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Uracil dna glycosylase

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https://www.readbyqxmd.com/read/28314872/rt-qpcr-with-chimeric-du-stem-loop-primer-is-efficient-for-the-detection-of-bacterial-small-rnas
#1
Yangfan Wu, Xuejiao Xing, Ting You, Rubing Liang, Jianhua Liu
Small non-coding RNAs are considered be involved in the regulation of multiple cellular processes. Quantitative reverse transcription PCR (RT-qPCR) is widely used in the detection of eukaryotic microRNA, and the stem-loop primers can improve the specificity and efficiency of reverse transcription. However, the loop structure of primers probably influence the next quantitative amplification due to the base stacking and steric hindrance. Here, we designed a chimeric stem-loop primer with a deoxyuracil (dU) base located near the RNA matching part...
March 17, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28306242/excision-repair-initiated-enzyme-assisted-bicyclic-cascade-signal-amplification-for-ultrasensitive-detection-of-uracil-dna-glycosylase
#2
Li-Juan Wang, Ming Ren, Qianyi Zhang, Bo Tang, Chun-Yang Zhang
Uracil-DNA glycosylase (UDG) is an important base excision repair (BER) enzyme responsible for the repair of uracil-induced DNA lesion and the maintenance of genomic integrity, while the aberrant expression of UDG is associated with a variety of cancers. Thus the accurate detection of UDG activity is essential to biomedical research and clinical diagnosis. Here, we develop a fluorescent method for ultrasensitive detection of UDG activity using excision repair-initiated enzyme-assisted bicyclic cascade signal amplification...
March 17, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28283534/pms2-and-uracil-dna-glycosylases-act-jointly-in-the-mismatch-repair-pathway-to-generate-ig-gene-mutations-at-a-t-base-pairs
#3
Giulia Girelli Zubani, Marija Zivojnovic, Annie De Smet, Olivier Albagli-Curiel, François Huetz, Jean-Claude Weill, Claude-Agnès Reynaud, Sébastien Storck
During somatic hypermutation (SHM) of immunoglobulin genes, uracils introduced by activation-induced cytidine deaminase are processed by uracil-DNA glycosylase (UNG) and mismatch repair (MMR) pathways to generate mutations at G-C and A-T base pairs, respectively. Paradoxically, the MMR-nicking complex Pms2/Mlh1 is apparently dispensable for A-T mutagenesis. Thus, how detection of U:G mismatches is translated into the single-strand nick required for error-prone synthesis is an open question. One model proposed that UNG could cooperate with MMR by excising a second uracil in the vicinity of the U:G mismatch, but it failed to explain the low impact of UNG inactivation on A-T mutagenesis...
March 10, 2017: Journal of Experimental Medicine
https://www.readbyqxmd.com/read/28159613/the-vaccinia-virus-dna-polymerase-and-its-processivity-factor
#4
REVIEW
Maciej W Czarnecki, Paula Traktman
Vaccinia virus is the prototypic poxvirus. The 192 kilobase double-stranded DNA viral genome encodes most if not all of the viral replication machinery. The vaccinia virus DNA polymerase is encoded by the E9L gene. Sequence analysis indicates that E9 is a member of the B family of replicative polymerases. The enzyme has both polymerase and 3'-5' exonuclease activities, both of which are essential to support viral replication. Genetic analysis of E9 has identified residues and motifs whose alteration can confer temperature-sensitivity, drug resistance (phosphonoacetic acid, aphidicolin, cytosine arabinsode, cidofovir) or altered fidelity...
February 1, 2017: Virus Research
https://www.readbyqxmd.com/read/28110804/differential-role-of-base-excision-repair-proteins-in-mediating-cisplatin-cytotoxicity
#5
Akshada Sawant, Ashley M Floyd, Mohan Dangeti, Wen Lei, Robert W Sobol, Steve M Patrick
Interstrand crosslinks (ICLs) are covalent lesions formed by cisplatin. The mechanism for the processing and removal of ICLs by DNA repair proteins involves nucleotide excision repair (NER), homologous recombination (HR) and fanconi anemia (FA) pathways. In this report, we monitored the processing of a flanking uracil adjacent to a cisplatin ICL by the proteins involved in the base excision repair (BER) pathway. Using a combination of extracts, purified proteins, inhibitors, functional assays and cell culture studies, we determined the specific BER proteins required for processing a DNA substrate with a uracil adjacent to a cisplatin ICL...
