, but this is rare within the cellular environment. The discovery of topoisomerases and gyrases, enzymes that can change the linking number of circular nucleic acids and thus "unwind" and "rewind" the replicating bacterial chromosome, solved the topological objections to the B-form DNA helical structure.

Another use of Phred quality scores by Phrap that contributed to the program's success was the determination of consensus sequences using sequence qualities. In effect, Phrap automated a step that was a major bottleneck in the early phases of the Human Genome Project: to determine the correct consensus sequence at all positions where the assembled sequences had discrepant bases. This approach had been suggested by Bonfield and Staden in 1995,Bonfield JK, Staden R (1995): The application of numerical estimates of base calling accuracy to DNA sequencing projects. Nucleic Acids Res. 1995 Apr 25;23(8):1406-10.

LB buffer, also known as lithium borate buffer, is a buffer solution used in agarose electrophoresis, typically for the separation of nucleic acids such as DNA and RNA. It is made up of Lithium borate (lithium hydroxide monohydrate and boric acid). LB(R) is a registered (USPTO) trademark of Faster Better Media LLC, which owns US patent 7,163,610 covering low-conductance lithium borate polynucleotide electrophoresis. Lithium Borate buffer has a lower conductivity, produces crisper resolution, and can be run at higher speeds than can gels made from TBE or TAE (5-50 V/cm as compared to 5-10 V/cm).

The polymerase that performs the sequencing reaction in the zero-mode waveguides produces kinetic data that can be used to distinguish base modifications. In October 2012, scientists used SMRT sequencing to generate the methylomes of six bacteria, reporting their results in a paper in Nucleic Acids Research. With increasing read length and throughput, mammalian studies increased using the product. In April 2012, scientists from Pacific Biosciences, the University of California, and other institutes used SMRT sequencing to prove the validity of activating internal tandem duplication mutations in FLT3 as a therapeutic target in acute myeloid leukemia.

HTH motif alignment of three TetR family members: MtrR (magenta), SimR (cyan), & AmtR (green) As of June 2005, this family of proteins had about 2,353 members that are transcriptional regulators. (Transcriptional regulators control gene expression.) These proteins contain a helix-turn-helix (HTH) motif that is the DNA-binding domain. The second helix is considered to be most important for DNA sequence specificity and often recognizes nucleic acids within the major groove of the double helix. In the majority of the family members, this motif is on the N-terminal end of the protein and is highly conserved.

Ludwig Karl Martin Leonhard Albrecht Kossel (16 September 1853 – 5 July 1927) was a German biochemist and pioneer in the study of genetics. He was awarded the Nobel Prize for Physiology or Medicine in 1910 for his work in determining the chemical composition of nucleic acids, the genetic substance of biological cells. Kossel isolated and described the five organic compounds that are present in nucleic acid: adenine, cytosine, guanine, thymine, and uracil. These compounds were later shown to be nucleobases, and are key in the formation of DNA and RNA, the genetic material found in all living cells.

A low-pressure mercury-vapor discharge tube floods the inside of a biosafety cabinet with shortwave UV light when not in use, sterilizing microbiological contaminants from irradiated surfaces. Ultraviolet germicidal irradiation (UVGI) is a disinfection method that uses short-wavelength ultraviolet (ultraviolet C or UV-C) light to kill or inactivate microorganisms by destroying nucleic acids and disrupting their DNA, leaving them unable to perform vital cellular functions. UVGI is used in a variety of applications, such as food, air, and water purification. UV-C light is weak at the Earth's surface since the ozone layer of the atmosphere blocks it.

Technologies based upon the polymerase chain reaction (PCR) method will become nearly ubiquitous gold standards of diagnostics of the near future, for several reasons. First, the catalog of infectious agents has grown to the point that virtually all of the significant infectious agents of the human population have been identified. Second, an infectious agent must grow within the human body to cause disease; essentially it must amplify its own nucleic acids in order to cause a disease. This amplification of nucleic acid in infected tissue offers an opportunity to detect the infectious agent by using PCR.

BioModels is a free and open-source repository for storing, exchanging and retrieving quantitative models of biological interest created in 2006.Le Novère N., Bornstein B., Broicher A., Courtot M., Donizelli M., Dharuri H., Li L., Sauro H., Schilstra M., Shapiro B., Snoep J.L., Hucka M. BioModels Database: A Free, Centralized Database of Curated, Published, Quantitative Kinetic Models of Biochemical and Cellular Systems. Nucleic Acids Research (2006), 34: D689-D691.Chelliah V., Juty N., Ajmera I., Raza A., Dumousseau M., Glont M., Hucka M., Jalowicki G., Keating S., Knight-Schrijver V., Lloret- Villas A., Natarajan K., Pettit J.-B.

