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Uracil dna glycosylase

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https://www.readbyqxmd.com/read/28879561/backbone-1-h-13-c-and-15-n-chemical-shift-assignment-of-full-length-human-uracil-dna-glycosylase-ung2
#1
Edith Buchinger, Siv Å Wiik, Anna Kusnierczyk, Renana Rabe, Per A Aas, Bodil Kavli, Geir Slupphaug, Finn L Aachmann
Human uracil N-glycosylase isoform 2-UNG2 consists of an N-terminal intrinsically disordered regulatory domain (UNG2 residues 1-92, 9.3 kDa) and a C-terminal structured catalytic domain (UNG2 residues 93-313, 25.1 kDa). Here, we report the backbone (1)H, (13)C, and (15)N chemical shift assignment as well as secondary structure analysis of the N-and C-terminal domains of UNG2 representing the full-length UNG2 protein.
September 6, 2017: Biomolecular NMR Assignments
https://www.readbyqxmd.com/read/28875174/improved-base-excision-repair-inhibition-and-bacteriophage-mu-gam-protein-yields-c-g-to-t-a-base-editors-with-higher-efficiency-and-product-purity
#2
Alexis C Komor, Kevin T Zhao, Michael S Packer, Nicole M Gaudelli, Amanda L Waterbury, Luke W Koblan, Y Bill Kim, Ahmed H Badran, David R Liu
We recently developed base editing, the programmable conversion of target C:G base pairs to T:A without inducing double-stranded DNA breaks (DSBs) or requiring homology-directed repair using engineered fusions of Cas9 variants and cytidine deaminases. Over the past year, the third-generation base editor (BE3) and related technologies have been successfully used by many researchers in a wide range of organisms. The product distribution of base editing-the frequency with which the target C:G is converted to mixtures of undesired by-products, along with the desired T:A product-varies in a target site-dependent manner...
August 2017: Science Advances
https://www.readbyqxmd.com/read/28846663/chemopreventive-potential-of-ethanolic-extracts-of-luobuma-leaves-apocynum-venetum-l-in-androgen-insensitive-prostate-cancer
#3
Szu-Ping Huang, Tzu-Ming Ho, Chih-Wen Yang, Ya-Ju Chang, Jie-Fu Chen, Ning-Sing Shaw, Jia-Cherng Horng, Shih-Lan Hsu, Ming-Yuan Liao, Li-Chen Wu, Ja-An Annie Ho
Luobuma (Apocynum venetum L. (AVL)) is a popular beverage in Asia and has been reportedly to be associated with the bioactivities such as cardiotonic, diuretic, antioxidative, and antihypertensive. However, its biofunction as chemoprevention activity is seldom addressed. Herein, we aimed to characterize the anti-androgen-insensitive-prostate-cancer (anti-AIPC) bioactive compounds of Luobuma, and to investigate the associated molecular mechanisms. Activity-guided-fractionation (antioxidative activity and cell survivability) of Luobuma ethanolic extracts was performed to isolate and characterize the major bioactive compounds using Ultra Performance Liquid Chromatography (UPLC), Liquid Chromatography-Mass Spectrometry (LC-MS), and Nuclear Magnetic Resonance (NMR)...
August 28, 2017: Nutrients
https://www.readbyqxmd.com/read/28775312/uracil-accumulation-and-mutagenesis-dominated-by-cytosine-deamination-in-cpg-dinucleotides-in-mice-lacking-ung-and-smug1
#4
Lene Alsøe, Antonio Sarno, Sergio Carracedo, Diana Domanska, Felix Dingler, Lisa Lirussi, Tanima SenGupta, Nuriye Basdag Tekin, Laure Jobert, Ludmil B Alexandrov, Anastasia Galashevskaya, Cristina Rada, Geir Kjetil Sandve, Torbjørn Rognes, Hans E Krokan, Hilde Nilsen
Both a DNA lesion and an intermediate for antibody maturation, uracil is primarily processed by base excision repair (BER), either initiated by uracil-DNA glycosylase (UNG) or by single-strand selective monofunctional uracil DNA glycosylase (SMUG1). The relative in vivo contributions of each glycosylase remain elusive. To assess the impact of SMUG1 deficiency, we measured uracil and 5-hydroxymethyluracil, another SMUG1 substrate, in Smug1 (-/-) mice. We found that 5-hydroxymethyluracil accumulated in Smug1 (-/-) tissues and correlated with 5-hydroxymethylcytosine levels...
