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Nuclease

Index Nuclease

A nuclease (also archaically known as nucleodepolymerase or polynucleotidase) is an enzyme capable of cleaving the phosphodiester bonds between monomers of nucleic acids. [1]

123 relations: Active site, Adenine, Amino acid, AP endonuclease, AP site, Archaea, Artemis complex, Aspergillus nuclease S1, Ataxia-telangiectasia, Bacillus amyloliquefaciens, Backbone chain, BamHI, Base (chemistry), Base excision repair, Base pair, Crosslinking of DNA, Crossover junction endodeoxyribonuclease, Cut, copy, and paste, Cytosine, D-loop, Deamination, Deletion (genetics), Deoxyribonuclease, DNA, DNA adduct, DNA damage (naturally occurring), DNA glycosylase, DNA methylation, DNA mismatch repair, DNA polymerase, DNA repair, DNA replication, DNA-binding domain, DNA-PKcs, EcoRI, EcoRV, Endonuclease, Enzyme, Enzyme Commission number, ERCC1, ERCC4, ERCC5, Escherichia coli, Esterase, Eukaryote, Exodeoxyribonuclease I, Exonuclease, Exonuclease VII, Flap endonuclease, Flap structure-specific endonuclease 1, ..., Genetic engineering, Genetic recombination, Genome editing, Genome instability, Guanine, Haemophilus influenzae, HindII, HindIII, Holliday junction, Homologous chromosome, Homologous recombination, Hydrolase, Immunodeficiency, International Union of Biochemistry and Molecular Biology, Ionizing radiation, Johns Hopkins University, Ligase, Lipase, Meganuclease, Meiosis, Methyl group, Methylation, Methyltransferase, Micrococcal nuclease, Microorganism, Molecular cloning, Monomer, MRE11A, MUS81, MutS-1, Nick (DNA), Non-homologous end joining, Nuclease protection assay, Nucleic acid, Nucleic acid double helix, Nucleic acid notation, Nucleic acid tertiary structure, Nucleotide, Nucleotide excision repair, Okazaki fragments, P1 nuclease, Phosphatase, Phosphodiester bond, Phosphodiesterase, PIN domain, Point mutation, Polymerase, Polymerization, Primer (molecular biology), Proofreading (biology), Protein complex, Protein domain, Protein primary structure, R.EcoRII, Rad50, Reactive oxygen species, Recognition sequence, Restriction enzyme, Ribonuclease, Ribonuclease H, RNA, RuvABC, Stem-loop, Sticky and blunt ends, Thymine, Turn (biochemistry), Ultraviolet, UvrABC endonuclease, V(D)J recombination, Very short patch repair, Werner Arber, Ydc2 protein domain, Yeast. Expand index (73 more) »

Active site

In biology, the active site is the region of an enzyme where substrate molecules bind and undergo a chemical reaction.

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Adenine

Adenine (A, Ade) is a nucleobase (a purine derivative).

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Amino acid

Amino acids are organic compounds containing amine (-NH2) and carboxyl (-COOH) functional groups, along with a side chain (R group) specific to each amino acid.

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AP endonuclease

Apurinic/apyrimidinic (AP) endonuclease is an enzyme that is involved in the DNA base excision repair pathway (BER).

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AP site

In biochemistry and molecular genetics, an AP site (apurinic/apyrimidinic site), also known as an abasic site, is a location in DNA (also in RNA but much less likely) that has neither a purine nor a pyrimidine base, either spontaneously or due to DNA damage.

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Archaea

Archaea (or or) constitute a domain of single-celled microorganisms.

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Artemis complex

The Artemis complex is a protein complex that functions in V(D)J recombination, the somatic recombination process which generates diversity in T cell receptors and immunoglobulins.

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Aspergillus nuclease S1

Aspergillus nuclease S1 is an endonuclease enzyme derived from Aspergillus oryzae that splits single-stranded DNA (ssDNA) and RNA into oligo- or mononucleotides.