Electrophoresis is the process of separating nucleic acid species based on their length by applying an electric field to them. As nucleic acids are negatively charged, they are pushed by an electric field through a matrix, usually an agarose gel, with the smaller molecules being pushed farther, faster. Capillary electrophoresis is a technique whereby small amounts of a nucleic acid sample can be run on a gel in a very thin tube. There is a detector in the machine that can tell when nucleic acid samples pass through a specific point in the tube, with smaller samples passing through first.

Almost immediately, Marshall Nirenberg and J. Heinrich Matthaei put it to use to form the first three-nucleotide RNA codons, which coded for the amino acid phenylalanine. This first step in cracking the genetic code entirely depended on the availability of Grunberg-Manago’s enzyme. In 1959, Ochoa and Arthur Kornberg won the 1959 Nobel Prize in Physiology or Medicine "for the synthesis of the nucleic acids RNA and DNA." She was elected a Foreign Honorary Member of the American Academy of Arts and Sciences in 1978 and a Foreign Associate Member of the National Academy of Sciences in 1982.

Eigen made several assumptions about conditions that led to the formation of the first hypercycles. Some of them were the consequence of the lack of knowledge about ribozymes, which were discovered a few years after the introduction of the hypercycle concept and negated Eigen's assumptions in the strict sense. The primary of them was that the formation of hypercycles had required the availability of both types of chains: nucleic acids forming a quasispecies population and proteins with enzymatic functions. Nowadays, taking into account the knowledge about ribozymes, it may be possible that a hypercycle's members were selected from the quasispecies population and the enzymatic function was performed by RNA.

His research has been published in leading peer reviewed scientific journals including Nature, Science, Cell, Nucleic Acids Research, PNAS, the Biochemical Journal, the Journal of Molecular Biology, Genome Research, Bioinformatics, PLOS Genetics,Nature Genetics and the Journal of Bacteriology. Gough's research has been funded by the Biotechnology and Biological Sciences Research Council (BBSRC), the Engineering and Physical Sciences Research Council (EPSRC), the Natural Environment Research Council (NERC), the European Union (EU) Seventh Research Framework Programme (FP7), the Japan Society for the Promotion of Science (JSPS) and the Royal Society of London. His former doctoral students and postdocs include Ralph Pethica, Owen Rackham, Hashem Shihab, Matt Oates, and Dimitrios Vavoulis.

The virus counter was developed in 2001 at University of Colorado in Boulder. The Single Nanometric Particle Enumerator (SNaPE) instrument was based on the principle of fluorescence detection from single stained nucleic acids aggregates by evaluating respiratory viruses. Quantification results from the instrument correlated with expected virus concentration and the values would be significantly higher than those obtained by standard plaque titer methods typically used for virus quantification. The measured concentrations were similar in magnitude to quantitative PCR results, both being substantially higher than plaque titer values. In 2004 the virus counter’s added a second detection channel to the SNaPE instrument which improved data analysis substantially to increase specificity.

Assays such as MNase-seq, DNase-seq, ATAC-seq or FAIRE-seq are routinely used to understand the accessible chromatin landscape of cells. The main feature of all these methods is that they're able to selectively isolate either the DNA sequences that are bounded to the histones, or those that are not. These sequences are then compared to a reference genome that allows to identify their relative position. MNase-seq and DNase-seq both follow the same principles, as they employ lytic enzymes that target nucleic acids to cut the DNA strands unbounded by nucleosomes or other proteic factors, while the bounded pieces are sheltered, and can be retrieved and analysed.

Proteinase K is commonly used in molecular biology to digest protein and remove contamination from preparations of nucleic acid. Addition of Proteinase K to nucleic acid preparations rapidly inactivates nucleases that might otherwise degrade the DNA or RNA during purification. It is highly suited to this application since the enzyme is active in the presence of chemicals that denature proteins, such as SDS and urea, chelating agents such as EDTA, sulfhydryl reagents, as well as trypsin or chymotrypsin inhibitors. Proteinase K is used for the destruction of proteins in cell lysates (tissue, cell culture cells) and for the release of nucleic acids, since it very effectively inactivates DNases and RNases.

In clinical microbiology labs, the quantitation of microbial burden is considered a routine function as it is associated with the severity and progression of the disease. To achieve a good quantitation a high sensitivity of the technique is needed. A key limitation of metagenomic next- generation sequencing (mNGS) is its decreased sensitivity with high background as these can be clinically relevant as the pathogen load in infections can be very low. Whereas interfering substances represent a common problem to clinical chemistry or to PCR diagnostics, the degree of interference from host (for example, in tissue biopsies) or nonpathogen nucleic acids (for example, in stool) in metagenomics is a new twist.

For large-scale structure, these local parameters must be supplemented with other structural assumptions or models, because errors add up as the double helix is traversed, and unlike with proteins, the double helix does not have a compact interior and does not fold back upon itself. However, long-range orientation information can be obtained through residual dipolar coupling experiments in a medium which imposes a weak alignment on the nucleic acid molecules. Recently, solid-state NMR methodology has been introduced for the structure determination of nucleic acids. The protocol implies two approaches: nucleotide-type selective labeling of RNA and usage of heteronuclear correlation experiments.

