Deamination: The removal of an amino group (NH2) from a chemical compound.Cytidine Deaminase: An enzyme that catalyzes the deamination of cytidine, forming uridine. EC 3.5.4.5.Cytosine: A pyrimidine base that is a fundamental unit of nucleic acids.5-Methylcytosine: A methylated nucleotide base found in eukaryotic DNA. In ANIMALS, the DNA METHYLATION of CYTOSINE to form 5-methylcytosine is found primarily in the palindromic sequence CpG. In PLANTS, the methylated sequence is CpNpGp, where N can be any base.Cytidine: A pyrimidine nucleoside that is composed of the base CYTOSINE linked to the five-carbon sugar D-RIBOSE.Adenosine Deaminase: An enzyme that catalyzes the hydrolysis of ADENOSINE to INOSINE with the elimination of AMMONIA.Uracil-DNA Glycosidase: An enzyme that catalyzes the HYDROLYSIS of the N-glycosidic bond between sugar phosphate backbone and URACIL residue during DNA synthesis.RNA Editing: A process that changes the nucleotide sequence of mRNA from that of the DNA template encoding it. Some major classes of RNA editing are as follows: 1, the conversion of cytosine to uracil in mRNA; 2, the addition of variable number of guanines at pre-determined sites; and 3, the addition and deletion of uracils, templated by guide-RNAs (RNA, GUIDE).Nitrous Acid: Nitrous acid (HNO2). A weak acid that exists only in solution. It can form water-soluble nitrites and stable esters. (From Merck Index, 11th ed)Inosine: A purine nucleoside that has hypoxanthine linked by the N9 nitrogen to the C1 carbon of ribose. It is an intermediate in the degradation of purines and purine nucleosides to uric acid and in pathways of purine salvage. It also occurs in the anticodon of certain transfer RNA molecules. (Dorland, 28th ed)Nucleoside Deaminases: Catalyze the hydrolysis of nucleosides with the elimination of ammonia.Guanine Deaminase: An enzyme that catalyzes the deamination of guanine to form xanthine. EC 3.5.4.3.Amine Oxidase (Copper-Containing): A group of enzymes including those oxidizing primary monoamines, diamines, and histamine. They are copper proteins, and, as their action depends on a carbonyl group, they are sensitive to inhibition by semicarbazide.UracilAdenosine Deaminase Inhibitors: Drugs that inhibit ADENOSINE DEAMINASE activity.Cytosine Deaminase: An enzyme which catalyzes the deamination of CYTOSINE resulting in the formation of URACIL. It can also act on 5-methylcytosine to form THYMIDINE.Somatic Hypermutation, Immunoglobulin: A programmed mutation process whereby changes are introduced to the nucleotide sequence of immunoglobulin gene DNA during development.Amination: The creation of an amine. It can be produced by the addition of an amino group to an organic compound or reduction of a nitro group.Thymine DNA Glycosylase: An enzyme that removes THYMINE and URACIL bases mispaired with GUANINE through hydrolysis of their N-glycosidic bond. These mispaired nucleotides generally occur through the hydrolytic DEAMINATION of 5-METHYLCYTOSINE to thymine.Monoamine Oxidase: An enzyme that catalyzes the oxidative deamination of naturally occurring monoamines. It is a flavin-containing enzyme that is localized in mitochondrial membranes, whether in nerve terminals, the liver, or other organs. Monoamine oxidase is important in regulating the metabolic degradation of catecholamines and serotonin in neural or target tissues. Hepatic monoamine oxidase has a crucial defensive role in inactivating circulating monoamines or those, such as tyramine, that originate in the gut and are absorbed into the portal circulation. (From Goodman and Gilman's, The Pharmacological Basis of Therapeutics, 8th ed, p415) EC 1.4.3.4.Coformycin: A ribonucleoside antibiotic synergist and adenosine deaminase inhibitor isolated from Nocardia interforma and Streptomyces kaniharaensis. It is proposed as an antineoplastic synergist and immunosuppressant.Nucleotide