DNA-(Apurinic or Apyrimidinic Site) Lyase: A DNA repair enzyme that catalyses the excision of ribose residues at apurinic and apyrimidinic DNA sites that can result from the action of DNA GLYCOSYLASES. The enzyme catalyzes a beta-elimination reaction in which the C-O-P bond 3' to the apurinic or apyrimidinic site in DNA is broken, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate. This enzyme was previously listed under EC 3.1.25.2.Apurinic Acid: Hydrolysate of DNA in which purine bases have been removed.Deoxyribonuclease IV (Phage T4-Induced): An enzyme which catalyzes the endonucleolytic cleavage of phosphodiester bonds at purinic or apyrimidinic sites (AP-sites) to produce 5'-Phosphooligonucleotide end products. The enzyme prefers single-stranded DNA (ssDNA) and was formerly classified as EC 3.1.4.30.Nucleic Acid Conformation: The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.PolynucleotidesCarbon-Oxygen Lyases: Enzymes that catalyze the cleavage of a carbon-oxygen bond by means other than hydrolysis or oxidation. EC 4.2.DNA: A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).Organophosphates: Carbon-containing phosphoric acid derivatives. Included under this heading are compounds that have CARBON atoms bound to one or more OXYGEN atoms of the P(=O)(O)3 structure. Note that several specific classes of endogenous phosphorus-containing compounds such as NUCLEOTIDES; PHOSPHOLIPIDS; and PHOSPHOPROTEINS are listed elsewhere.N-Glycosyl Hydrolases: A class of enzymes involved in the hydrolysis of the N-glycosidic bond of nitrogen-linked sugars.Oligonucleotides: Polymers made up of a few (2-20) nucleotides. In molecular genetics, they refer to a short sequence synthesized to match a region where a mutation is known to occur, and then used as a probe (OLIGONUCLEOTIDE PROBES). (Dorland, 28th ed)Endodeoxyribonucleases: A group of enzymes catalyzing the endonucleolytic cleavage of DNA. They include members of EC 3.1.21.-, EC 3.1.22.-, EC 3.1.23.- (DNA RESTRICTION ENZYMES), EC 3.1.24.- (DNA RESTRICTION ENZYMES), and EC 3.1.25.-.DNA Repair: The reconstruction of a continuous two-stranded DNA molecule without mismatch from a molecule which contained damaged regions. The major repair mechanisms are excision repair, in which defective regions in one strand are excised and resynthesized using the complementary base pairing information in the intact strand; photoreactivation repair, in which the lethal and mutagenic effects of ultraviolet light are eliminated; and post-replication repair, in which the primary lesions are not repaired, but the gaps in one daughter duplex are filled in by incorporation of portions of the other (undamaged) daughter duplex. Excision repair and post-replication repair are sometimes referred to as "dark repair" because they do not require light.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.DNA Glycosylases: A family of DNA repair enzymes that recognize damaged nucleotide bases and remove them by hydrolyzing the N-glycosidic bond that attaches them to the sugar backbone of the DNA molecule. The process called BASE EXCISION REPAIR can be completed by a DNA-(APURINIC OR APYRIMIDINIC SITE) LYASE which excises the remaining RIBOSE sugar from the DNA.Deoxyribonuclease (Pyrimidine Dimer): An enzyme which catalyzes an endonucleolytic cleavage near PYRIMIDINE DIMERS to produce a 5'-phosphate product. The enzyme acts on the damaged DNA strand, from the 5' side of the damaged site.Models, Molecular: Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.Molecular Sequence Data: Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.Uracil-DNA Glycosidase: An enzyme that catalyzes the HYDROLYSIS of the N-glycosidic bond between sugar phosphate backbone and URACIL residue during DNA synthesis.Oligodeoxyribonucleotides: A group of deoxyribonucleotides (up to 12) in which the phosphate residues of each deoxyribonucleotide act as bridges in forming diester linkages between the deoxyribose moieties.DNA-Formamidopyrimidine Glycosylase: A DNA repair enzyme that is an N-glycosyl hydrolase with specificity for DNA-containing ring-opened N(7)-methylguanine residues.Endonucleases: Enzymes that catalyze the hydrolysis of the internal bonds and thereby the formation of polynucleotides or oligonucleotides from ribo- or deoxyribonucleotide chains. EC 3.1.-.Deoxyribonucleases: Enzymes which catalyze the hydrolases of ester bonds within DNA. EC 3.1.-.Magnetic Resonance Spectroscopy: Spectroscopic method of measuring the magnetic moment of elementary particles such as atomic nuclei, protons or electrons. It is employed in clinical applications such as NMR Tomography (MAGNETIC RESONANCE IMAGING).Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.Substrate Specificity: A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.DNA Damage: Injuries to DNA that introduce deviations from its normal, intact structure and which may, if left unrepaired, result in a MUTATION or a block of DNA REPLICATION. These deviations may be caused by physical or chemical agents and occur by natural or unnatural, introduced circumstances. They include the introduction of illegitimate bases during replication or by deamination or other modification of bases; the loss of a base from the DNA backbone leaving an abasic site; single-strand breaks; double strand breaks; and intrastrand (PYRIMIDINE DIMERS) or interstrand crosslinking. Damage can often be repaired (DNA REPAIR). If the damage is extensive, it can induce APOPTOSIS.Escherichia coli: A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.Escherichia coli Proteins: Proteins obtained from ESCHERICHIA COLI.Purines: A series of heterocyclic compounds that are variously substituted in nature and are known also as purine bases. They include ADENINE and GUANINE, constituents of nucleic acids, as well as many alkaloids such as CAFFEINE and THEOPHYLLINE. Uric acid is the metabolic end product of purine metabolism.ATP