Nucleic acid NMR studies were performed as early as 1971, and focused on using the low-field imino proton resonances to probe base pairing interactions. These early studies focussed on tRNA because these nucleic acids were the only samples available at that time with low enough molecular weight that the NMR spectral line-widths were practical. The study focussed on the low-field protons because they were the only protons that could be reliably observed in aqueous solution using the best spectrometers available at that time. It was quickly realized that spectra of the low-field imino protons were providing clues to the tertiary structure of tRNA in solution.

This size selectively allows the passage of small water- soluble molecules while preventing larger molecules, such as nucleic acids and larger proteins, from inappropriately entering or exiting the nucleus. These large molecules must be actively transported into the nucleus instead. The nucleus of a typical mammalian cell will have about 3000 to 4000 pores throughout its envelope, each of which contains an eightfold-symmetric ring- shaped structure at a position where the inner and outer membranes fuse. Attached to the ring is a structure called the nuclear basket that extends into the nucleoplasm, and a series of filamentous extensions that reach into the cytoplasm.

Competent S. pneumoniae can also secrete an enzyme (murein hydrolase) that destroys non-competent cells (fratricide) causing DNA to be released into the surrounding medium for potential use by the competent cells. The insect antimicrobial peptide cecropin A can destroy planktonic and sessile biofilm-forming uropathogenic E. Coli cells, either alone or when combined with the antibiotic nalidixic acid, synergistically clearing infection in vivo (in the insect host Galleria mellonella) without off-target cytotoxicity. The multi-target mechanism of action involves outer membrane permeabilization followed by biofilm disruption triggered by the inhibition of efflux pump activity and interactions with extracellular and intracellular nucleic acids.

Autopoiesis was originally presented as a system description that was said to define and explain the nature of living systems. A canonical example of an autopoietic system is the biological cell. The eukaryotic cell, for example, is made of various biochemical components such as nucleic acids and proteins, and is organized into bounded structures such as the cell nucleus, various organelles, a cell membrane and cytoskeleton. These structures, based on an external flow of molecules and energy, produce the components which, in turn, continue to maintain the organized bounded structure that gives rise to these components (not unlike a wave propagating through a medium).

Formation of PSI+ prion causes S. cerevisiae cells with nonsense-mutation in ade1 gene to convert red pigment (colony below) into a colourless compound, causing colonies to become white (above) A fungal prion is a prion that infects fungal hosts. Fungal prions are naturally occurring proteins that can switch between multiple, structurally distinct conformations, at least one of which is self-propagating and transmissible to other prions. This transmission of protein state represents an epigenetic phenomenon where information is encoded in the protein structure itself, instead of in nucleic acids. Several prion-forming proteins have been identified in fungi, primarily in the yeast Saccharomyces cerevisiae.

32P, a beta-emitter (1.71 MeV) with a half-life of 14.3 days, is used routinely in life-science laboratories, primarily to produce radiolabeled DNA and RNA probes, e.g. for use in Northern blots or Southern blots. Because the high-energy beta particles produced penetrate skin and corneas, and because any 32P ingested, inhaled, or absorbed is readily incorporated into bone and nucleic acids, OSHA requires that a lab coat, disposable gloves, and safety glasses or goggles be worn when working with 32P, and that working directly over an open container be avoided in order to protect the eyes. Monitoring personal, clothing, and surface contamination is also required.

This has led to the development of other hypotheses, such as 'proteins first', which states that proteins arose prior to RNA, or coevolved with RNA. This has also led to the proposal of other primordial molecules that may have developed into RNA and DNA, such as peptide nucleic acids, which also show evidence of self replication. Despite the fact that criticisms might exist on the primordial or prebiotic nature of rRNA, these criticisms are not aimed at Woese's Dogma on the whole, as Woese's Dogma only claims that the evolution of rRNA was a necessary precursor to modern life, not that rRNA arose prebiotically.

DNA nanotechnology is an area of current research that uses the bottom-up, self-assembly approach for nanotechnological goals. DNA nanotechnology uses the unique molecular recognition properties of DNA and other nucleic acids to create self-assembling branched DNA complexes with useful properties. DNA is thus used as a structural material rather than as a carrier of biological information, to make structures such as complex 2D and 3D lattices (both tile-based as well as using the "DNA origami" method) and three-dimensional structures in the shapes of polyhedra. These DNA structures have also been used as templates in the assembly of other molecules such as gold nanoparticles and streptavidin proteins.