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Ataxia-telangiectasia

Ataxia-telangiectasia (AT or A-T), also referred to as ataxia-telangiectasia syndrome or Louis–Bar syndrome, is a rare, neurodegenerative, autosomal recessive disease causing severe disability.

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Bacillus amyloliquefaciens

Bacillus amyloliquefaciens is a species of bacterium in the genus Bacillus that is the source of the BamH1 restriction enzyme.

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Backbone chain

In polymer science, the backbone chain of a polymer is the longest series of covalently bonded atoms that together create the continuous chain of the molecule.

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BamHI

BamH I (from Bacillus amyloliquefaciens) is a type II restriction endonuclease, having the capacity for recognizing short sequences (6 b.p.) of DNA and specifically cleaving them at a target site.

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Base (chemistry)

In chemistry, bases are substances that, in aqueous solution, release hydroxide (OH−) ions, are slippery to the touch, can taste bitter if an alkali, change the color of indicators (e.g., turn red litmus paper blue), react with acids to form salts, promote certain chemical reactions (base catalysis), accept protons from any proton donor, and/or contain completely or partially displaceable OH− ions.

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Base excision repair

In biochemistry and genetics, base excision repair (BER) is a cellular mechanism that repairs damaged DNA throughout the cell cycle.

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Base pair

A base pair (bp) is a unit consisting of two nucleobases bound to each other by hydrogen bonds.

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Crosslinking of DNA

In genetics, crosslinking of DNA occurs when various exogenous or endogenous agents react with two nucleotides of DNA, forming a covalent linkage between them.

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Crossover junction endodeoxyribonuclease

Crossover junction endodeoxyribonuclease (Hje endonuclease, Holliday junction endonuclease CCE1, Holliday junction resolvase, Holliday junction-cleaving endonuclease, Holliday junction-resolving endoribonuclease, RusA Holliday junction resolvase, RusA endonuclease, RuvC endonuclease, SpCCe1 Holliday junction resolvase, crossover junction endoribonuclease, cruciform-cutting endonuclease, endo X3, endonuclease RuvC, endonuclease VII, endonuclease X3, resolving enzyme CCE1) is an enzyme.

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Cut, copy, and paste

In human–computer interaction, cut, copy and paste are related commands that offer a user-interface interprocess communication technique for transferring data.

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Cytosine

Cytosine (C) is one of the four main bases found in DNA and RNA, along with adenine, guanine, and thymine (uracil in RNA).

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D-loop

In molecular biology, a displacement loop or D-loop is a DNA structure where the two strands of a double-stranded DNA molecule are separated for a stretch and held apart by a third strand of DNA.

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Deamination

Deamination is the removal of an amine group from a protein molecule.

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Deletion (genetics)

In genetics, a deletion (also called gene deletion, deficiency, or deletion mutation) (sign: Δ) is a mutation (a genetic aberration) in which a part of a chromosome or a sequence of DNA is lost during DNA replication.

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Deoxyribonuclease

A deoxyribonuclease (DNase, for short) is an enzyme that catalyzes the hydrolytic cleavage of phosphodiester linkages in the DNA backbone, thus degrading DNA.

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DNA

Deoxyribonucleic acid (DNA) is a thread-like chain of nucleotides carrying the genetic instructions used in the growth, development, functioning and reproduction of all known living organisms and many viruses.

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DNA adduct

In molecular genetics, a DNA adduct is a segment of DNA bound to a cancer-causing chemical.

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DNA damage (naturally occurring)

DNA damage is distinctly different from mutation, although both are types of error in DNA.

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DNA glycosylase

DNA glycosylases are a family of enzymes involved in base excision repair, classified under EC number EC 3.2.2.

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DNA methylation

DNA methylation is a process by which methyl groups are added to the DNA molecule.

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DNA mismatch repair

DNA mismatch repair (MMR) is a system for recognizing and repairing erroneous insertion, deletion, and mis-incorporation of bases that can arise during DNA replication and recombination, as well as repairing some forms of DNA damage.