March 2017: DNA Repair
https://www.readbyqxmd.com/read/28106786/sulfolobus-acidocaldarius-udg-can-remove-du-from-the-rna-backbone-insight-into-the-specific-recognition-of-uracil-linked-with-deoxyribose
#6
Gang-Shun Yi, Wei-Wei Wang, Wei-Guo Cao, Feng-Ping Wang, Xi-Peng Liu
Sulfolobus acidocaldarius encodes family 4 and 5 uracil-DNA glycosylase (UDG). Two recombinant S. acidocaldarius UDGs (SacUDG) were prepared and biochemically characterized using oligonucleotides carrying a deaminated base. Both SacUDGs can remove deoxyuracil (dU) base from both double-stranded DNA and single-stranded DNA. Interestingly, they can remove U linked with deoxyribose from single-stranded RNA backbone, suggesting that the riboses on the backbone have less effect on the recognition of dU and hydrolysis of the C-N glycosidic bond...
January 18, 2017: Genes
https://www.readbyqxmd.com/read/28049757/smug2-dna-glycosylase-from-pedobacter-heparinus-as-a-new-subfamily-in-udg-superfamily
#7
Panjiao Pang, Ye Yang, Jing Li, Zhong Wang, Weiguo Cao, Wei Xie
Base deamination is a common type of DNA damage that occurs in all organisms. DNA repair mechanisms are essential to maintain genome integrity, in which the base excision repair (BER) pathway plays a major role in the removal of base damage. In the BER pathway, the uracil DNA glycosylase superfamily is responsible for excising the deaminated bases from DNA and generates apurinic/apyrimidinic (AP) sites. Using bioinformatics tools, we identified a family 3 SMUG1-like DNA glycoyslase from Pedobacter heparinus (named as Phe SMUG2), which display catalytic activities towards DNA containing uracil or hypoxanthine/xanthine...
January 3, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/27974818/cadmium-ii-inhibition-of-human-uracil-dna-glycosylase-by-catalytic-water-supplantation
#8
Trevor Gokey, Bo Hang, Anton B Guliaev
Toxic metals are known to inhibit DNA repair but the underlying mechanisms of inhibition are still not fully understood. DNA repair enzymes such as human uracil-DNA glycosylase (hUNG) perform the initial step in the base excision repair (BER) pathway. In this work, we showed that cadmium [Cd(II)], a known human carcinogen, inhibited all activity of hUNG at 100 μM. Computational analyses based on 2 μs equilibrium, 1.6 μs steered molecular dynamics (SMD), and QM/MM MD determined that Cd(II) ions entered the enzyme active site and formed close contacts with both D145 and H148, effectively replacing the catalytic water normally found in this position...
December 15, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27933035/life-without-dutpase
#9
Csaba Kerepesi, Judit E Szabó, Veronika Papp-Kádár, Orsolya Dobay, Dóra Szabó, Vince Grolmusz, Beáta G Vértessy
Fine-tuned regulation of the cellular nucleotide pools is indispensable for faithful replication of Deoxyribonucleic Acid (DNA). The genetic information is also safeguarded by DNA damage recognition and repair processes. Uracil is one of the most frequently occurring erroneous bases in DNA; it can arise from cytosine deamination or thymine-replacing incorporation. Two enzyme activities are primarily involved in keeping DNA uracil-free: dUTPase (dUTP pyrophosphatase) activity that prevent thymine-replacing incorporation and uracil-DNA glycosylase activity that excise uracil from DNA and initiate uracil-excision repair...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27875297/glycogen-synthase-kinase-3-gsk-3-mediated-phosphorylation-of-uracil-n-glycosylase-2-ung2-facilitates-the-repair-of-floxuridine-induced-dna-lesions-and-promotes-cell-survival
#10
Carly A Baehr, Catherine J Huntoon, Song-My Hoang, Calvin R Jerde, Larry M Karnitz
Uracil N-glycosylase 2 (UNG2), the nuclear isoform of UNG, catalyzes the removal of uracil or 5-fluorouracil lesions that accumulate in DNA following treatment with the anticancer agents 5-fluorouracil and 5-fluorodeoxyuridine (floxuridine), a 5-fluorouracil metabolite. By repairing these DNA lesions before they can cause cell death, UNG2 promotes cancer cell survival and is therefore critically involved in tumor resistance to these agents. However, the mechanisms by which UNG2 is regulated remain unclear. Several phosphorylation sites within the N-terminal regulatory domain of UNG2 have been identified, although the effects of these modifications on UNG2 function have not been fully explored, nor have the identities of the kinases involved been determined...
