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)
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)
The position of the residues that activate the water nucleophile and protonate the uracil leaving group are widely debated, though the most commonly followed mechanism employs the water activating loop detailed in the enzyme structure. (wikipedia.org)
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. (lu.se)
Archaeal family B-type polymerases can incorporate/tolerate a variety of modified nucleotides but will stall upon encountering uracil and inosine residues. (neb.com)
Inhibitors2
UDG activity is controlled by various cellular factors, including the uracil-DNA glycosylase inhibitors, which are DNA mimic proteins that prevent the DNAbinding sites of UDGs from interacting with their DNA substrate. (tmu.edu.tw)
Muselmani, Wael and Kashif-Khan, Naail and Bagneris, Claire and Santangelo, Rosalia and Williams, Mark A and Savva, Renos (2023) A multimodal approach towards genomic identification of protein inhibitors of Uracil-DNA Glycosylase . (bbk.ac.uk)
Proteins1
Uracil-DNA glycosylases (UDGs) are highly conserved proteins that can be found in a wide range of organisms, and are involved in the DNA repair and host defense systems. (tmu.edu.tw)
DUTP5
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)
Uracil is a natural base of RNA but may appear in DNA through two different pathways including cytosinedeamination or misincorporation of deoxyuridine 5'-triphosphate nucleotide (dUTP) during DNA replication and constitutes one of the most frequent DNA lesions. (bvsalud.org)
Q5U Hot Start High-Fidelity DNA Polymerase is a modified Q5 High-Fidelity DNA polymerase which efficiently incorporates dUTP and amplifies uracil-containing templates. (neb.com)
The WarmStart Colorimetric LAMP Master Mix with UDG contains a low-Tris reaction buffer with all necessary cofactors at optimized 2X concentrations for LAMP assays: Bst 2.0 WarmStart DNA Polymerase, WarmStart RTx, Antarctic Thermolabile Uracil- DNA Glycosylase (UDG), dTTP/dUTP and Phenol Red for pH detection of LAMP. (neb.com)
Polymerase4
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)
Once unzipped, mismatched guanine and uracil pairs are separated, and DNA polymerase inserts complementary bases to form a guanine-cytosine (GC) pair in one daughter strand and an adenine-uracil (AU) pair in the other. (wikipedia.org)
Uracil N-glycosylase (UNG) is utilized to eliminate carryover polymerase chain reaction (PCR) products in PCR. (wikipedia.org)
Structural basis of transcription: RNA Polymerase II substrate binding and metal coordination at 3.0 A using a free-electron laser. (stanford.edu)
Coli1
The glycosylases studied here include Escherichia coli uracil-DNA glycosylase (UNG), E. coli mismatch uracil-DNA glycosylase (MUG), and the Methanobacterium thermoautotrophicum mismatch thymine-DNA glycosylase (TDG). (utmb.edu)
Mutagenic4
After a mutation occurs, the mutagenic threat of uracil propagates through any subsequent DNA replication steps. (wikipedia.org)
Subsequent steps generate single-strand breaks [ 17 ], which become substrates for mutagenic repair or recombination. (biomedcentral.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)
Excision4
Its most important function is to prevent mutagenesis by eliminating uracil from DNA molecules by cleaving the N-glycosidic bond and initiating the base-excision repair (BER) pathway. (wikipedia.org)
One important function of uracil-DNA glycosylases is to prevent mutagenesis by eliminating uracil from DNA molecules by cleaving the N-glycosidic bond and initiating the base-excision repair (BER) pathway. (wikipedia.org)
Human cells express five to six types of DNA glycosylases, all of which share a common mechanism of base eversion and excision as a means of DNA repair. (wikipedia.org)
In collaboration with Laurence Pearl , he elucidated the structural basis of excision repair by Uracil-DNA glycosylase . (wikimili.com)
Protein4
Protein p56 encoded by the Bacillus subtilis phage phi29 inhibits host uracil-DNA glycosylase (UDG) activity. (nih.gov)
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)
Furthermore, transfection activity of uracil-containing phi29 DNA was significantly higher in cells that constitutively synthesized p56 than in cells lacking this protein. (nih.gov)
The encoded protein has additionally been identified to have uracilDNA glycosylase activity in the nucleus. (ebiocell.com)
Thymine3
Contrary to predictions based upon the crystal structure, the preference of MUG for mispaired uracil over thymine is not based upon steric exclusion. (utmb.edu)