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DNA polymerase

DNA polymerases are enzymes that synthesize DNA molecules from deoxyribonucleotides, the building blocks of DNA.

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DNA repair

DNA repair is a collection of processes by which a cell identifies and corrects damage to the DNA molecules that encode its genome.

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DNA replication

In molecular biology, DNA replication is the biological process of producing two identical replicas of DNA from one original DNA molecule.

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DNA-binding domain

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.

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DNA-PKcs

DNA-dependent protein kinase, catalytic subunit, also known as DNA-PKcs, is an enzyme that in humans is encoded by the gene designated as PRKDC or XRCC7.

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EcoRI

EcoRI (pronounced "eco R one") is a restriction endonuclease enzyme isolated from species E. coli. The Eco part of the enzyme's name originates from the species from which it was isolated, while the R represents the particular strain, in this case RY13.

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EcoRV

EcoRV (pronounced "eco R five") is a type II restriction endonuclease isolated from certain strains of Escherichia coli.

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Endonuclease

Endonucleases are enzymes that cleave the phosphodiester bond within a polynucleotide chain.

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Enzyme

Enzymes are macromolecular biological catalysts.

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Enzyme Commission number

The Enzyme Commission number (EC number) is a numerical classification scheme for enzymes, based on the chemical reactions they catalyze.

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ERCC1

DNA excision repair protein ERCC-1 is a protein that in humans is encoded by the ERCC1 gene.

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ERCC4

ERCC4 is a protein designated as DNA repair endonuclease XPF that in humans is encoded by the ERCC4 gene.

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ERCC5

DNA repair protein complementing XP-G cells is a protein that in humans is encoded by the ERCC5 gene.

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Escherichia coli

Escherichia coli (also known as E. coli) is a Gram-negative, facultatively anaerobic, rod-shaped, coliform bacterium of the genus Escherichia that is commonly found in the lower intestine of warm-blooded organisms (endotherms).

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Esterase

An esterase is a hydrolase enzyme that splits esters into an acid and an alcohol in a chemical reaction with water called hydrolysis.

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Eukaryote

Eukaryotes are organisms whose cells have a nucleus enclosed within membranes, unlike Prokaryotes (Bacteria and other Archaea).

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Exodeoxyribonuclease I

Exodeoxyribonuclease I (Escherichia coli exonuclease I, E. coli exonuclease I, exonuclease I) is an enzyme.

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Exonuclease

Exonucleases are enzymes that work by cleaving nucleotides one at a time from the end (exo) of a polynucleotide chain.

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Exonuclease VII

In molecular biology, exonuclease VII (Escherichia coli exonuclease VII, E. coli exonuclease VII, endodeoxyribonuclease VII, Exodeoxyribonuclease VII) is a bacterial exonuclease enzyme.

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Flap endonuclease

Flap endonucleases (FENs, also known as 5' nucleases in older references) are a class of nucleolytic enzymes that act as both 5'-3' exonucleases and structure-specific endonucleases on specialised DNA structures that occur during the biological processes of DNA replication, DNA repair, and DNA recombination.

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Flap structure-specific endonuclease 1

Flap endonuclease 1 is an enzyme that in humans is encoded by the FEN1 gene.

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Genetic engineering

Genetic engineering, also called genetic modification or genetic manipulation, is the direct manipulation of an organism's genes using biotechnology.

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Genetic recombination

Genetic recombination (aka genetic reshuffling) is the production of offspring with combinations of traits that differ from those found in either parent.

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Genome editing

Genome editing, or genome engineering is a type of genetic engineering in which DNA is inserted, deleted, modified or replaced in the genome of a living organism.

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Genome instability

Genome instability (also genetic instability or genomic instability) refers to a high frequency of mutations within the genome of a cellular lineage.

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Guanine

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).

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Haemophilus influenzae

Haemophilus influenzae (formerly called Pfeiffer's bacillus or Bacillus influenzae) is a Gram-negative, coccobacillary, facultatively anaerobic pathogenic bacterium belonging to the Pasteurellaceae family.