December 23, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27871818/oxidatively-generated-base-modifications-in-dna-not-only-carcinogenic-risk-factor-but-also-regulatory-mark
#11
REVIEW
Marco Seifermann, Bernd Epe
The generation of DNA modifications in cells is in most cases accidental and associated with detrimental consequences such as increased mutation rates and an elevated risk of malignant transformation. Accordingly, repair enzymes involved in the removal of the modifications have primarily a protective function. Among the well-established exceptions of this rule are 5-methylcytosine and uracil, which are generated in DNA enzymatically under controlled conditions and fulfill important regulatory functions in DNA as epigenetic marks and in antibody diversification, respectively...
November 18, 2016: Free Radical Biology & Medicine
https://www.readbyqxmd.com/read/27836975/a-conserved-tripeptide-sequence-at-the-c-terminus-of-the-poxvirus-dna-processivity-factor-d4-is-essential-for-protein-integrity-and-function
#12
Manunya Nuth, Hancheng Guan, Robert P Ricciardi
Vaccinia virus (VACV) is a poxvirus, and the VACV D4 protein serves both as a uracil-DNA glycosylase and as an essential component required for processive DNA synthesis. The VACV A20 protein has no known catalytic function itself but associates with D4 to form the D4-A20 heterodimer that functions as the poxvirus DNA processivity factor. The heterodimer enables the DNA polymerase to efficiently synthesize extended strands of DNA. Upon characterizing the interaction between D4 and A20, we observed that the C terminus of D4 is susceptible to perturbation...
December 30, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27825529/toehold-mediated-strand-displacement-reaction-dependent-fluorescent-strategy-for-sensitive-detection-of-uracil-dna-glycosylase-activity
#13
Yushu Wu, Lei Wang, Wei Jiang
Sensitive detection of uracil-DNA glycosylase (UDG) activity is beneficial for evaluating the repairing process of DNA lesions. Here, toehold-mediated strand displacement reaction (TSDR)-dependent fluorescent strategy was constructed for sensitive detection of UDG activity. A single-stranded DNA (ssDNA) probe with two uracil bases and a trigger sequence were designed. A hairpin probe with toehold domain was designed, and a reporter probe was also designed. Under the action of UDG, two uracil bases were removed from ssDNA probe, generating apurinic/apyrimidinic (AP) sites...
March 15, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/27815903/analysis-of-nuclear-uracil-dna-glycosylase-nudg-turnover-during-the-cell-cycle
#14
Jennifer A Fischer, Salvatore J Caradonna
Uracil-DNA glycosylases (UDG/UNG) are enzymes that remove uracil from DNA and initiate base-excision repair. These enzymes play a key role in maintaining genomic integrity by reducing the mutagenic events caused by G:C to A:T transition mutations. The recent finding that a family of RNA editing enzymes (AID/APOBECs) can deaminate cytosine in DNA has raised the interest in these base-excision repair enzymes. The methodology presented here focuses on determining the regulation of the nuclear isoform of uracil-DNA glycosylase (nUDG), a 36,000 Da protein...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27723754/targeted-aid-mediated-mutagenesis-tam-enables-efficient-genomic-diversification-in-mammalian-cells
#15
Yunqing Ma, Jiayuan Zhang, Weijie Yin, Zhenchao Zhang, Yan Song, Xing Chang
A large number of genetic variants have been associated with human diseases. However, the lack of a genetic diversification approach has impeded our ability to interrogate functions of genetic variants in mammalian cells. Current screening methods can only be used to disrupt a gene or alter its expression. Here we report the fusion of activation-induced cytidine deaminase (AID) with nuclease-inactive clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein 9 (dCas9) for efficient genetic diversification, which enabled high-throughput screening of functional variants...