August 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28763516/crystal-structure-of-mimivirus-uracil-dna-glycosylase
#5
Eunju Kwon, Deepak Pathak, Hyeun Wook Chang, Dong Young Kim
Cytosine deamination induced by stresses or enzymatic catalysis converts deoxycytidine into deoxyuridine, thereby introducing a G to A mutation after DNA replication. Base-excision repair to correct uracil to cytosine is initiated by uracil-DNA glycosylase (UDG), which recognizes and eliminates uracil from DNA. Mimivirus, one of the largest known viruses, also encodes a distinctive UDG gene containing a long N-terminal domain (N-domain; residues 1-130) and a motif-I (residues 327-343), in addition to the canonical catalytic domain of family I UDGs (also called UNGs)...
2017: PloS One
https://www.readbyqxmd.com/read/28746850/investigation-of-n-terminal-phospho-regulation-of%C3%A2-uracil-dna-glycosylase-using-protein-semisynthesis
#6
Brian P Weiser, James T Stivers, Philip A Cole
Uracil DNA Glycosylase (UNG2) is the primary enzyme in humans that prevents the stable incorporation of deoxyuridine monophosphate into DNA in the form of U/A basepairs. During S-phase, UNG2 remains associated with the replication fork through its interactions with two proteins, Proliferating Cell Nuclear Antigen (PCNA) and Replication Protein A (RPA), which are critical for DNA replication and repair. In this work, we used protein semisynthesis and fluorescence anisotropy assays to explore the interactions of UNG2 with PCNA and RPA and to determine the effects of two UNG2 phosphorylation sites (Thr(6) and Tyr(8)) located within its PCNA-interacting motif (PIP-box)...
July 25, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28720682/reducing-artifactual-egfr-t790m-mutations-in-dna-from-formalin-fixed-paraffin-embedded-tissue-by-use-of-thymine-dna-glycosylase
#7
Hongdo Do, Ramyar Molania, Paul L Mitchell, Rita Vaiskunaite, John D Murdoch, Alexander Dobrovic
BACKGROUND: False-positive EGFR T790M mutations have been reported in formalin-fixed lung tumors, but the cause of the false positives has not been identified. The T790M mutation results from a C>T change at the cytosine of a CpG dinucleotide. The presence or absence of methylation at this cytosine has different consequences following deamination, resulting in a thymine or uracil, respectively, both of which however result in an artifactual change. Uracil-DNA glycosylase (UDG) can be used to eliminate DNA templates with uracil residues but is not active against artifactual thymines...
September 2017: Clinical Chemistry
https://www.readbyqxmd.com/read/28719838/identification-of-a-prototypical-single-stranded-uracil-dna-glycosylase-from-listeria-innocua
#8
Jing Li, Ye Yang, Jose Guevara, Liangjiang Wang, Weiguo Cao
A recent phylogenetic study on UDG superfamily estimated a new clade of family 3 enzymes (SMUG1-like), which shares a lower homology with canonic SMUG1 enzymes. The enzymatic properties of the newly found putative DNA glycosylase are unknown. To test the potential UDG activity and evaluate phylogenetic classification, we isolated one SMUG1-like glycosylase representative from Listeria innocua (Lin). A biochemical screening of DNA glycosylase activity in vitro indicates that Lin SMUG1-like glycosylase is a single-strand selective uracil DNA glycosylase...
September 2017: DNA Repair
https://www.readbyqxmd.com/read/28675037/sensitive-detection-of-dna-lesions-by-bulge-enhanced-highly-specific-coamplification-at-lower-denaturation-temperature-polymerase-chain-reaction
#9
Yu Feng, Shuang Cai, Guoliang Xiong, Guanfei Zhang, Shihui Wang, Xin Su, Changyuan Yu
Mutagenic modifications of nucleotides or DNA lesions that result from environmental stress have proven to be associated with a variety of diseases, particularly cancer. The method for accurately detecting the lesions is therefore of great importance for biomedical research and toxicity study. We develop a sensitive and low-cost bulge-enhanced coamplification at lower denaturation temperature polymerase chain reaction (COLD-PCR) method for detecting DNA lesions (uracil and 8-oxoguanine) by combining an in vitro base excision repair (BER) pathway and COLD-PCR...
