• This deamination process is normally counteracted by uracil-N-glycosylase, the product of the ung gene, and organisms defective in the removal of uracil from DNA have an increased spontaneous mutation rate and more G:C→A:T base-pair transitions ( 7 ). (cdc.gov)
  • The EZ1&2 DNA FFPE protocol uses double lysis to recover DNA effectively, while the optional uracil-N-glycosylase (UNG) step removes deaminated cytosine artifacts to limit the risk of nucleotide read errors. (qiagen.com)
  • Protein p56 encoded by the Bacillus subtilis phage phi29 inhibits host uracil-DNA glycosylase (UDG) activity. (nih.gov)
  • Belongs to the uracil-DNA glycosylase family. (abcam.cn)
  • A rapid, safe, and quantitative in vitro assay for measurement of uracil-DNA glycosylase activity. (cirn-na.com)
  • Organisms counteract the mutagenic effects of uracil in DNA using the BER repair system, which is mediated by a member of the uracil-DNA glycosylase (UDG) superfamily. (cirn-na.com)
  • The mutagenic effects of uracil in DNA are mitigated by the uracil-DNA glycosylase. (cirn-na.com)
  • The crenarchaeal Sulfolobus species probably suffer more than most, due to growth at 80°C, leading to more rapid reactions such as hydrolytic deamination of nucleotide bases, an aerobic lifestyle resulting in DNA damage by reactive oxygen species (ROS) and exposure to UV irradiation. (biomedcentral.com)
  • The enzyme/prodrug strategy using cytosine deaminase (CD) and 5-fluorocytosine (5-FC) has been used for cancer gene therapy. (biomedcentral.com)
  • Adenoviral vectors were constructed encoding one or both subunits of murine IL-12 (Ad.p35, Ad.p40 and Ad.IL-12) or cytosine deaminase (Ad.CD). (biomedcentral.com)
  • We are currently attempting to engineer SECURE adenine base editors and exploring the off-target RNA effects of cytosine base editors that use other deaminase enzymes than the one in the editor we investigated. (irbic.ir)
  • Structural basis of sequence-specific cytosine deamination by double-stranded DNA deaminase toxin DddA. (anl.gov)
  • The interbacterial deaminase toxin DddA catalyzes cytosine-to-uracil conversion in double-stranded (ds) DNA and enables CRISPR-free mitochondrial base editing, but the molecular mechanisms underlying its unique substrate selectivity have remained elusive. (anl.gov)
  • The modified cytosine residues are not distinguished from cytosine in traditional polymerase based sequencing. (helsinki.fi)
  • Using the phi29 DNA amplification system, we found that phi29 DNA polymerase is also able to carry out the extension of the dA:dUMP pair and replicate past uracil. (nih.gov)
  • Additionally, UDG and apurinic-apyrimidinic endonuclease treatment of viral DNA isolated from phi29-infected cells revealed that uracil residues arise in phi29 DNA during replication, probably as a result of misincorporation of dUMP by the phi29 DNA polymerase. (nih.gov)
  • Reference: Visualization of the interaction between archaeal DNA polymerase and uracil-containing DNA by atomic force microscopy. (neb.com)
  • To better understand the recognition mechanism, the binding modes of DNA polymerase B1 of Sulfolobus solfataricus (Pol B1) to uracil-containing DNA were examined by gel mobility shift assays and atomic force microscopy. (neb.com)
  • Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or due to deamination of cytosine. (abcam.cn)
  • Furthermore, pathogenic mycobacteria are at increased risk for deamination because of the production of reactive oxygen and nitrogen intermediates inside host macrophages. (cdc.gov)
  • The generation of ds DNA was significantly inhibited, however, by the presence of template uracil, and intermediates where monomeric forms of Pol B1 appeared to bind to uracil-containing DNA were observed. (neb.com)
  • However, several recent studies have brought some pieces of evidence that introduction of uracil bases in viral genomic DNA intermediates during genome replication might be a way of innate immune defence against some viruses. (bvsalud.org)
  • They may also comprise intermediates like Dihydrouridine that is found as an intermediate in uracil catabolism. (notesbard.com)
  • However, treating DNA with bisulfite prior to sequencing leads to deamination of cytosine, but leaves the modified cytosine residues unchanged. (helsinki.fi)
  • It was recently suggested that the methylated and hydroxymethylated cytosine residues could be distinguished from each other by selectively oxidizing the 5-hydroxymethyl cytosine to 5-formyl cytosine prior to bisulfite treatment. (helsinki.fi)
  • Thus, our data support a model in which protein p56 ensures an efficient viral DNA replication, preventing the deleterious effect caused by UDG when it eliminates uracil residues present in the phi29 genome. (nih.gov)
  • Other examples of non-primary pyrimidine bases include 5-hydroxymethyl and cytosine 5,6-dihydrouracil. (notesbard.com)
  • The pyrimidine bases are - Cytosine (2-Oxy-4-amino pyrimidine): (C5H6O2N5), found in both RNA and DNA, is a white crystalline substance, with MW=111.12 daltons and a melting point 320 to 325 C. (tuiasi.ro)