He is the winner of the Lilly Prize (1996), the Pfizer Academic Award (1997), the British Pharmaceutical Conference Science Medal (1998), the Controlled Release Society (USA) Young Investigator Research Achievement Award (2001) and the Kappa Society Science Award (2005). His current research interests include studying molecular pharmacology and signal transduction pathways involved in diabetes and/or hypertension-induced cardiovascular dysfunction, and understanding the biological and pharmaceutical challenges associated with the development of gene silencing nucleic acids (RNA interference/ siRNA/ antisense oligonucleotides) as potential therapeutic agents; and c) studying the toxicogenomics of novel drugs and non-viral drug delivery systems. Akhtar has also provided health advice for fasting during Ramadan.

Hans-Jürgen Bandelt, Vincent Macaulay, Dr. Martin Richards, Human mitochondrial DNA and the evolution of Homo sapiens, Volume 18 of Nucleic acids and molecular biology, (シュプリンガー・ジャパン株式会社: 2006), p.235.AD. Holden (2005), MtDNA variation in North, East, and Central African populations gives clues to a possible back-migration from the Middle East , Program of the Seventy-Fourth Annual Meeting of the American Association of Physical Anthropologists (2005) This mitochondrial clade is common among Ethiopians and North Africans, particularly Egyptians and Algerians. M1 is believed to have originated in Asia, where its parent M clade represents the majority of mtDNA lineages.

Dimethyl sulfate, known as DMS, is a chemical that can be used to modify nucleic acids in order to determine secondary structure. Reaction with DMS adds a methyl adduct at the site, known as methylation. In particular, DMS methylates N1 of adenine (A) and N3 of cytosine (C), both located at the site of natural hydrogen bonds upon base-pairing. Therefore, modification can only occur at A and C nucleobases that are single-stranded, base paired at the end of a helix, or in a base pair at or next to a GU wobble pair, the latter two being positions where the base-pairing can occasionally open up.

Synthesis of Okazaki fragments The work of Kiwako Sakabe, Reiji Okazaki and Tsuneko Okazaki provided experimental evidence supporting the hypothesis that DNA replication is a discontinuous process. Previously, it was commonly accepted that replication was continuous in both the 3' to 5' and 5' to 3' directions. 3' and 5' are specifically numbered carbons on the deoxyribose ring in nucleic acids, and refer to the orientation or directionality of a strand. In 1967, the Tsuneko Okazaki and Toru Ogawa suggested that there is no found mechanism that showed continuous replication in the 3' to 5' direction, only 5' to 3' using DNA polymerase, a replication enzyme.

Their studies revealed both a biological purpose of the receptor and how to use it for therapeutic purposes in pneumococcal sepsis. In 2008, Dr. Marth published an enumeration of the building blocks of life, all of which fall under the 4 types of macromolecules present in all cells (glycans, lipids, nucleic acids, and proteins). This concept is becoming a feature of modern cell biology texts. Marth and other colleagues have called attention to the fact that only half of these macromolecules are encoded in the genome, suggesting that a more holistic and rigorous approach is needed to fully understand cell biology and the origins of disease.

The RNA chain is synthesized from the 5' end to the 3' end as the 3'-hydroxyl group of the last ribonucleotide in the chain acts as a nucleophile and launches a hydrophilic attack on the 5'-triphosphate of the incoming ribonucleotide, releasing pyrophosphate as a by- product. Due to the physical properties of the nucleotides, the backbone of RNA is very hydrophilic and polar. At neutral pH, nucleic acids are highly charged as each phosphate group carries a negative charge. Both DNA and RNA are built from nucleoside phosphates, also known as mononucleotide monomers, which are thermodynamically less likely to combine than amino acids.

The identification of RNA molecules in microvesicles supports the hypothesis that they are a biological vehicle for the transfer of nucleic acids and subsequently modulate the target cell's protein synthesis. Messenger RNA transported from one cell to another through microvesicles can be translated into proteins, conferring new function to the target cell. The discovery that microvesicles may shuttle specific mRNA and miRNA suggests that this may be a new mechanism of genetic exchange between cells. Exosomes produced by cells exposed to oxidative stress can mediate protective signals, reducing oxidative stress in recipient cells, a process which is proposed to depend on exosomal RNA transfer.

The location of two-chain- superposition correspond in these experiments to twice the thickness of single chain (0.8 nm in the case of the mentioned example). At the application of proper scanning parameters, conformation of such molecules remain unchanged for hours that allows the performance of experiments under liquid media having various properties., Furthermore, by controlling the force between the tip and the sample high resolution images can be obtained.D. Murugesapillai et al, DNA bridging and looping by HMO1 provides a mechanism for stabilizing nucleosome- free chromatin, Nucleic Acids Res (2014) 42 (14): 8996-9004 Optical tweezers have also been used to study and quantify DNA-protein interactions.

Numbered ribose carbons on cytidine. Molecular biologists use several shorthand terms when referring to nucleic acid molecules, such as DNA and RNA, collectively referred to as nucleic acid nomenclature. The most common is the representation of the base pairs as letters--an adenine nucleotide is abbreviated as A, guanine as G, cytosine as C, thymine as T, and in RNA, uracil as U. Additionally, the positions of the carbons in the ribose sugar that forms the backbone of the nucleic acid chain are numbered, and are used to indicate the direction of nucleic acids (5'->3' versus 3'->5'). This is referred to as directionality.