Citrate (pro-S)-Lyase: An enzyme that, in the presence of ATP and COENZYME A, catalyzes the cleavage of citrate to yield acetyl CoA, oxaloacetate, ADP, and ORTHOPHOSPHATE. This reaction represents an important step in fatty acid biosynthesis. This enzyme was formerly listed as EC 4.1.3.8.Kinetics: The rate dynamics in chemical or physical systems.Lyases: A class of enzymes that catalyze the cleavage of C-C, C-O, and C-N, and other bonds by other means than by hydrolysis or oxidation. (Enzyme Nomenclature, 1992) EC 4.DNA Polymerase beta: A DNA repair enzyme that catalyzes DNA synthesis during base excision DNA repair. EC 2.7.7.7.Methyl Methanesulfonate: An alkylating agent in cancer therapy that may also act as a mutagen by interfering with and causing damage to DNA.DNA Ligases: Poly(deoxyribonucleotide):poly(deoxyribonucleotide)ligases. Enzymes that catalyze the joining of preformed deoxyribonucleotides in phosphodiester linkage during genetic processes during repair of a single-stranded break in duplex DNA. The class includes both EC 6.5.1.1 (ATP) and EC 6.5.1.2 (NAD).Phosphoric Diester Hydrolases: A class of enzymes that catalyze the hydrolysis of one of the two ester bonds in a phosphodiester compound. EC 3.1.4.DeoxyriboseExonucleases: Enzymes that catalyze the release of mononucleotides by the hydrolysis of the terminal bond of deoxyribonucleotide or ribonucleotide chains.Amino Acid Sequence: The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.Deoxycytidine Monophosphate: Deoxycytidine (dihydrogen phosphate). A deoxycytosine nucleotide containing one phosphate group esterified to the deoxyribose moiety in the 2'-,3'- or 5- positions.Polysaccharide-Lyases: A group of carbon-oxygen lyases. These enzymes catalyze the breakage of a carbon-oxygen bond in polysaccharides leading to an unsaturated product and the elimination of an alcohol. EC 4.2.2.Exodeoxyribonucleases: A family of enzymes that catalyze the exonucleolytic cleavage of DNA. It includes members of the class EC 3.1.11 that produce 5'-phosphomonoesters as cleavage products.Adenylosuccinate Lyase: An enzyme that, in the course of purine ribonucleotide biosynthesis, catalyzes the conversion of 5'-phosphoribosyl-4-(N-succinocarboxamide)-5-aminoimidazole to 5'-phosphoribosyl-4-carboxamide-5-aminoimidazole and the conversion of adenylosuccinic acid to AMP. EC 4.3.2.2.Ribosemonophosphates: Ribose substituted in the 1-, 3-, or 5-position by a phosphoric acid moiety.UracilPyrimidine Dimers: Dimers found in DNA chains damaged by ULTRAVIOLET RAYS. They consist of two adjacent PYRIMIDINE NUCLEOTIDES, usually THYMINE nucleotides, in which the pyrimidine residues are covalently joined by a cyclobutane ring. These dimers block DNA REPLICATION.Borohydrides: A class of inorganic or organic compounds that contain the borohydride (BH4-) anion.DNA Polymerase I: A DNA-dependent DNA polymerase characterized in prokaryotes and may be present in higher organisms. It has both 3'-5' and 5'-3' exonuclease activity, but cannot use native double-stranded DNA as template-primer. It is not inhibited by sulfhydryl reagents and is active in both DNA synthesis and repair. EC 2.7.7.7.T-Phages: A series of 7 virulent phages which infect E. coli. The T-even phages T2, T4; (BACTERIOPHAGE T4), and T6, and the phage T5 are called "autonomously virulent" because they cause cessation of all bacterial metabolism on infection. Phages T1, T3; (BACTERIOPHAGE T3), and T7; (BACTERIOPHAGE T7) are called "dependent virulent" because they depend on continued bacterial metabolism during the lytic cycle. The T-even phages contain 5-hydroxymethylcytosine in place of ordinary cytosine in their DNA.Catalysis: The facilitation of a chemical reaction by material (catalyst) that is not consumed by the reaction.Oxo-Acid-Lyases: Enzymes that catalyze the cleavage of a carbon-carbon bond of a 3-hydroxy acid. (Dorland, 28th ed) EC 4.1.3.GuanineHydrolysis: The process of cleaving a chemical compound by the addition of a molecule of water.DioxolanesProtein Conformation: The characteristic 3-dimensional shape of a protein, including the secondary, supersecondary (motifs), tertiary (domains) and quaternary structure of the peptide chain. PROTEIN STRUCTURE, QUATERNARY describes the conformation assumed by multimeric proteins (aggregates of more than one polypeptide chain).DNA Adducts: The products of chemical reactions that result in the addition of extraneous chemical groups to DNA.Mutation: Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.Aldehyde-Lyases: Enzymes that catalyze a reverse aldol condensation. A molecule containing a hydroxyl group and a carbonyl group is cleaved at a C-C bond to produce two smaller molecules (ALDEHYDES or KETONES). EC 4.1.2.Models, Chemical: Theoretical representations that simulate the behavior or activity of chemical processes or phenomena; includes the use of mathematical equations, computers, and other electronic equipment.Oligoribonucleotides: A group of ribonucleotides (up to 12) in which the phosphate residues of each ribonucleotide act as bridges in forming diester linkages between the ribose moieties.Structure-Activity Relationship: The relationship between the chemical structure of a compound and its biological or pharmacological activity. Compounds are often classed together because they have structural characteristics in common including shape, size, stereochemical arrangement, and distribution of functional groups.Ultraviolet Rays: That portion of the electromagnetic spectrum immediately below the visible range and extending into the x-ray frequencies. The longer wavelengths (near-UV or biotic or vital rays) are necessary for the endogenous synthesis of vitamin D and are also called antirachitic rays; the shorter, ionizing wavelengths (far-UV or abiotic or extravital rays) are viricidal, bactericidal, mutagenic, and carcinogenic and are used as disinfectants.Catalytic Domain: The region of an enzyme that interacts with its substrate to cause the enzymatic reaction.Crystallography, X-Ray: The study of crystal structure using X-RAY DIFFRACTION techniques. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)Osmium Tetroxide: (T-4)-Osmium oxide (OsO4). A highly toxic and volatile oxide of osmium used in industry as an oxidizing agent. It is also used as a histological fixative and stain and as a synovectomy agent in arthritic joints. Its vapor can cause eye, skin, and lung damage.DNA-Directed DNA Polymerase: DNA-dependent DNA polymerases found in bacteria, animal and plant cells. During the replication process, these enzymes catalyze the addition of deoxyribonucleotide residues to the end of a DNA strand in the presence of DNA as template-primer. They also possess exonuclease activity and therefore function in DNA repair.Glycolates: Derivatives of ACETIC ACID which contain an hydroxy group attached to the methyl carbon.Hydrogen-Ion Concentration: The normality of a solution with respect to HYDROGEN ions; H+. It is related to acidity measurements in most cases by pH = log 1/2[1/(H+)], where (H+) is the hydrogen ion concentration in gram equivalents per liter of solution. (McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed)Oxidation-Reduction: A chemical reaction in which an electron is transferred from one molecule to another. The electron-donating molecule is the reducing agent or reductant; the electron-accepting molecule is the oxidizing agent or oxidant. Reducing and oxidizing agents function as conjugate reductant-oxidant pairs or redox pairs (Lehninger, Principles of Biochemistry, 1982, p471).Phosphorus-Oxygen Lyases: Enzymes that catalyze the cleavage of a phosphorus-oxygen bond by means other than hydrolysis or oxidation. EC 4.6.RNA Ligase (ATP): An enzyme that catalyzes the conversion of linear RNA to a circular form by the transfer of the 5'-phosphate to the 3'-hydroxyl terminus. It also catalyzes the covalent joining of two polyribonucleotides in phosphodiester linkage. EC 6.5.1.3.Protein Binding: The process in which substances, either endogenous or exogenous, bind to proteins, peptides, enzymes, protein precursors, or allied compounds. Specific protein-binding measures are often used as assays in diagnostic assessments.Sequence Homology, Amino Acid: The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.Organophosphorus Compounds: Organic compounds that contain phosphorus as an integral part of the molecule. Included under this heading is broad array of synthetic compounds that are used as PESTICIDES and DRUGS.Base Pair Mismatch: The presence of an uncomplimentary base in double-stranded DNA caused by spontaneous deamination of cytosine or adenine, mismatching during homologous recombination, or errors in DNA replication. Multiple, sequential base pair mismatches lead to formation of heteroduplex DNA; (NUCLEIC ACID HETERODUPLEXES).Molecular Structure: The location of the atoms, groups or ions relative to one another in a molecule, as well as the number, type and location of covalent bonds.Recombinant Proteins: Proteins prepared by recombinant DNA technology.DNA, Single-Stranded: A single chain of deoxyribonucleotides that occurs in some bacteria and viruses. It usually exists as a covalently closed circle.RNA: A polynucleotide consisting essentially of chains with a repeating backbone of phosphate and ribose units to which nitrogenous bases are attached. RNA is unique among biological macromolecules in that it can encode genetic information, serve as an abundant structural component of cells, and also possesses catalytic activity. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)Nuclear Magnetic Resonance, Biomolecular: NMR spectroscopy on small- to medium-size biological macromolecules. This is often used for structural investigation of proteins and nucleic acids, and often involves more than one isotope.Phosphorothioate Oligonucleotides: Modified oligonucleotides in which one of the oxygens of the phosphate group is replaced with a sulfur atom.Flap Endonucleases: Endonucleases that remove 5' DNA sequences from a DNA structure called a DNA flap. The DNA flap structure occurs in double-stranded DNA containing a single-stranded break where the 5' portion of the downstream strand is too long and overlaps the 3' end of the upstream strand. Flap endonucleases cleave the downstream strand of the overlap flap structure precisely after the first base-paired nucleotide, creating a ligatable nick.Hydrogen Bonding: A low-energy attractive force between hydrogen and another element. It plays a major role in determining the properties of water, proteins, and other compounds.Magnesium: A metallic element that has the atomic symbol Mg, atomic number 12, and atomic weight 24.31. It is important for the activity of many enzymes, especially those involved in OXIDATIVE PHOSPHORYLATION.Cytosine: A pyrimidine base that is a fundamental unit of nucleic acids.Hydroxylamines: Organic compounds that contain the (-NH2OH) radical.Bacteriophage phi X 174: The type species of the genus MICROVIRUS. A prototype of the small virulent DNA coliphages, it is composed of a single strand of supercoiled circular DNA, which on infection, is converted to a double-stranded replicative form by a host enzyme.Protein Structure, Secondary: The level of protein structure in which regular hydrogen-bond interactions within contiguous stretches of polypeptide chain give rise to alpha helices, beta strands (which align to form beta sheets) or other types of coils. This is the first folding level of protein conformation.Protein Structure, Tertiary: The level of protein structure in which combinations of secondary protein structures (alpha helices, beta sheets, loop regions, and motifs) pack together to form folded shapes called domains. Disulfide bridges between cysteines in two different parts of the polypeptide chain along with other interactions between the