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HindII

HindII is a type II restriction enzyme found in Haemophilus influenzae.

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HindIII

HindIII (pronounced "Hin D Three") is a type II site-specific deoxyribonuclease restriction enzyme isolated from Haemophilus influenzae that cleaves the DNA palindromic sequence AAGCTT in the presence of the cofactor Mg2+ via hydrolysis.

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Holliday junction

A Holliday junction is a branched nucleic acid structure that contains four double-stranded arms joined together.

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Homologous chromosome

A couple of homologous chromosomes, or homologs, are a set of one maternal and one paternal chromosome that pair up with each other inside a cell during meiosis.

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Homologous recombination

Homologous recombination is a type of genetic recombination in which nucleotide sequences are exchanged between two similar or identical molecules of DNA.

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Hydrolase

Hydrolase is a class of enzyme that is commonly used as biochemical catalysts that utilize water to break a chemical bond.

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Immunodeficiency

Immunodeficiency (or immune deficiency) is a state in which the immune system's ability to fight infectious disease and cancer is compromised or entirely absent.

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International Union of Biochemistry and Molecular Biology

The International Union of Biochemistry and Molecular Biology (IUBMB) is an international non-governmental organisation concerned with biochemistry and molecular biology.

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Ionizing radiation

Ionizing radiation (ionising radiation) is radiation that carries enough energy to liberate electrons from atoms or molecules, thereby ionizing them.

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Johns Hopkins University

Johns Hopkins University is an American private research university in Baltimore, Maryland.

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Ligase

In biochemistry, a ligase is an enzyme that can catalyze the joining of two large molecules by forming a new chemical bond, usually with accompanying hydrolysis of a small pendant chemical group on one of the larger molecules or the enzyme catalyzing the linking together of two compounds, e.g., enzymes that catalyze joining of C-O, C-S, C-N, etc.

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Lipase

A lipase is any enzyme that catalyzes the hydrolysis of fats (lipids).

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Meganuclease

Meganucleases are endodeoxyribonucleases characterized by a large recognition site (double-stranded DNA sequences of 12 to 40 base pairs); as a result this site generally occurs only once in any given genome.

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Meiosis

Meiosis (from Greek μείωσις, meiosis, which means lessening) is a specialized type of cell division that reduces the chromosome number by half, creating four haploid cells, each genetically distinct from the parent cell that gave rise to them.

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Methyl group

A methyl group is an alkyl derived from methane, containing one carbon atom bonded to three hydrogen atoms — CH3.

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Methylation

In the chemical sciences, methylation denotes the addition of a methyl group on a substrate, or the substitution of an atom (or group) by a methyl group.

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Methyltransferase

Methyltransferases are a large group of enzymes that all methylate their substrates but can be split into several subclasses based on their structural features.

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Micrococcal nuclease

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.

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Microorganism

A microorganism, or microbe, is a microscopic organism, which may exist in its single-celled form or in a colony of cells. The possible existence of unseen microbial life was suspected from ancient times, such as in Jain scriptures from 6th century BC India and the 1st century BC book On Agriculture by Marcus Terentius Varro. Microbiology, the scientific study of microorganisms, began with their observation under the microscope in the 1670s by Antonie van Leeuwenhoek. In the 1850s, Louis Pasteur found that microorganisms caused food spoilage, debunking the theory of spontaneous generation. In the 1880s Robert Koch discovered that microorganisms caused the diseases tuberculosis, cholera and anthrax. Microorganisms include all unicellular organisms and so are extremely diverse. Of the three domains of life identified by Carl Woese, all of the Archaea and Bacteria are microorganisms. These were previously grouped together in the two domain system as Prokaryotes, the other being the eukaryotes. The third domain Eukaryota includes all multicellular organisms and many unicellular protists and protozoans. Some protists are related to animals and some to green plants. Many of the multicellular organisms are microscopic, namely micro-animals, some fungi and some algae, but these are not discussed here. They live in almost every habitat from the poles to the equator, deserts, geysers, rocks and the deep sea. Some are adapted to extremes such as very hot or very cold conditions, others to high pressure and a few such as Deinococcus radiodurans to high radiation environments. Microorganisms also make up the microbiota found in and on all multicellular organisms. A December 2017 report stated that 3.45 billion year old Australian rocks once contained microorganisms, the earliest direct evidence of life on Earth. Microbes are important in human culture and health in many ways, serving to ferment foods, treat sewage, produce fuel, enzymes and other bioactive compounds. They are essential tools in biology as model organisms and have been put to use in biological warfare and bioterrorism. They are a vital component of fertile soils. In the human body microorganisms make up the human microbiota including the essential gut flora. They are the pathogens responsible for many infectious diseases and as such are the target of hygiene measures.