October 10, 2016: Nature Methods
https://www.readbyqxmd.com/read/27721668/archaeal-dna-polymerase-b-as-a-dna-template-guardian-links-between-polymerases-and-base-alternative-excision-repair-enzymes-in-handling-the-deaminated-bases-uracil-and-hypoxanthine
#16
Javier Abellón-Ruiz, Sonoko Ishino, Yoshizumi Ishino, Bernard A Connolly
In Archaea repair of uracil and hypoxanthine, which arise by deamination of cytosine and adenine, respectively, is initiated by three enzymes: Uracil-DNA-glycosylase (UDG, which recognises uracil); Endonuclease V (EndoV, which recognises hypoxanthine); and Endonuclease Q (EndoQ), (which recognises both uracil and hypoxanthine). Two archaeal DNA polymerases, Pol-B and Pol-D, are inhibited by deaminated bases in template strands, a feature unique to this domain. Thus the three repair enzymes and the two polymerases show overlapping specificity for uracil and hypoxanthine...
2016: Archaea: An International Microbiological Journal
https://www.readbyqxmd.com/read/27704075/a-dna-array-based-on-clickable-lesion-containing-hairpin-probes-for-multiplexed-detection-of-base-excision-repair-activities
#17
Mélanie Flaender, Guillaume Costa, Guillaume Nonglaton, Christine Saint-Pierre, Didier Gasparutto
DNA is under continuous assault by environmental and endogenous reactive oxygen and alkylating species, inducing the formation of mutagenic, toxic and genome destabilizing nucleobase lesions. Due to the implications of such genetic alterations in cell death, aging, inflammation, neurodegenerative diseases and cancer, many efforts have been devoted to developing assays that aim at analyzing DNA repair activities from purified enzymes or cell extracts. The present work deals with the conception and application of a new, miniaturized and parallelized on surface-DNA biosensor to measure base excision repair (BER) activities...
September 22, 2016: Analyst
https://www.readbyqxmd.com/read/27697833/ung-protects-b-cells-from-aid-induced-telomere-loss
#18
Elena M Cortizas, Astrid Zahn, Shiva Safavi, Joseph A Reed, Francisco Vega, Javier M Di Noia, Ramiro E Verdun
Activation-induced deaminase (AID) initiates antibody gene diversification by creating G:U mismatches in the immunoglobulin loci. However, AID also deaminates nonimmunoglobulin genes, and failure to faithfully repair these off-target lesions can cause B cell lymphoma. In this study, we identify a mechanism by which processing of G:U produced by AID at the telomeres can eliminate B cells at risk of genomic instability. We show that telomeres are off-target substrates of AID and that B cell proliferation depends on protective repair by uracil-DNA glycosylase (UNG)...
October 17, 2016: Journal of Experimental Medicine
https://www.readbyqxmd.com/read/27684934/poxvirus-uracil-dna-glycosylase-an-unusual-member-of-the-family-i-uracil-dna-glycosylases
#19
REVIEW
Norbert Schormann, Natalia Zhukovskaya, Gregory Bedwell, Manunya Nuth, Richard Gillilan, Peter E Prevelige, Robert P Ricciardi, Surajit Banerjee, Debasish Chattopadhyay
Uracil-DNA glycosylases are ubiquitous enzymes, which play a key role repairing damages in DNA and in maintaining genomic integrity by catalyzing the first step in the base excision repair pathway. Within the superfamily of uracil-DNA glycosylases family I enzymes or UNGs are specific for recognizing and removing uracil from DNA. These enzymes feature conserved structural folds, active site residues and use common motifs for DNA binding, uracil recognition and catalysis. Within this family the enzymes of poxviruses are unique and most remarkable in terms of amino acid sequences, characteristic motifs and more importantly for their novel non-enzymatic function in DNA replication...
December 2016: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/27640531/actinomyces-spp-gene-expression-in-root-caries-lesions
#20
Naile Dame-Teixeira, Clarissa Cavalcanti Fatturi Parolo, Marisa Maltz, Aradhna Tugnait, Deirdre Devine, Thuy Do
BACKGROUND: The studies of the distribution of Actinomyces spp. on carious and non-carious root surfaces have not been able to confirm the association of these bacteria with root caries, although they were extensively implicated as a prime suspect in root caries. OBJECTIVE: The aim of this study was to observe the gene expression of Actinomyces spp. in the microbiota of root surfaces with and without caries. DESIGN: The oral biofilms from exposed sound root surface (SRS; n=10) and active root caries (RC; n=30) samples were collected...
2016: Journal of Oral Microbiology
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