chains play a role in the formation and stabilization of tertiary structure. Small proteins usually consist of only one domain but larger proteins may contain a number of domains connected by segments of polypeptide chain which lack regular secondary structure.Cell Extracts: Preparations of cell constituents or subcellular materials, isolates, or substances.HeLa Cells: The first continuously cultured human malignant CELL LINE, derived from the cervical carcinoma of Henrietta Lacks. These cells are used for VIRUS CULTIVATION and antitumor drug screening assays.Thionucleotides: Nucleotides in which the base moiety is substituted with one or more sulfur atoms.Molecular Weight: The sum of the weight of all the atoms in a molecule.Cloning, Molecular: The insertion of recombinant DNA molecules from prokaryotic and/or eukaryotic sources into a replicating vehicle, such as a plasmid or virus vector, and the introduction of the resultant hybrid molecules into recipient cells without altering the viability of those cells.Deoxyguanosine: A nucleoside consisting of the base guanine and the sugar deoxyribose.Phosphates: Inorganic salts of phosphoric acid.Mutagenesis, Site-Directed: Genetically engineered MUTAGENESIS at a specific site in the DNA molecule that introduces a base substitution, or an insertion or deletion.Alkylation: The covalent bonding of an alkyl group to an organic compound. It can occur by a simple addition reaction or by substitution of another functional group.Electrophoresis, Polyacrylamide Gel: Electrophoresis in which a polyacrylamide gel is used as the diffusion medium.Sequence Alignment: The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.Plasmids: Extrachromosomal, usually CIRCULAR DNA molecules that are self-replicating and transferable from one organism to another. They are found in a variety of bacterial, archaeal, fungal, algal, and plant species. They are used in GENETIC ENGINEERING as CLONING VECTORS.Lucanthone: One of the SCHISTOSOMICIDES, it has been replaced largely by HYCANTHONE and more recently PRAZIQUANTEL. (From Martindale The Extrapharmacopoeia, 30th ed., p46)Oligonucleotides, Antisense: Short fragments of DNA or RNA that are used to alter the function of target RNAs or DNAs to which they hybridize.Bacterial Proteins: Proteins found in any species of bacterium.Mutagens: Chemical agents that increase the rate of genetic mutation by interfering with the function of nucleic acids. A clastogen is a specific mutagen that causes breaks in chromosomes.Chromatography, Ion Exchange: Separation technique in which the stationary phase consists of ion exchange resins. The resins contain loosely held small ions that easily exchange places with other small ions of like charge present in solutions washed over the resins.DNA Primers: Short sequences (generally about 10 base pairs) of DNA that are complementary to sequences of messenger RNA and allow reverse transcriptases to start copying the adjacent sequences of mRNA. Primers are used extensively in genetic and molecular biology techniques.DNA, Viral: Deoxyribonucleic acid that makes up the genetic material of viruses.
DNA-(apurinic or apyrimidinic site) lyase is an enzyme that in humans is encoded by the APEX1 gene. Apurinic/apyrimidinic (AP) ... Class II AP endonucleases cleave the phosphodiester backbone 5' to the AP site, thereby initiating a process known as base ... Mol CD, Hosfield DJ, Tainer JA (2000). "Abasic site recognition by two apurinic/apyrimidinic endonuclease families in DNA base ... sites (also called "abasic sites") occur frequently in DNA molecules by spontaneous hydrolysis, by DNA damaging agents or by ...
... apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination ... and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; EC). Fpg ... DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These ... The FPG IleRS zinc finger domain represents a zinc finger domain found at the C-terminal in both DNA glycosylase/AP lyase ...
... apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination ... and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity;EC 4.2. ... is a DNA-binding domain found in DNA glycosylase/AP lyase enzymes, which are involved in base excision repair of DNA damaged by ... These enzymes are primarily from bacteria, and have both DNA glycosylase activity EC 3.2.2.- and AP lyase activity EC 4.2.99.18 ...
... of damaged or mismatched nucleotides in DNA is to create a nick in the phosphodiester backbone of the AP site created when DNA ... Levin, Joshua D; Demple, Bruce (1990). "Analysis of class II (hydrolytic) and class I (beta-lyase) apurinic/apyrimidinic ... Class I AP endonucleases (EC 4.2.99.18) cleave 3' to AP sites by a β-lyase mechanism, leaving an unsaturated aldehyde, termed a ... Apurinic/apyrimidinic (AP) endonuclease is an enzyme that is involved in the DNA base excision repair pathway (BER). Its main ...
... creating an apurinic/apyrimidinic site, commonly referred to as an AP site. This is accomplished by flipping the damaged base ... whereas bifunctional glycosylases also possess AP lyase activity that permits them to cut the phosphodiester bond of DNA, ... Uracil-DNA glycosylases are DNA repair enzymes that excise uracil residues from DNA by cleaving the N-glycosydic bond, ... and this hydrolysed the N-glycosidic bond connecting the base to the deoxyribose sugar of the DNA backbone. The function of UDG ...
DNA-(apurinic or apyrimidinic site) lyase is an enzyme that in humans is encoded by the APEX1 gene. Apurinic/apyrimidinic (AP) ... Class II AP endonucleases cleave the phosphodiester backbone 5 to the AP site, thereby initiating a process known as base ... Mol CD, Hosfield DJ, Tainer JA (2000). "Abasic site recognition by two apurinic/apyrimidinic endonuclease families in DNA base ... sites (also called "abasic sites") occur frequently in DNA molecules by spontaneous hydrolysis, by DNA damaging agents or by ...
... apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination ... and cleaves both the 3- and 5-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; EC 4.2. ... zinc ion binding (GO:0008270), DNA-(apurinic or apyrimidinic site) endonuclease activity (GO:0003906), hydrolase activity, ... and Arg-258 form hydrogen bonds tothe phosphodiester backbone of DNA, which is sharply kinked at the lesion site.Residues Met- ...
... apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination ... and cleaves both the 3- and 5-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; EC 4.2. ... and Arg-258 form hydrogen bonds tothe phosphodiester backbone of DNA, which is sharply kinked at the lesion site.Residues Met- ... apurinic or apyrimidinic site) endonuclease activity (GO:0003906), damaged DNA binding (GO:0003684). ...
... apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination ... and cleaves both the 3- and 5-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; EC). Fpg ... DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These ... The FPG IleRS zinc finger domain represents a zinc finger domain found at the C-terminal in both DNA glycosylase/AP lyase ...
DNA-(apurinic or apyrimidinic site) lyase,OTTHUMP00000163988,apurinic/apyrimidinic (abasic) endonuclease,apurinic/apyrimidinic ... Class II AP endonucleases cleave the phosphodiester backbone 5 to the AP site. This gene encodes the major AP endonuclease in ... Apurinic/apyrimidinic (AP) sites occur frequently in DNA molecules by spontaneous hydrolysis, by DNA damaging agents or by DNA ... AP sites are pre-mutagenic lesions that can prevent normal DNA replication so the cell contains systems to identify and repair ...
... multifunctional DNA repair enzyme) 1 (APEX1), transcript variant 3, mRNA. (H00000328-R03) - Products - Abnova ... DNA-(apurinic or apyrimidinic site) lyase,OTTHUMP00000163988,apurinic/apyrimidinic (abasic) endonuclease,apurinic/apyrimidinic ... Class II AP endonucleases cleave the phosphodiester backbone 5 to the AP site. This gene encodes the major AP endonuclease in ... Apurinic/apyrimidinic (AP) sites occur frequently in DNA molecules by spontaneous hydrolysis, by DNA damaging agents or by DNA ...
Apurinic/Apyrimidinic Endodeoxyribonuclease 2, including: function, proteins, disorders, pathways, orthologs, and expression. ... apurinic or apyrimidinic site) lyase 2 (EC 4.2.99.18) (B7ZA71_HUMAN). *DNA-apurinic or apyrimidinic site lyase 2 (E5KN95_HUMAN) ... Class II AP endonucleases cleave the phosphodiester backbone 5 to the AP site. This gene encodes a protein shown to have a ... Apurinic/apyrimidinic (AP) sites occur frequently in DNA molecules by spontaneous hydrolysis, by DNA damaging agents or by DNA ...
... and processed with AP lyase activity that cleaves the 3 side of AP sites [22] or with APE1 that cleaves the phosphate backbone ... Cloning and characterization of mammalian 8-hydroxyguanine-specific DNA glycosylase/apurinic, apyrimidinic lyase, a functional ... base damage and is recognized by monofunctional DNA glycosylases that lack lyase activity which leaves the phosphodiester bond ... side of the intact apurinic/apyrimidinic site, this will be incised by apurinic/apyrimidinic endonuclease (APE1/APEX1). Finally ...
... generating an apurinic (AP site), where the phosphodiester backbone is optionally intact. The AP-lyase activity cleaves both 3 ... apyrimidinic) site while leaving the phosphodiester backbone intact, and where the lyase activity of Endonuclease VIII breaks ... to form an apurinic site. One suitable enzyme is formamidopyrimidine [fapy]-DNA glycosylase, also known as 8-oxoguanine DNA ... Optionally, the abasic site is modified by a lyase to generate a base gap. The lyase for example cleaves 3 and/or 5 to the ...
Each day our DNA is damaged by UV radiation, free radicals and other carcinogenic substances, but even without such external ... the apurinic/apyrimidinic (AP) endonuclease, which cleaves the DNA backbone at the 5′ side of the abasic position. The AP ... Verly, W.G., Y. Paquette, and L. Thibodeau, Nuclease for DNA apurinic sites may be involved in the maintenance of DNA in normal ... With UV-irradiated DNA as a substrate, the proteins hydrolysed two phosphodiester-bonds on the damaged DNA strand. The ...
... apyrimidinic (AP) site, whereas others cleave off the base by a lyase mechanism and catalyze a subsequent AP lyase reaction. In ... but is thought to recognize the phosphodiester backbone conformations created by the damage. Recognition of abnormal backbone ... Some DNA glycosylases are simple glycosylases, catalyzing only the hydrolytic removal of the base so as to form an apurinic/ ... DNA Backbone Damages Backbone damages include abasic sites and single- and double-strand DNA breaks. Abasic sites are generated ...
Initiates repair of AP sites in DNA by catalyzing hydrolytic incision of the phosphodiester backbone immediately adjacent to ... Plays a role in regulating MYC mRNA turnover by preferentially cleaving in between UA and CA dinucleotides of the MYC coding ... The C-O-P bond 3 to the apurinic or apyrimidinic site in DNA is broken by a beta-elimination reaction, leaving a 3-terminal ... Functions as a apurinic/apyrimidinic (AP) endodeoxyribonuclease in the DNA base excision repair (BER) pathway of DNA lesions ...
DNA (apurinic or apyrimidinic site) lyase antibody. *DNA-(apurinic or apyrimidinic site) lyase, mitochondrial antibody ... Initiates repair of AP sites in DNA by catalyzing hydrolytic incision of the phosphodiester backbone immediately adjacent to ... Plays a role in regulating MYC mRNA turnover by preferentially cleaving in between UA and CA dinucleotides of the MYC coding ... Functions as a apurinic/apyrimidinic (AP) endodeoxyribonuclease in the DNA base excision repair (BER) pathway of DNA lesions ...