July 12, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28621520/homogeneously-sensitive-detection-of-multiple-dna-glycosylases-with-intrinsically-fluorescent-nucleotides
#10
Yan Zhang, Chen-Chen Li, Bo Tang, Chun-Yang Zhang
DNA glycosylases are responsible for recognition and excision of the damaged bases in the base excision repair pathway, and all mammals express multiple DNA glycosylases to maintain genome stability. However, simultaneous detection of multiple DNA glycosylase still remains a great challenge. Here, we develop a rapid and sensitive fluorescent method for simultaneous detection of human 8-oxoG DNA glycosylase 1 (hOGG1) and uracil DNA glycolase (UDG) using exonuclease-assisted recycling signal amplification in combination with fluorescent bases 2-aminopurine (2-AP) and pyrrolo-dC (P-dC) as the fluorophores...
June 30, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28601074/role-of-glyceraldehyde-3-phosphate-dehydrogenase-gapdh-in-dna-repair
#11
REVIEW
A A Kosova, S N Khodyreva, O I Lavrik
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is widely known as a glycolytic enzyme. Nevertheless, various functions of GAPDH have been found that are unrelated to glycolysis. Some of these functions presume interaction of GAPDH with DNA, but the mechanism of its translocation to the nucleus is not fully understood. When in the nucleus, GAPDH participates in the initiation of apoptosis and transcription of genes involved in antiapoptotic pathways and cell proliferation and plays a role in the regulation of telomere length...
June 2017: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/28541550/integrity-of-immunoglobulin-variable-regions-is-supported-by-ganp-during-aid-induced-somatic-hypermutation-in-germinal-center-b-cells
#12
Mohammed Mansour Abbas Eid, Mayuko Shimoda, Shailendra Kumar Singh, Sarah Ameen Almofty, Phuong Pham, Myron F Goodman, Kazuhiko Maeda, Nobuo Sakaguchi
Immunoglobulin affinity maturation depends on somatic hypermutation (SHM) in immunoglobulin variable (IgV) regions initiated by activation-induced cytidine deaminase (AID). AID induces transition mutations by C→U deamination on both strands, causing C:G→T:A. Error-prone repairs of U by base excision and mismatch repairs (MMRs) create transversion mutations at C/G and mutations at A/T sites. In Neuberger's model, it remained to be clarified how transition/transversion repair is regulated. We investigate the role of AID-interacting GANP (germinal center-associated nuclear protein) in the IgV SHM profile...
May 1, 2017: International Immunology
https://www.readbyqxmd.com/read/28514671/evaluation-of-improved-is6110-lamp-assay-for-diagnosis-of-pulmonary-and-extra-pulmonary-tuberculosis
#13
Deepali Joon, Manoj Nimesh, Mandira Varma-Basil, Daman Saluja
In the present study, IS6110 loop mediated isothermal amplification (LAMP) assay was modified using dUTP-UNG (uracil-DNA N-glycosylase) strategy to prevent carryover contamination, and was evaluated using clinical specimens. The clinical specimens were collected from 236 suspected patients of pulmonary tuberculosis and 315 specimens of suspected patients of extra pulmonary tuberculosis. DNA was extracted from specimens and used as template for nucleic acid amplification. The results were evaluated with culture method as gold standard...
May 14, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/28447972/wild-type-blocking-pcr-combined-with-direct-sequencing-as-a-highly-sensitive-method-for-detection-of-low-frequency-somatic-mutations
#14
Adam Z Albitar, Wanlong Ma, Maher Albitar
Accurate detection and identification of low frequency mutations can be problematic when assessing residual disease after therapy, screening for emerging resistance mutations during therapy, or when patients have few circulating tumor cells. Wild-type blocking PCR followed by sequencing analysis offers high sensitivity, flexibility, and simplicity as a methodology for detecting these low frequency mutations. By adding a custom designed locked nucleic acid oligonucleotide to a new or previously established conventional PCR based sequencing assay, sensitivities of approximately 1 mutant allele in a background of 1,000 WT alleles can be achieved (1:1,000)...