In the fields of histology, pathology, and cell biology, fixation is the preservation of biological tissues from decay due to autolysis or putrefaction. It terminates any ongoing biochemical reactions and may also increase the treated tissues' mechanical strength or stability. Tissue fixation is a critical step in the preparation of histological sections, its broad objective being to preserve cells and tissue components and to do this in such a way as to allow for the preparation of thin, stained sections. This allows the investigation of the tissues' structure, which is determined by the shapes and sizes of such macromolecules (in and around cells) as proteins and nucleic acids.

At the University of Würzburg he worked with Emil Fischer on the chemistry of sugars, receiving his PhD in 1890. In 1891, they published the preparation of a novel unnatural sugar, -ribose, by the epimerisation of -arabonic acid and reduction of the resulting lactone. It was not until work by Phoebus Levene and Walter Jacobs in 1909 that it was recognised that -ribose is a natural product, the enantiomer of Fischer and Piloty's product, and an essential component of nucleic acids. In 1892, he followed Fischer to the University of Berlin where he worked until his father- in-law offered him a position at the University of Munich in 1900.

Most of a grape's YAN content is found in the skins and seeds which gets left behind as pomace after pressing. YAN is a measurement of the primary organic (free amino acids) and inorganic (ammonia and ammonium) sources of nitrogen that can be assimilated by S. cerevisiae. There are several nitrogenous compounds found in must and wine including peptides, larger proteins, amides, biogenic amines, pyridines, purines and nucleic acids but these cannot be directly used by yeast for metabolism. Taken together, the total nitrogen content of grape must can range from 60 to 2400 mg of nitrogen per liter, however not all of this nitrogen will be assimilable.

Additionally, bacteria have a multi-component cytoskeleton to control the localisation of proteins and nucleic acids within the cell, and to manage the process of cell division. Many important biochemical reactions, such as energy generation, occur due to concentration gradients across membranes, creating a potential difference analogous to a battery. The general lack of internal membranes in bacteria means these reactions, such as electron transport, occur across the cell membrane between the cytoplasm and the outside of the cell or periplasm. However, in many photosynthetic bacteria the plasma membrane is highly folded and fills most of the cell with layers of light-gathering membrane.

Advances in the fields of histology and cytology began in the late 19th century along with advances in surgical techniques allowing for the painless and safe removal of biopsy specimens. The invention of the electron microscope brought a great advance in resolution power and allowed research into the ultrastructure of cells and the organelles and other structures within them. About the same time, in the 1950s, the use of X-ray diffraction for studying the crystal structures of proteins, nucleic acids and other biological molecules gave rise to a new field of molecular anatomy. Equally important advances have occurred in non-invasive techniques for examining the interior structures of the body.

Metabolic reactions may be categorized as catabolic – the breaking down of compounds (for example, the breaking down of glucose to pyruvate by cellular respiration); or anabolic – the building up (synthesis) of compounds (such as proteins, carbohydrates, lipids, and nucleic acids). Usually, catabolism releases energy, and anabolism consumes energy. The chemical reactions of metabolism are organized into metabolic pathways, in which one chemical is transformed through a series of steps into another chemical, each step being facilitated by a specific enzyme. Enzymes are crucial to metabolism because they allow organisms to drive desirable reactions that require energy that will not occur by themselves, by coupling them to spontaneous reactions that release energy.

However, because several aromatic amino acids exist, this method has low accuracy; in order to mitigate this issue, the desired protein must be pure, and its molar absorptivity is known. In addition, a protein without aromatic amino acids will not have an absorption maximum at approximately 280 nm. The presence of nucleic acids in the protein can further decrease the method's accuracy due to the presence of purine and pyrimidine rings, which have an absorption maximum at approximately 260 nm. Phenylalanine has a relatively weak absorbance in comparison to the other standard aromatic amino acids; its presence in a protein can only be detected if tryptophan and tyrosine are not present.

He has brought synthesis and design to the field of biopolymers and the methodology of nucleic acids to the field of molecular recognition. His pioneering research at the interface of chemistry and biology has contributed greatly to a set of general chemical principles for sequence specific recognition at single sites in the human genome." # M. Frederick Hawthorne 1994 "For outstanding contributions to the fields of inorganic chemistry and organometallic chemistry through his seminal discoveries n the rapidly expanding area of borane clusters. Inparticular, his work has provided pioneering insights into the syntheses, structures, bonding, and reactivity patterns of polyhedral borane anions, carboranes, and metallocarboranes.