... apurinic/apyrimidinic) site. The AP-lyase activity cleaves the phosphodiester bond 3 to the AP site by a beta-elimination, ... apurinic/apyrimidinic) lyase activity and introduces nicks in the DNA strand. Cleaves the DNA backbone by beta-delta ... apurinic/apyrimidinic) site. The AP-lyase activity cleaves the phosphodiester bond 3 to the AP site by a beta-elimination, ... apurinic/apyrimidinic) site. The AP-lyase activity cleaves the phosphodiester bond 3 to the AP site by a beta-elimination, ...
DNA-(apurinic or apyrimidinic site) lyase. General function:. Replication, recombination and repair. Specific function:. ... Initiates repair of AP sites in DNA by catalyzing hydrolytic incision of the phosphodiester backbone immediately adjacent to ... Can also cleave the linkage between a glucuronic acid unit and an N-sulfo glucosamine unit carrying a 2-O-sulfo group, but not ... Functions as a apurinic/apyrimidinic (AP) endodeoxyribonuclease in the DNA base excision repair (BER) pathway of DNA lesions ...
... which cleaves the phosphodiester backbone 5 to Py,,Py. To detect apurinic/apyrimidinic (AP) sites, DNA was first digested with ... The nucleotide excision repair (NER) and spore photoproduct (SP) lyase DNA repair pathways are major determinants of spore ... In contrast, no apurinic/apyrimidinic sites were detected in any of our DNA preparations as revealed by digestion with Endo IV ... Photoiupac home page. Discussion. Photobiology.com home DNA in dormant Bacillus subtilis spores exposed to solar radiation ...
Other than apurinic/apyrimidinic (AP) lyases, human cells contain two known AP endonucleases, APE1 and APE2, that cleave the ... Lines above and below the text represent the DNA backbone, triangles show sites of ligation by X4L4, and red bars between the ... phosphodiester bond between the 5′-phosphate of the AP site and the preceding nucleotide, leaving a 3′-hydroxyl end [92]. Both ... Ku also has a potent lyase activity that serves to cleave abasic sites near DNA ends [18]. This lyase activity also removes ...
DNA Repair * DNA-(Apurinic or Apyrimidinic Site) Lyase * Deoxyribonuclease IV (Phage T4-Induced) ... endonuclease family that primes DNA repair synthesis by cleaving the DNA backbone 5 of AP sites. The crystal structures of ... These structures suggest three Zn2+ ions directly participate in phosphodiester bond cleavage and prompt hypotheses that double ... Enzyme loops intercalate side chains at the abasic site, compress the DNA backbone, bend the DNA approximately 90 degrees, and ...
Multifunctional DNA Repair Enzyme) 1 Antikörper für Western Blotting (WB) vergleichen & kaufen. ... Class II AP endonucleases cleave the phosphodiester backbone 5 to the AP site. This gene encodes the major AP endonuclease in ... APEX nuclease (multifunctional DNA repair enzyme) 1 L homeolog * DNA-(apurinic or apyrimidinic site) lyase ... Apurinic/apyrimidinic (AP) sites occur frequently in DNA molecules by spontaneous hydrolysis, by DNA damaging agents or by DNA ...
... and cleaves both the 3′‐ and 5′‐phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity). The ... The H2TH motif of the C‐terminal domain is situated near the active site and may interact with the DNA backbone with the ... A DNA glycosylase which excises imidazole ring‐opened purines and nicks DNA at apurinic/apyrimidinic sites. J Biol Chem, 265, ... DNA glycosylase of Escherichia coli and an activity nicking DNA at apurinic/apyrimidinic sites. Proc Natl Acad Sci USA, 86, ...
... apurinic/apyrimidinic (AP) sites, mutagenized nucleotides, modified nucleotides, nicks, gaps and DNA-DNA or DNA-protein cross- ... Abasic sites can be recognized and cleaved by AP endonucleases and/or AP lyases. Class II AP endonucleases cleave at AP sites ... activity that cleaves the phosphate backbone at the abasic site. This leaves an extendable 3 OH on the DNA fragment 5 to the ... 0081] Lyases break the phosphodiester bond in a polynucleotide. [0082] Examples of AP endonucleases belong to 4 classes. [0083] ...
Abasic sites can be recognized and cleaved by AP endonucleases and/or AP lyases. Class II AP endonucleases cleave at AP sites ... an apurinic/apyrimidinic endonuclease, UDG, FPG, and T4 pdg.. As an example, Chromatin IP (ChIP) is performed on HeLa cell DNA ... This is achieved in one embodiment by Endo IV activity that cleaves the phosphate backbone at the abasic site. This leaves an ... Another type of repair enzyme is a lyase. This enzyme can break the phosphodiester bond in a polynucleotide.. Examples of AP ...
Oxidized base-specific DNA glycosylases have intrinsic AP lyase activity and cleaves the DNA strand 3 to the AP site (Hazra TK ... It acts on apurinic/apyrimidinic (AP) sites in DNA as a major member of the base excision repair (BER) pathway, is involved in ... then hydrolyzes the phosphodiester backbone immediately 5 to an AP site to produce 3OH group and 5 deoxyribose-5-phosphate ( ... Mutagenesis by apurinic/ apyrimidinic sites. Annu Rev Genet 20: 201-230, 1986.  L pez-Abente G, Poll n M, Aragon s N, G mez BP ...