The side chain of Tyr147 interferes sterically with the thymine C5 methyl group, while a specific hydrogen bond between the uracil O2 carbonyl and Gln144 discriminates against a cytosine substrate, which lacks the necessary carbonyl. (wikipedia.org)
Uracil is selected over cytosine by a pattern of specific hydrogen bonds, and thymine is excluded by steric clash of its 5-methyl group with Y66. (ox.ac.uk)
Mutation1
Q5U contains a mutation in the uracil-binding pocket that enables the ability to read and amplify templates containing uracil and inosine bases. (neb.com)
Replication2
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)
Many proofreading polymerases derived from archaeal Family B DNA polymerases stall replication in response to uracil bases in DNA templates (Wardle, J. et al. (neb.com)
Bases1
Damaged pyrimidines are generally removed by glycosylases that must scan the entire genome to locate lesions with sufficient fidelity to selectively remove the damage without inadvertent removal of normal bases. (utmb.edu)
Furthermore, the preference for mispaired uracil over uracil paired with adenine is more likely due to reduced thermal stability as opposed to specific recognition of the mispaired guanine. (utmb.edu)
In the first pathway, the uracil will preferentially pair with adenine, leading to C:G → T:A transition. (cirn-na.com)
Excises2
UDG excises uracil in both AU and GU pairs to prevent propagation of the base mismatch to downstream transcription and translation processes. (wikipedia.org)
This N123D:L191A mutant excises C when it is mispaired with A or opposite an abasic site, but not when it is paired with G. In contrast no cleavage is observed with any substrates that contain 5-methylcytosine. (ox.ac.uk)
Pyrimidines1
Purines are too large to fit in the active site, while unfavorable interactions with other pyrimidines discourage binding alternative substrates. (wikipedia.org)
Cleavage2
The active site comprises five highly conserved motifs that collectively catalyze glycosidic bond cleavage: Water-activating loop: 63-QDPYH-67 Pro-rich loop: 165-PPPPS-169 Uracil-binding motif: 199-GVLLLN-204 Gly-Ser loop: 246-GS-247 Minor groove intercalation loop: 268-HPSPLS-273 Glycosidic bond cleavage follows a "pinch-push-pull" mechanism using the five conserved motifs. (wikipedia.org)
Once uracil is recognized, cleavage of the glycosidic bond proceeds according to the mechanism below. (wikipedia.org)
Enzyme1
Uracil-DNA glycosylase (also known as UNG or UDG) is an enzyme. (wikipedia.org)
Endonuclease1
Oxidative DNA Damage and Cisplatin Neurotoxicity Is Exacerbated by Inhibition of OGG1 Glycosylase Activity and APE1 Endonuclease Activity in Sensory Neurons), inhibition of enzymes that play a role in repairing oxidative DNA damage exacerbated neurotoxic effects of the chemotherapeutic agent, cisplatin. (scientificarchives.com)
Vitro1
A rapid, safe, and quantitative in vitro assay for measurement of uracil-DNA glycosylase activity. (cirn-na.com)
Utilize1
The results of this study suggest that these glycosylases utilize several strategies for base identification, including (1) steric limitations on the size of the 5-substituent, (2) electronic-inductive properties of the 5-substituent, (3) reduced thermal stability of mispairs, and (4) specific functional groups on the purine base in the opposing strand. (utmb.edu)
Structural1
We report here studies conducted with a series of base analogues designed to test mechanisms of base recognition suggested by structural studies of glycosylase complexes. (utmb.edu)
Efficiently1
Uracil DNA glycosylase (UDG) efficiently removes uracil from DNA in a reaction in which the base is flipped into the enzyme's active site. (ox.ac.uk)
Viral1
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)
Lesions1
Uracil is one of the most prevalent lesions that appears in DNA. (cirn-na.com)
Recognition1
Backbone compression favors eversion of the now extrahelical nucleotide, which is positioned for recognition by the uracil-binding motif. (wikipedia.org)
Family1
Belongs to the uracil-DNA glycosylase family. (lu.se)
Strand1
Pinch: UDG scans DNA for uracil by nonspecifically binding to the strand and creating a kink in the backbone, thereby positioning the selected base for detection. (wikipedia.org)
Repair1
These results provide new insights into the mechanisms of base selection by DNA repair glycosylases. (utmb.edu)
Removes1
The shaded box illustrates how AID first deaminates C to U, and then uracil-DNA glycosylase removes U, leaving an abasic site. (biomedcentral.com)
Include1
Substrates for T4 RNA Ligase I include single-stranded RNA and DNA as well as dinucleoside pyrophosphates. (genomics-online.com)
Site1
Pull: Now accessible to the active site, the nucleotide interacts with the uracil binding motif. (wikipedia.org)