Alongside proteins, lipids and complex carbohydrates (polysaccharides), nucleic acids are one of the four major types of macromolecules that are essential for all known forms of life. The two DNA strands are known as polynucleotides as they are composed of simpler monomeric units called nucleotides. Each nucleotide is composed of one of four nitrogen-containing nucleobases (cytosine [C], guanine [G], adenine [A] or thymine [T]), a sugar called deoxyribose, and a phosphate group. The nucleotides are joined to one another in a chain by covalent bonds (known as the phospho-diester linkage) between the sugar of one nucleotide and the phosphate of the next, resulting in an alternating sugar-phosphate backbone.

When scientific research resumed after the end of the Cultural Revolution, in 1978 she was admitted for the second time to the Shanghai Institute of Biochemistry and became the first graduate student of the renowned scientist Wang Yinglai after the Cultural Revolution. She was awarded a Fogarty Fellowship by the US National Institutes of Health to conduct postdoctoral research at the University of California, Davis from 1984 to 1987. After she returned to Shanghai in 1987, Wang Yinglai chose her to succeed him as principal investigator of the institute's research on the interaction between enzymes and nucleic acids. However, she was soon diagnosed with breast cancer and underwent surgery.

Directed evolution (DE) is a method used in protein engineering that mimics the process of natural selection to steer proteins or nucleic acids toward a user-defined goal. It consists of subjecting a gene to iterative rounds of mutagenesis (creating a library of variants), selection (expressing those variants and isolating members with the desired function) and amplification (generating a template for the next round). It can be performed in vivo (in living organisms), or in vitro (in cells or free in solution). Directed evolution is used both for protein engineering as an alternative to rationally designing modified proteins, as well as studies of fundamental evolutionary principles in a controlled, laboratory environment.

Albert Jakob Eschenmoser (born 5 August 1925) is a Swiss organic chemist best known for his work on the synthesis of complex heterocyclic natural compounds, most notably vitamin B12. In addition to his significant contributions to the field of organic synthesis, Eschenmoser pioneered work in the Origins of Life (OoL) field with work on the synthetic pathways of artificial nucleic acids. Before retiring in 2009, Eschenmoser held tenured teaching positions at the ETH Zurich and The Skaggs Institute for Chemical Biology at The Scripps Research Institute in La Jolla, California as well as visiting professorships at the University of Chicago, Cambridge University, and Harvard.

James Andrew McCammon (born 1947, Lafayette, Indiana, USA) is an American physical chemist known for his application of principles and methods from theoretical and computational chemistry to biological systems. A professor at the University of California, San Diego, McCammon's research focuses on the theoretical aspects of biomolecular and cellular activity. In 2011 he was elected to the National Academy of Sciences. Prof. McCammon co-authored Dynamics of Proteins and Nucleic Acids (Cambridge University Press, 1987; ), an important contribution to molecular mechanics and molecular dynamics, with Stephen Harvey, while the first published reports on molecular mechanics and molecular dynamics can be found as early as 1976, most likely even earlier.

Showing the arrangement of nucleotides within the structure of nucleic acids: At lower left, a monophosphate nucleotide; its nitrogenous base represents one side of a base-pair. At upper right, four nucleotides form two base-pairs: thymine and adenine (connected by double hydrogen bonds) and guanine and cytosine (connected by triple hydrogen bonds). The individual nucleotide monomers are chain-joined at their sugar and phosphate molecules, forming two 'backbones' (a double helix) of a nucleic acid, shown at upper left. A nucleo _tide_ is composed of three distinctive chemical sub-units: a five-carbon sugar molecule, a nitrogenous base—which two together are called a nucleo _side_ —and one phosphate group.

Nucleic acid types differ in the structure of the sugar in their nucleotides–DNA contains 2'-deoxyribose while RNA contains ribose (where the only difference is the presence of a hydroxyl group). Also, the nucleobases found in the two nucleic acid types are different: adenine, cytosine, and guanine are found in both RNA and DNA, while thymine occurs in DNA and uracil occurs in RNA. The sugars and phosphates in nucleic acids are connected to each other in an alternating chain (sugar- phosphate backbone) through phosphodiester linkages. In conventional nomenclature, the carbons to which the phosphate groups attach are the 3'-end and the 5'-end carbons of the sugar.

Multicolor optical coding for biological assays has been achieved by embedding different-sized quantum dots into polymeric microbeads. Nanopore technology for analysis of nucleic acids converts strings of nucleotides directly into electronic signatures. Sensor test chips containing thousands of nanowires, able to detect proteins and other biomarkers left behind by cancer cells, could enable the detection and diagnosis of cancer in the early stages from a few drops of a patient's blood. Nanotechnology is helping to advance the use of arthroscopes, which are pencil-sized devices that are used in surgeries with lights and cameras so surgeons can do the surgeries with smaller incisions.

Samples may be any material containing proteins or nucleic acids. These may be biologically derived, for example from prokaryotic or eukaryotic cells, tissues, viruses, environmental samples, or purified proteins. In the case of solid tissues or cells, these are often first broken down mechanically using a blender (for larger sample volumes), using a homogenizer (smaller volumes), by sonicator or by using cycling of high pressure, and a combination of biochemical and mechanical techniques - including various types of filtration and centrifugation - may be used to separate different cell compartments and organelles prior to electrophoresis. Synthetic biomolecules such as oligonucleotides may also be used as analytes.