Deaminases: Catalyze the hydrolysis of nucleotides with the elimination of ammonia.AminohydrolasesDNA 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.Sulfites: Inorganic salts of sulfurous acid.AMP Deaminase: An enzyme that catalyzes the deamination of AMP to IMP. EC 3.5.4.6.Glutamate Dehydrogenase: An enzyme that catalyzes the conversion of L-glutamate and water to 2-oxoglutarate and NH3 in the presence of NAD+. (From Enzyme Nomenclature, 1992) EC 1.4.1.2.Tetrahydrouridine: An inhibitor of nucleotide metabolism.Ammonia: A colorless alkaline gas. It is formed in the body during decomposition of organic materials during a large number of metabolically important reactions. Note that the aqueous form of ammonia is referred to as AMMONIUM HYDROXIDE.N-Glycosyl Hydrolases: A class of enzymes involved in the hydrolysis of the N-glycosidic bond of nitrogen-linked sugars.Ethanolamine Ammonia-Lyase: An enzyme that catalyzes the deamination of ethanolamine to acetaldehyde. EC 4.3.1.7.Substrate Specificity: A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.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.Pentoxyl: 5-Hydroxymethyl-6-methyl- 2,4-(1H,3H)-pyrimidinedione. Uracil derivative used in combination with toxic antibiotics to lessen their toxicity; also to stimulate leukopoiesis and immunity. Synonyms: pentoksil; hydroxymethylmethyluracil.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.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.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).ThymineAmino Acid Oxidoreductases: A class of enzymes that catalyze oxidation-reduction reactions of amino acids.Alanine Dehydrogenase: An NAD-dependent enzyme that catalyzes the reversible DEAMINATION of L-ALANINE to PYRUVATE and AMMONIA. The enzyme is needed for growth when ALANINE is the sole CARBON or NITROGEN source. It may also play a role in CELL WALL synthesis because L-ALANINE is an important constituent of the PEPTIDOGLYCAN layer.Ammonia-Lyases: Enzymes that catalyze the formation of a carbon-carbon double bond by the elimination of AMMONIA. EC 4.3.1.DNA-Cytosine Methylases: Methylases that are specific for CYTOSINE residues found on DNA.Kinetics: The rate dynamics in chemical or physical systems.Leucine Dehydrogenase: An octameric enzyme belonging to the superfamily of amino acid dehydrogenases. Leucine dehydrogenase catalyzes the reversible oxidative deamination of L-LEUCINE, to 4-methyl-2-oxopentanoate (2-ketoisocaproate) and AMMONIA, with the corresponding reduction of the cofactor NAD+.Adenosine: A nucleoside that is composed of ADENINE and D-RIBOSE. Adenosine or adenosine derivatives play many important biological roles in addition to being components of DNA and RNA. Adenosine itself is a neurotransmitter.Monoamine Oxidase Inhibitors: A chemically heterogeneous group of drugs that have in common the ability to block oxidative deamination of naturally occurring monoamines. (From Gilman, et al., Goodman and Gilman's The Pharmacological Basis of Therapeutics, 8th ed, p414)Deoxyuridine: 2'-Deoxyuridine. An antimetabolite that is converted to deoxyuridine triphosphate during DNA synthesis. Laboratory suppression of deoxyuridine is used to diagnose megaloblastic anemias due to vitamin B12 and folate deficiencies.Immunoglobulin Class Switching: Gene rearrangement of the B-lymphocyte which results in a substitution in the type of heavy-chain constant region that is expressed. This allows the effector response to change while the antigen binding specificity (variable region) remains the same. The majority of class switching occurs by a DNA recombination event but it also can take place at the level of RNA processing.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.Guaninevif Gene Products, Human Immunodeficiency Virus: Proteins encoded by the VIF GENES of the HUMAN IMMUNODEFICIENCY VIRUS.