  • This gene encodes the enzyme responsible for pre-mRNA editing of the glutamate receptor subunit B by site-specific deamination of adenosines. (cancerindex.org)
  • Uracil is a natural base of RNA but may appear in DNA through two different pathways including cytosine deamination or misincorporation of deoxyuridine 5'-triphosphate nucleotide (dUTP) during DNA replication and constitutes one of the most frequent DNA lesions. (bvsalud.org)
  • Uracil is one of the most prevalent lesions that appears in DNA arising by spontaneous or enzymatic deamination of cytosine or misincorporation of the deoxyuridine 5'-triphosphate nucleotide (dUTP) in place of deoxythymidine 5'-triphosphate (dTTP) during DNA replication. (cirn-na.com)
  • When uracil in DNA arises from misincorporation of dUTP instead of dTTP, this process will result in A:U pairs. (cirn-na.com)
  • The oxidized base 8-oxo-7,8-dihydroguanine (8-oxoG), the product of deamination of cytosine uracil (U), and the sites of base loss [abasic (AP) sites] are among the most frequent mutagenic lesions formed in the human genome under physiological conditions. (utmb.edu)
  • In previous studies, we suggested that this inhibition is likely a defense mechanism developed by phage phi29 to prevent the action of UDG if uracilation occurs in DNA either from deamination of cytosine or the incorporation of dUMP during viral DNA replication. (nih.gov)
  • The resulting uracil pairs with adenine during DNA replication, thereby inducing G:C to A:T transitions in the progeny. (neb.com)
  • The experimental part of the thesis studies selective oxidation of 5-hydroxymethyl cytosine to 5-formyl cytosine. (helsinki.fi)
  • Taking advantage of this finding, we proposed a paper-assisted TdT (PAT) assay for absolute quantification of alkylated DNA lesions (N7-methylguanine), DNA deamination (cytosine-to-uracil) and DNA oxidation (8-oxo-7,8-dihydroguanine) by combining various DNA glycosylases. (rsc.org)
  • CRISPR Duo includes a RNA chain, which help to unravel the double helix structure, and the deamination enzyme is transported to the single-stranded on the precise target. (crisprinsider.com)
  • On the other hand, the action of UDG on uracil-containing phi29 DNA impaired in vitro viral DNA replication, which was prevented by the presence of protein p56. (nih.gov)
  • by using ung + and ung - Escherichia coli strains, demonstrated that total nitric oxide exposures in the μmol/L range can lead to C→T mutations by a mechanism probably involving cytosine deamination ( 8 ). (cdc.gov)
  • This tandem displacement mechanism allows DddA to locate a target cytosine without flipping it into the active site. (anl.gov)
  • Benzopyrene, a known carcinogen, has been shown to produce lesions at guanine bases in some genes, causing problems in the base's ability to pair to cytosine. (ukessays.com)
  • Uracil is one of the most prevalent lesions that appears in DNA. (cirn-na.com)
  • Isocytosine can be artificially produced by malic acid and guanidine is an isomer of cytosine and also has applications in hachimoji RNA. (notesbard.com)
  • For testing the agents, we used 5-hydroxymethyl uracil, 5-hydroxymethyl cytosine as model molecules. (helsinki.fi)
  • These results suggest that Pol B1 more efficiently recognizes uracil in DNA during DNA synthesis rather than during random diffusion in solution, and that single molecules of Pol B1 bind to template uracil and stall DNA synthesis. (neb.com)
  • As part of countermeasures, numerous viruses have developed powerful strategies to prevent emergence of uracilated viral genomes and/or to eliminate uracils already incorporated into DNA. (bvsalud.org)
  • As for the nitrogenous base (or nucleobase) component, the common bases are adenine (A), guanine (G), cytosine (C), and uracil (U). Depending on the number of phosphates that make up the compound, the ribonucleotide may be designated as monophosphate (having only one phosphate group), diphosphate (having two phosphate groups), and triphosphate (having three phosphate groups). (biologyonline.com)
  • These structures show that DddA binds to the minor groove of a sharply bent dsDNA and engages the target cytosine extruded from the double helix. (anl.gov)
  • DNA lacks uracil in its structures as one of the bases. (notesbard.com)
  • In the first pathway, the uracil will preferentially pair with adenine, leading to C:G → T:A transition. (cirn-na.com)
  • Interestingly, B-family DNA polymerases from hyperthermophilic Archaea recognize the presence of uracil in DNA and stall DNA synthesis. (neb.com)
  • Although PolB1 per se specifically binds to uracil-containing single-stranded DNA, the binding efficiency was substantially enhanced by the initiation of DNA synthesis. (neb.com)
  • We show that a cytosine base editor (CBE) with rat APOBEC1 can cause extensive transcriptome-wide RNA cytosine deamination in human cells, inducing tens of thousands of C-to-uracil (U) edits with frequencies ranging from 0.07 to 100% in 38-58% of expressed genes," the article's authors wrote. (irbic.ir)