... has an associated lyase activity that breaks the phosphodiester backbone 3′ to the abasic site with generation of 5′-phosphate ... 1997) 3′-phosphodiesterase activity of human apurinic/apyrimidinic endonuclease at DNA double-strand break ends. Nucleic Acids ... 2005) Human Tdp1 cleaves a broad spectrum of substrates, including phosphoamide linkages. J Biol Chem 280:36518-36528. ... Human tyrosyl-DNA phosphodiesterase (TDP1) hydrolyzes the phosphodiester bond at a DNA 3′-end linked to a tyrosyl moiety and ...
Cell division involves the duplication of the entire DNA so that two genetically identical daughter cells arise from a single ... An apurinic/apyrimidinic site (AP site) is formed.. * AP sites belong to the most common physiologically-occurring DNA lesions ... AP lyase cuts the DNA backbone on the 3 end of the AP site ... Cleaves only one of both DNA strands *Has a nuclease (cuts the ... Links newly synthesized DNA fragments (ATP or NAD+-dependent reaction) by catalyzing the formation of phosphodiester bonds DNA ...
  • Shows fairly strong 3-phosphodiesterase activity involved in the removal of 3-damaged termini formed in DNA by oxidative agents. (genecards.org)
  • Microbial dysbiosis promotes the release of bacterial genotoxins, metabolites, and causes chronic inflammation, which promote oxidative DNA damage. (jcancer.org)
  • In aerobic organisms, cellular DNA is frequently damaged by activated oxygen species from aerobic energy metabolism or oxidative stress. (embopress.org)
  • In particular, the 8‐oxoguanine (GO) lesion is one of the most stable products of oxidative DNA damage ( Dizdaroglu, 1985 ). (embopress.org)
  • We also show that mitochondrial base excision repair depends on TDP1 activity and provide evidence that TDP1 is required for efficient repair of oxidative damage in mitochondrial DNA. (pnas.org)
  • Because of the proximity of reactive oxygen species (ROS) generated by the mitochondrial oxidative phosphorylation chain, mtDNA is potentially exposed to oxidative DNA damage ( 3 , 4 ). (pnas.org)
  • Abasic endonuclease 1 (APE1) is the a well characterized enzyme in mammals for the repair of 3′-phosphoglycolate esters (3′-PG) during oxidative DNA damage ( 25 - 27 ). (pnas.org)
  • The four types of pathways elicited by DNA damage known, or presumed, to ameliorate harmful damage effects are DNA repair, DNA damage checkpoints, transcriptional response, and apoptosis (1) (Figure 1). (studylibtr.com)
  • DNA repair pathways have evolved to cope with recurring DNA damage, providing protection against carcinogenesis, neurodegeneration, and premature aging - . (prolekare.cz)
  • Shows robust 3-5 exonuclease activity on 3-recessed heteroduplex DNA and is able to remove mismatched nucleotides preferentially. (genecards.org)
  • Plays a role in regulating MYC mRNA turnover by preferentially cleaving in between UA and CA dinucleotides of the MYC coding region determinant (CRD). (rcsb.org)
  • These results were interpreted to indicate that environmentally-relevant UV wavelengths also induced non-SP photoproduct(s) in spore DNA which were preferentially repaired by NER (Xue and Nicholson, 1996). (photobiology.com)
  • The DNA damage checkpoints employ damage sensor proteins, such as ATM, ATR, the Rad17-RFC complex, and the 9-1-1 complex, to detect DNA damage and to initiate signal transduction cascades that employ Chk1 and Chk2 Ser/Thr kinases and Cdc25 phosphatases. (studylibtr.com)
  • Mitochondrial DNA (mtDNA) is an essential component of eukaryotic cells because it encodes a critical subset of mitochondrial proteins for the production of cellular ATP. (pnas.org)
  • Moreover, the mitochondrial genome does not encode DNA repair proteins, and is thus completely dependent on proteins encoded in the nucleus for its repair and integrity. (pnas.org)
  • Yet, the full spectrum of nuclear DNA repair proteins involved in mtDNA repair is not entirely known. (pnas.org)
  • DME and ROS1 encode two closely related DNA glycosylase domain proteins, but it is unknown whether they participate directly in a DNA demethylation process or counteract silencing through an indirect effect on chromatin structure. (pnas.org)
  • Paul Modrich has demonstrated how the cell corrects errors that occur when DNA is replicated during cell division. (slideshare.net)
  • On the basis of the three‐dimensional structure and taking account of previous biochemical experiments, we propose a DNA‐binding mode and reaction mechanism for MutM. (embopress.org)
  • Initiates repair of AP sites in DNA by catalyzing hydrolytic incision of the phosphodiester backbone immediately adjacent to the damage, generating a single-strand break with 5-deoxyribose phosphate and 3-hydroxyl ends. (genecards.org)
  • The cellular consequences of DNA oxidation by RONs can lead to a number of different types of damage such as generation of 7, 8-hydroxy-2'-deoxyguanosine (8-Oxod-G), thymine glycol (Tg), abasic sites (AP), and oxidized deoxyribose sugars which lead to single and double strand DNA breaks (SSBs and DSBs) [ 8 ], crosslinking of DNA, and mutation [ 9 - 13 ]. (jcancer.org)
  • Acts as a loading factor for POLB onto non-incised AP sites in DNA and stimulates the 5'-terminal deoxyribose 5'-phosphate (dRp) excision activity of POLB . (rcsb.org)
  • Another proposed mechanism is disruption of the labile N -glycosidic bond between the 5-meC base and the deoxyribose moiety in DNA, followed by replacement with an unmodified cytosine. (pnas.org)
  • Our previous work showed that a 3′-DNA phosphatase, ZDP, functions downstream of ROS1 during active DNA demethylation in Arabidopsis. (prolekarniky.cz)