  • Comparison of the differential context-dependence of DNA deamination by APOBEC enzymes: correlation with mutation spectra in vivo. (nih.gov)
  • Further detailed studies revealed that APOBEC molecules are packaged into HIV-1 virions in virus producer cells via a specific interaction with Gag and viral RNA and then exert their deaminase activity in subsequent target cells on a single-stranded DNA (ssDNA) intermediate synthesized by reverse transcriptase ( 3 , 28 , 55 ). (asm.org)
  • Most mutations involved the C of TpC, the substrate of some single strand-specific APOBEC cytidine deaminases, similar to the mutations that can typify the 'mutator phenotype' of numerous tumors. (elifesciences.org)
  • Agitated APOBEC enzymes cause mutations at C's preceded by T. Loss of mismatch repair causes microsatellite instability (MSI), marked by expansion and contraction of simple-sequence repeats, as well as characteristic types of single-base changes. (massgeneral.org)
  • Single-stranded DNA binding proteins (SSBs) are ubiquotous systems involved in DNA replication, recombination, transcription and various modifications of DNA such as deamination (APOBEC proteins). (uiuc.edu)
  • In short, an enzyme called "activation-induced deoxycytidine deaminase" (or AID) moves up and down single-stranded DNA that encodes the pattern for antibodies and sporadically alters the strand by converting one nitrogen base to another, which is called "deamination. (medindia.net)
  • These skews reflect mainly those in protein coding sequences, which are driven by asymmetric mutation pressures during replication and transcription (notably asymmetric cytosine deamination) plus subsequent selection for preferred structures, signals, amino acid or codons. (biomedcentral.com)
  • DSBs can also be generated when DNA replication forks encounter DNA lesions, such as DNA single strand breaks or DNA cross-links ( Khanna and Jackson, 2001 ). (rupress.org)
  • 6 Theoretically, if the effective size of the stem cell population had been large enough, and it had been given enough replication cycles, it would have been reasonable to assume that almost every possible mutation can be found at the single cell level. (haematologica.org)
  • The positive control is a sequence with a U synthetically incorporated at the same position as the target C. b , Coomassie-stained denaturing PAGE of the expressed and purified proteins used in (c), (d), (e), and (f). c-f , Gel-based deaminase assay showing the deamination window of base editors with deaminase-Cas9 linkers of GGS (c), (GGS) 3 (d), XTEN (e), or (GGS) 7 (f). (nih.gov)
  • AID associates with single-stranded DNA with high affinity and a long complex half-life in a sequence-independent manner. (genome.jp)
  • 1b shows same sequence experiencing measured rates of deamination. (wordpress.com)
  • We use these data to quantify the relationship between sequence and functional divergence, and to identify CpG deamination as a potentially important force in driving changes in enhancer activity during primate evolution. (biomedcentral.com)
  • Formalin treatment and storage introduce cytosine deamination , which leads to DNA sequence changes and potentially wrong data interpretation. (thefreedictionary.com)
  • There was a single-base pair substitution in the Hindlll recognition sequence in the cDNA in four out of the 15 strains. (nii.ac.jp)
  • Deamination is the removal of an amino group from a molecule. (wikipedia.org)
  • A single-stranded DNA molecule with 2 million bases will experience a single deamination event involving cytosine every 2.8 hours (at pH 7.4 and 37 degree C). In contrast, it would take 140 hours for an adenine to experience deamination. (wordpress.com)
  • Notably, up to 14 bases were substituted simultaneously in a single DNA molecule, with a low indel frequency of 0.6%, when 32 gRNAs were co-transfected. (g3journal.org)
  • Here, we develop a single-molecule detection method for the simultaneous detection of human 8-oxoguanine DNA glycosylase 1 (hOGG1) and human alkyladenine DNA glycosylase (hAAG) on the basis of DNA glycosylase-mediated cleavage of molecular beacons. (rsc.org)
  • Both of the Cy3 and Cy5 signals can be simply quantified by total internal reflection fluorescence-based single-molecule detection. (rsc.org)
  • Time lapse AFM is the technique with a great potential for single molecule biophysics. (uiuc.edu)
  • Ammonia is toxic to the human system, and enzymes convert it to urea or uric acid by addition of carbon dioxide molecules (which is not considered a deamination process) in the urea cycle, which also takes place in the liver. (wikipedia.org)