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Molecular cloning

Molecular cloning is a set of experimental methods in molecular biology that are used to assemble recombinant DNA molecules and to direct their replication within host organisms.

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Monomer

A monomer (mono-, "one" + -mer, "part") is a molecule that "can undergo polymerization thereby contributing constitutional units to the essential structure of a macromolecule".

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MRE11A

Double-strand break repair protein MRE11A is a protein that in humans is encoded by the MRE11A gene.

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MUS81

Crossover junction endonuclease MUS81 is an enzyme that in humans is encoded by the MUS81 gene.

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MutS-1

Mismatch repair contributes to the overall fidelity of DNA replication and is essential for combating the adverse effects of damage to the genome.

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Nick (DNA)

A nick is a discontinuity in a double stranded DNA molecule where there is no phosphodiester bond between adjacent nucleotides of one strand typically through damage or enzyme action.

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Non-homologous end joining

Non-homologous end joining (NHEJ) is a pathway that repairs double-strand breaks in DNA.

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Nuclease protection assay

Nuclease protection assay is a laboratory technique used in biochemistry and genetics to identify individual RNA molecules in a heterogeneous RNA sample extracted from cells.

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Nucleic acid

Nucleic acids are biopolymers, or small biomolecules, essential to all known forms of life.

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Nucleic acid double helix

In molecular biology, the term double helix refers to the structure formed by double-stranded molecules of nucleic acids such as DNA.

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Nucleic acid notation

The nucleic acid notation currently in use was first formalized by the International Union of Pure and Applied Chemistry (IUPAC) in 1970.

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Nucleic acid tertiary structure

Nucleic acid tertiary structure is the three-dimensional shape of a nucleic acid polymer.

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Nucleotide

Nucleotides are organic molecules that serve as the monomer units for forming the nucleic acid polymers deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), both of which are essential biomolecules within all life-forms on Earth.

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Nucleotide excision repair

Nucleotide excision repair is a DNA repair mechanism.

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Okazaki fragments

Okazaki fragments are short, newly synthesized DNA fragments that are formed on the lagging template strand during DNA replication.

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P1 nuclease

P1 nuclease is a nuclease that works on single-stranded DNA as well as RNA.

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Phosphatase

A phosphatase is an enzyme that uses water to cleave a phosphoric acid monoester into a phosphate ion and an alcohol.

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Phosphodiester bond

A phosphodiester bond occurs when exactly two of the hydroxyl groups in phosphoric acid react with hydroxyl groups on other molecules to form two ester bonds.

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Phosphodiesterase

A phosphodiesterase (PDE) is an enzyme that breaks a phosphodiester bond.

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PIN domain

In molecular biology the PIN domain is a protein domain that is about 130 amino acids in length.

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Point mutation

A point mutation is a genetic mutation where a single nucleotide base is changed, inserted or deleted from a sequence of DNA or RNA.

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Polymerase

A polymerase is an enzyme (EC 2.7.7.6/7/19/48/49) that synthesizes long chains of polymers or nucleic acids.

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Polymerization

In polymer chemistry, polymerization is a process of reacting monomer molecules together in a chemical reaction to form polymer chains or three-dimensional networks.

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Primer (molecular biology)

A primer is a short strand of RNA or DNA (generally about 18-22 bases) that serves as a starting point for DNA synthesis.