  • Our results show that APE1L and ZDP act jointly downstream of DME to regulate gene imprinting in plants, and suggest that DME-initiated active DNA demethylation in the central cell and endosperm uses both APE- and ZDP-dependent mechanisms. (prolekarniky.cz)
  • Finally, BER is completed upon ligation of the nick by DNA Ligase I or the Xrcc1/Ligase IIIα complex ( Figure 1A ). (prolekare.cz)
  • However, the 3′-PG removal activity of APE1 is highly selective and APE1 is relatively ineffective when the 3′-PG is in single-stranded DNA, at 3′-overhangs or at blunt or recessed 3′-ends of DSBs ( 27 , 29 - 32 ). (pnas.org)
  • Functional dissection of siRNA sequence by systematic DNA substitution: modified siRNA with a DNA seed arm is a powerful tool for mammalian gene silencing with significantly reduced off-target effect. (abnova.com)
  • Acts as DNA glycosylase that recognizes and removes damaged bases. (string-db.org)
  • Free radical-mediated DSBs typically bear unligatable 3′-phosphate or 3′-phosphoglycolate termini and often have oxidized bases and/or abasic sites near the break. (hindawi.com)
  • This process uses uracil DNA glycosylase (UDG) to eliminate those PCR products containing uracil to prevent contaminating subsequent PCR reactions* U.S. patent publication No. 2004-0067559 Al also relies on modified bases in primer DNA prior to amplification and uses, for example, dUTP for incorporation into the amplicon. (allindianpatents.com)
  • Methylation patterns are established and maintained by DNA methyltransferases that catalyze transfer of a methyl group from S -adenosyl- l -methionine to cytosine bases in DNA. (pnas.org)
  • [email protected] Key Words damage recognition, excision repair, PIKK family, Rad17-RFC/9-11 complex, signal transduction f Abstract DNA damage is a relatively common event in the life of a cell and may lead to mutation, cancer, and cellular or organismic death. (studylibtr.com)
  • DNA cytosine methylation (5-methylcytosine, 5-meC) is an important epigenetic mark, and methylation patterns are coordinately controlled by methylation and demethylation reactions during development and reproduction. (prolekarniky.cz)
  • Most of mammalian and plant DNA methylation is restricted to symmetrical CpG sequences, but plants also have significant levels of cytosine methylation in the symmetric context CpNpG (where N is any nucleotide) and even in asymmetric contexts ( 2 , 7 ). (pnas.org)
  • The reason our genetic material does not disintegrate into complete chemical chaos is that a host of molecular systems continuously monitor and repair DNA. (slideshare.net)
  • 2. 1 (15) The Royal Swedish Academy of Sciences has decided to award Tomas Lindahl, Paul Modrich and Aziz Sancar the Nobel Prize in Chemistry 2015 for their "Mechanistic studies of DNA repair" Damage to the genetic material poses a threat to all organisms. (slideshare.net)
  • While UV irradiation of dormant B. subtilis endospores results mainly in formation of the 'spore photoproduct' (SP) 5-thyminyl-5,6-dihydrothymine, genetic evidence indicates that additional DNA photoproduct(s) may be formed in spores exposed to solar UV-B and UV-A radiation (Xue,Y. and W.L. Nicholson, Appl. (photobiology.com)
  • Understandably, loss of function mutations have been extensively studied, whereas genetic variants that result in increased DNA repair activity have not received the same attention, primarily because decreased DNA repair is thought to be more relevant for increased cancer risk. (prolekare.cz)
  • Has a 3'-5' exoribonuclease activity on mismatched deoxyribonucleotides at the 3' termini of nicked or gapped DNA molecules during short-patch BER. (rcsb.org)
  • DME and ROS1 show a preference for 5-meC over thymine in the symmetric dinucleotide CpG context, where most plant DNA methylation occurs. (pnas.org)
  • External factors as well as internal cellular processes lead to alterations in the chemical structure of DNA . (amboss.com)
  • Py), AP sites and strand breaks in DNA are possible candidates for solar radiation-induced damage in spore DNA. (photobiology.com)
  • Most DNA double-strand breaks (DSBs) formed in a natural environment have chemical modifications at or near the ends that preclude direct religation and require removal or other processing so that rejoining can proceed. (hindawi.com)
  • Damage to DNA induces several cellular responses that enable the cell either to eliminate or cope with the damage or to activate a programmed cell death process, presumably to eliminate cells with potentially catastrophic mutations. (studylibtr.com)
  • 40 41 42 42 42 42 44 44 44 46 46 47 47 48 51 56 58 59 59 62 68 70 75 77 77 INTRODUCTION The primary structure of DNA is constantly subjected to alteration by cellular metabolites and exogenous DNA-damaging agents. (studylibtr.com)
  • DNA damage continually arises from environmental agents and reactive byproducts of normal cellular function. (prolekare.cz)
  • In plants, DNA methylation can occur within CG, CHG, and CHH motifs (H represents A, T, or C). Genome-wide mapping of DNA methylation in Arabidopsis has revealed that methylation in gene bodies is predominantly at CG context whereas methylation in transposon- and other repeat-enriched heterochromatin regions can be within all three motifs . (prolekarniky.cz)
  • DNA repair mechanisms are thus important to ensure a sufficient degree of genomic stability. (amboss.com)
  • In eukaryotes, DNA methylation is detected in protists, fungi, plants, and animals ( 3 ) and plays important roles in the establishment of developmental programs ( 4 , 5 ) and in genome defense against parasitic mobile elements ( 6 ). (pnas.org)