  • Such pre-treatment may alter the course of fermentation by two mechanisms-first, by rendering protein more available for degradative attack by micro organisms leading to escape of the by product of metabolic deamination and second, by effectively eliminating much of the heat-sensitive indigenous micro flora . (thefreedictionary.com)
  • The deaminated metabolite of benfluorex was not found as a metabolite of fenfluramine indicating that the N-ethyl-substitution had influenced the deamination route as well as the overall metabolic fate of the 1-(m-trifluoro-methylphenyl)-2-aminopropane nucleus. (surrey.ac.uk)
  • Ultra-performance liquid chromatography-mass spectrometry and radiodetection techniques were used to investigate the profiles and structures of metabolites in plasma, urine, and feces after a single oral dose of 14 C-pimasertib. (aspetjournals.org)
  • The identified metabolites were the products of N-deethylation (norfenfluramine) and deamination with subsequent side chain oxidation. (surrey.ac.uk)
  • Norfenfluramine and a single deamination product were minor urinary metabolites, although the deamination product was quantitatively important in plasma. (surrey.ac.uk)
  • The analysis includes the single- and multicopy seed storage proteins (zeins), the miniature inverted-repeat transposable elements (MITEs), and long terminal repeat (LTR) retrotransposons. (genetics.org)
  • After the penetration of retroviral nucleocapsids into target cells of infection and the initiation of reverse transcription, it can induce the conversion of cytosine to uracil in the minus-sense single-strand viral DNA, leading to G-to-A hypermutations in the subsequent plus-strand viral DNA. (uniprot.org)
  • AID is believed to initiate the formation of single-strand DNA breaks that are converted to the double-strand breaks (DSBs) that are necessary for the intrachromosomal deletions that result in CSR. (rupress.org)
  • Repair of damage to a single strand by base excision repair or nucleotide excision repair, for example, depends on just the two copies of genetic information contained in the two strands of the DNA double helix. (coursehero.com)
  • The bottom line is that spontaneous deamination of cytosine can lead to a base substitution known as a transition, where C is replaced by T (and G is replaced by A on the other strand of DNA). (wordpress.com)
  • Likelihood of any nucleotide being targeted for deamination along AGCTAGCTAGCT strand of DNA. (wordpress.com)
  • Normally, DNA polymerase β (Polβ) would replace the dC deaminated by AID, leading to correct repair of the single-strand break, thereby preventing CSR. (pubmedcentralcanada.ca)
  • The act of transcription creates single-strand DNA, the substrate for AID ( 8 , 9 , 12 - 15 ). (pubmedcentralcanada.ca)
  • In the BER pathway, abasic sites are subsequently recognized by apurinic/apyrimidic endonucleases (APEs), which nick the DNA backbone to create DNA single-strand breaks (SSBs) ( 24 ). (pubmedcentralcanada.ca)
  • In chapter 3 we have determined the structure of the complex of the XPF HhH domains bound to 10nt single strand DNA. (uu.nl)
  • that suggested a role for the XPF HhH domain in single strand DNA binding we find that the positively charged surface of the XPF interacts with the phosphate backbone of the single strand DNA. (uu.nl)
  • Next we show by NMR spectroscopy that in XPF/ERCC1 heterodimers the XPF HhH domains can bind single strand DNA using the same charged surface as found for XPF homodimers. (uu.nl)
  • For example, in a simple model for transcription elongation, the nontranscribed strand should be transiently in single-strand form when the transcription bubble passes through. (biology-online.org)
  • The three UV filter compounds underwent spontaneous deamination, such that at pH7 less than half of the starting materials [Kyn (42%), 3OHKG (30%) and 3OHKyn (21%)] remained after 7 days. (edu.au)
  • Krawczak M, Ball EV and Cooper DN (1998) Neighbouring‐nucleotide effects on the rates of germ‐line single‐base‐pair substitution in human genes. (els.net)
  • Analysis of the mutation spectra of single nucleotide substitutions associated with monogenic disorders strongly suggests that CG to TG mutations are among the most frequent causes of human genetic disease phenotypes. (els.net)
  • We observe groups of enhancer tiles with coherent trajectories, most of which can be potentially explained by a single gain or loss-of-activity event per tile. (biomedcentral.com)
  • Reaction of the UV filter deamination products with lens crystallins therefore appears to be more likely in the nucleus. (edu.au)