Various buffer systems are used in PAGE depending on the nature of the sample and the experimental objective. The buffers used at the anode and cathode may be the same or different. center center An electric field is applied across the gel, causing the negatively charged proteins or nucleic acids to migrate across the gel away from the negative electrode (which is the cathode being that this is an electrolytic rather than galvanic cell) and towards the positive electrode (the anode). Depending on their size, each biomolecule moves differently through the gel matrix: small molecules more easily fit through the pores in the gel, while larger ones have more difficulty.

CAR is a receptor for both Coxsackie B virus and adenovirus 2 and 5, which are structurally distinct. In patients with myocarditis or dilated cardiomyopathy, elevated Coxsackie B2 viral nucleic acids have been detected in myocardial biopsy samples. Adenoviral genomic DNA has also been detected in myocardial biopsies of patients with idiopathic cardiomyopathy, or impaired left ventricular function of unknown origin. Patients exhibiting sudden death from acute myocardial infarction had a higher proportion of active coxsackie B virus infection relative to matched controls, which was coordinate with disrupted sarcolemmal localization of dystrophin, suggesting that enteroviral infection may worsen the outcome of patients with acute myocardial infarction.

1\. T. S. Kumarevel, H. Mizuno, P. K. R. Kumar, Structural basis of HutP-mediated anti-termination and roles of the Mg2+ ion and L-histidine ligand, Nature 434 (2005) 183-191. 2\. T. S. Kumarevel, Z. Fujimoto, P. Karthe, M. Oda, H. Mizuno, P. K. R. Kumar, Crystal structure of activated HutP; an RNA binding protein that regulates transcription of the hut operon in Bacillus subtilis, Structure 12 (2004) 1269-1280. 3\. T. S. Kumarevel, H. Mizuno, P. K. R. Kumar, Allosteric activation of HutP protein, that regulates transcription of hut operon in Bacillus subtilis, mediated by various analogs of histidine, Nucleic Acids Res suppl. 3 (2003) 199-200. 4\.

Since its discovery in 1958, there have only been 150 reported human illnesses caused by POWV. The incidence rate of POWV in the United States was 1 case per year from 1958-2005, and has risen to an average of 10 cases per year since then. Currently, POWV is detected with IgM antibody capture ELISA of an IgM immunofluorescence antibody (IFA) assay, plaque reduction neutralization test (PRNT), detection of virus-specific nucleic acids, isolation in culture, or a >4-fold increase in antibody titers from paired acute and convalescent sera. These specific tests for POWV can only be done at a state lab or the CDC.

The mechanism is different from that of nuclear staining by basic (cationic) dyes such as thionine or toluidine blue. Staining by basic dyes occurs only from solutions that are less acidic than hemalum, and it is prevented by prior chemical or enzymatic extraction of nucleic acids. There is evidence to indicate that co-ordinate bonds, similar to those that hold aluminium and hematein together, bind the hemalum complex to DNA and to carboxy groups of proteins in the nuclear chromatin. The structures do not have to be acidic or basic to be called basophilic and eosinophilic; the terminology is based on the affinity of cellular components for the dyes.

Leslie Barnett helped set up Sydney Brenner's laboratory in Singapore, many years later. Esther Lederberg, Gunther Stent, Sydney Brenner and Joshua Lederberg pictured in 1965 Brenner, with George Pieczenik, created the first computer matrix analysis of nucleic acids using TRAC, which Brenner continued to use. Crick, Brenner, Klug and Pieczenik returned to their early work on deciphering the genetic code with a pioneering paper on the origin of protein synthesis, where constraints on mRNA and tRNA co-evolved allowing for a five-base interaction with a flip of the anticodon loop, and thereby creating a triplet code translating system without requiring a ribosome. This model requires a partially overlapping code.

Organic chemist Donna Blackmond described this finding as "strong evidence" in favour of the RNA world. However, John Sutherland said that while his team's work suggests that nucleic acids played an early and central role in the origin of life, it did not necessarily support the RNA world hypothesis in the strict sense, which he described as a "restrictive, hypothetical arrangement". The Sutherland group's 2009 paper also highlighted the possibility for the photo- sanitization of the pyrimidine-2',3'-cyclic phosphates. A potential weakness of these routes is the generation of enantioenriched glyceraldehyde, or its 3-phosphate derivative (glyceraldehyde prefers to exist as its keto tautomer dihydroxyacetone).

SB buffer is a buffer solution used in agarose and polyacrylamide gel electrophoresis for the separation of nucleic acids such as DNA and RNA. "SB" is a commercial trademark of Faster Better Media LLC for their sodium boric acid-based conductive medium (US Patent # 7811437), which is based on the publications of Brody and Kern. It is made up of sodium borate, usually 1-10 mM at pH 8.0. It has a lower conductivity, produces sharper bands, and can be run at higher speeds than can gels made from TBE buffer or TAE buffer (5-35 V/cm as compared to 5-10 V/cm).