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Proofreading (biology)

The term proofreading is used in genetics to refer to the error-correcting processes, first proposed by John Hopfield and Jacques Ninio, involved in DNA replication, immune system specificity, enzyme-substrate recognition among many other processes that require enhanced specificity.

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Protein complex

A protein complex or multiprotein complex is a group of two or more associated polypeptide chains.

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Protein domain

A protein domain is a conserved part of a given protein sequence and (tertiary) structure that can evolve, function, and exist independently of the rest of the protein chain.

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Protein primary structure

Protein primary structure is the linear sequence of amino acids in a peptide or protein.

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R.EcoRII

Restriction endonuclease (REase) EcoRII (pronounced "eco R two") is an enzyme of restriction modification system (RM) naturally found in Escherichia coli, a Gram-negative bacteria.

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Rad50

DNA repair protein RAD50, also known as RAD50, is a protein that in humans is encoded by the RAD50 gene.

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Reactive oxygen species

Reactive oxygen species (ROS) are chemically reactive chemical species containing oxygen.

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Recognition sequence

The recognition sequence, sometimes also referred to as recognition site, of any DNA-binding protein motif that exhibits binding specificity, refers to the DNA sequence (or subset thereof), to which the domain is specific.

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Restriction enzyme

A restriction enzyme or restriction endonuclease is an enzyme that cleaves DNA into fragments at or near specific recognition sites within the molecule known as restriction sites.

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Ribonuclease

Ribonuclease (commonly abbreviated RNase) is a type of nuclease that catalyzes the degradation of RNA into smaller components.

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Ribonuclease H

Ribonuclease H (abbreviated RNase H or RNH) is a family of non-sequence-specific endonuclease enzymes that catalyze the cleavage of RNA in an RNA/DNA substrate via a hydrolytic mechanism.

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RNA

Ribonucleic acid (RNA) is a polymeric molecule essential in various biological roles in coding, decoding, regulation, and expression of genes.

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RuvABC

RuvABC is a complex of three proteins that mediate branch migration and resolve the Holliday junction created during homologous recombination in bacteria.

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Stem-loop

Stem-loop intramolecular base pairing is a pattern that can occur in single-stranded DNA or, more commonly, in RNA.

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Sticky and blunt ends

DNA ends refer to the properties of the end of DNA molecules, which may be sticky ends (cohesive ends), blunt ends or in other forms.

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Thymine

---> Thymine (T, Thy) is one of the four nucleobases in the nucleic acid of DNA that are represented by the letters G–C–A–T.

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Turn (biochemistry)

A turn is an element of secondary structure in proteins where the polypeptide chain reverses its overall direction.

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Ultraviolet

Ultraviolet (UV) is electromagnetic radiation with a wavelength from 10 nm to 400 nm, shorter than that of visible light but longer than X-rays.

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UvrABC endonuclease

UvrABC endonuclease is a multienzyme complex in Escherichia coli involved in DNA repair by nucleotide excision repair, and it is, therefore, sometimes called an excinuclease.

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V(D)J recombination

V(D)J recombination is the unique mechanism of genetic recombination that occurs only in developing lymphocytes during the early stages of T and B cell maturation.

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Very short patch repair

Very short patch (VSP) repair is a DNA repair system that removes GT mismatches created by the deamination of 5-methylcytosine to thymine.

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Werner Arber

Werner Arber (born 3 June 1929 in Gränichen, Aargau) is a Swiss microbiologist and geneticist.

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Ydc2 protein domain

In molecular biology, the protein domain, Ydc2 (also known as SpCce1), is a Holliday junction resolvase from the fission yeast Schizosaccharomyces pombe that is involved in the maintenance of mitochondrial DNA.

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Yeast

Yeasts are eukaryotic, single-celled microorganisms classified as members of the fungus kingdom.

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Nucleases, Nucleodepolymerase, Polynucleotidase.

References

[1] https://en.wikipedia.org/wiki/Nuclease

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