Nuclear magnetic resonance spectroscopy of proteins (usually abbreviated protein NMR) is a field of structural biology in which NMR spectroscopy is used to obtain information about the structure and dynamics of proteins, and also nucleic acids, and their complexes. The field was pioneered by Richard R. Ernst and Kurt Wüthrich at the ETH, and by Ad Bax, Marius Clore, Angela Gronenborn at the NIH,, and Gerhard Wagner at Harvard University, among others. Structure determination by NMR spectroscopy usually consists of several phases, each using a separate set of highly specialized techniques. The sample is prepared, measurements are made, interpretive approaches are applied, and a structure is calculated and validated.

The Growth Rate Hypothesis (GRH) addresses this phenomenon and states that the demands for phosphorus increase during active growth phases to produce P-rich nucleic acids in biomass production and are reflected in the P content of the consumer. During early growth stages, or earlier in-stars, invertebrates may have higher demands for N and P enriched resources to fuel the ribosomal production of proteins and RNA. At later stages, the demand for particular elements may shift as they are no longer actively growing as rapidly or generating protein rich biomass. Growth rates of invertebrate organisms can also be limited by the resources that are available to them.

Kossel was awarded the Nobel Prize in Physiology or Medicine in 1910 for his research in cell biology, the chemical composition of the cell nucleus, and for his work in isolating and describing nucleic acids. The award was presented on 10 December 1910. In the autumn of 1911, Kossel was invited to the United States to deliver the Herter Lecture at Johns Hopkins. Traveling with his wife Luise and daughter Gertrude, he took the opportunity to travel and to visit acquaintances, one of which was Eugene W. Hilgard, professor emeritus of agricultural chemistry at the University of California at Berkeley, who was also his wife's cousin.

For analysis of RNA, samples should be cryogenically frozen (−196 °C) almost immediately upon collection, or stored in an RNA stabilization and preservation reagent (e.g. RNAlater). The next step is to extract the desired nucleic acids from the sample, which can be performed manually using various published extraction methods or by using one of the many commercially available DNA/RNA extraction kits. Due to the labile nature of RNA, synthesis of complementary DNA (cDNA) using extracted RNA as a template is performed for further analysis. For most molecular genetic sequencing methods of AM fungi a PCR step is required to increase the total amount of target DNA/RNA/cDNA.

Depiction of the adenine–thymine Watson–Crick base pair A base pair (bp) is a fundamental unit of double-stranded nucleic acids consisting of two nucleobases bound to each other by hydrogen bonds. They form the building blocks of the DNA double helix and contribute to the folded structure of both DNA and RNA. Dictated by specific hydrogen bonding patterns, "Watson–Crick" base pairs (guanine–cytosine and adenine–thymine) allow the DNA helix to maintain a regular helical structure that is subtly dependent on its nucleotide sequence. The complementary nature of this based-paired structure provides a redundant copy of the genetic information encoded within each strand of DNA.

This ammonia can then be assimilated into organic matter like amino and nucleic acids, by both photoautrophic and heterotrophic plankton, it can also be nitrified to NO3 for energy production by nitrifying bacteria. Finally the use of NO3 or NO2 as terminal electron acceptors reduces the nitrogen back into N2, which is then released back into the atmosphere thus closing the cycle. Another important process involved in the regeneration of atmospheric N2 is anammox. Anammox, a process in which ammonia is combined with nitrite in order to produce diatomic nitrogen and water, could account for 30-50% of production of N2 in the ocean.

Initially influenced by the herpetologist Bayard Brattstrom, with whom she co- authored her first two research papers on the salamander Eurycea bislineata, she subsequently became interested in the then-novel disciplines of molecular biology and molecular genetics. She briefly studied under geneticist David Bonner at the Yale School of Medicine's Department of Microbiology, with a National Science Foundation fellowship. In 1960, she transferred to the microbiology department of New York University (NYU) Medical School, supervised initially by the bacterial geneticist Werner Maas and then by the biochemist Jerard Hurwitz, who was researching nucleic acids. She received her Ph.D. from NYU in 1964; her thesis was on histones.

The HIV-1 nucleocapsid protein 7 (NCp7) is the protein targeted by zinc ejectors. NCp7 is initially formed as part of the gag polypeptide and follows a gag-knuckle zinc finger conformation. In its lifetime, NCp7 facilitates the unwinding of tRNA, acts as a primer for reverse transcription, chaperones nucleic acids within the capsid of HIV-1, helps integrate the viral RNA into budding virions, and is intimately involved in the replication of HIV-1 in both the early phase and late phase. These processes play critical roles in the replication of HIV-1 thus making NCp7 a prime target for drugs seeking to contravene the replication process.