March 29, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28427352/point-of-sampling-detection-of-zika-virus-within-a-multiplexed-kit-capable-of-detecting-dengue-and-chikungunya
#15
Ozlem Yaren, Barry W Alto, Priyanka V Gangodkar, Shatakshi R Ranade, Kunal N Patil, Kevin M Bradley, Zunyi Yang, Nikhil Phadke, Steven A Benner
BACKGROUND: Zika, dengue, and chikungunya are three mosquito-borne viruses having overlapping transmission vectors. They cause diseases having similar symptoms in human patients, but requiring different immediate management steps. Therefore, rapid (< one hour) discrimination of these three viruses in patient samples and trapped mosquitoes is needed. The need for speed precludes any assay that requires complex up-front sample preparation, such as extraction of nucleic acids from the sample...
April 20, 2017: BMC Infectious Diseases
https://www.readbyqxmd.com/read/28397787/correlated-mutation-in-the-evolution-of-catalysis-in-uracil-dna-glycosylase-superfamily
#16
Bo Xia, Yinling Liu, Jose Guevara, Jing Li, Celeste Jilich, Ye Yang, Liangjiang Wang, Brian N Dominy, Weiguo Cao
Enzymes in Uracil DNA glycosylase (UDG) superfamily are essential for the removal of uracil. Family 4 UDGa is a robust uracil DNA glycosylase that only acts on double-stranded and single-stranded uracil-containing DNA. Based on mutational, kinetic and modeling analyses, a catalytic mechanism involving leaving group stabilization by H155 in motif 2 and water coordination by N89 in motif 3 is proposed. Mutual Information analysis identifies a complexed correlated mutation network including a strong correlation in the EG doublet in motif 1 of family 4 UDGa and in the QD doublet in motif 1 of family 1 UNG...
April 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28395718/-over-expression-of-uracil-dna-glycosylase-2-ung2-enhances-the-resistance-to-oxidative-damage-in-hepg2-cells
#17
Liyan Cao, Shan Cheng, Juan Du, Yanhai Guo, Xiaofeng Huang
Objective To investigate the uracil glycosidic enzyme activity of uracil DNA glycosylase 2 (UNG2) and study the role of UNG2 in the resistance of antioxidant stress of HepG2 cells. Methods The UNG2-expressing vector was built. Western blotting was used to detect the expression of UNG2. Immunofluorescence staining was performed to observe the cellular location of UNG2. Oligonucleotide was used as substrate for the determination of the UNG2 glycosidic enzyme activity. H2O2 toxicity assay was done to study the function of UNG2 in the antioxidant resistance of hepatocellular carcinoma HepG2 cells...
April 2017: Xi Bao Yu Fen Zi Mian Yi Xue za Zhi, Chinese Journal of Cellular and Molecular Immunology
https://www.readbyqxmd.com/read/28369586/uracil-dna-glycosylase-udg-activities-in-bradyrhizobium-diazoefficiens-characterization-of-a-new-class-of-udg-with-broad-substrate-specificity
#18
Ullas Valiya Chembazhi, Vinod Vikas Patil, Shivjee Sah, Wayne Reeve, Ravi P Tiwari, Euijeon Woo, Umesh Varshney
Repair of uracils in DNA is initiated by uracil DNA glycosylases (UDGs). Family 1 UDGs (Ung) are the most efficient and ubiquitous proteins having an exquisite specificity for uracils in DNA. Ung are characterized by motifs A (GQDPY) and B (HPSPLS) sequences. We report a novel dimeric UDG, Blr0248 (BdiUng) from Bradyrhizobium diazoefficiens. Although BdiUng contains the motif A (GQDPA), it has low sequence identity to known UDGs. BdiUng prefers single stranded DNA and excises uracil, 5-hydroxymethyl-uracil or xanthine from it...
June 2, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334887/avoidance-of-apobec3b-induced-mutation-by-error-free-lesion-bypass
#19
James I Hoopes, Amber L Hughes, Lauren A Hobson, Luis M Cortez, Alexander J Brown, Steven A Roberts
APOBEC cytidine deaminases mutate cancer genomes by converting cytidines into uridines within ssDNA during replication. Although uracil DNA glycosylases limit APOBEC-induced mutation, it is unknown if subsequent base excision repair (BER) steps function on replication-associated ssDNA. Hence, we measured APOBEC3B-induced CAN1 mutation frequencies in yeast deficient in BER endonucleases or DNA damage tolerance proteins. Strains lacking Apn1, Apn2, Ntg1, Ntg2 or Rev3 displayed wild-type frequencies of APOBEC3B-induced canavanine resistance (CanR)...
May 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28314872/rt-qpcr-with-chimeric-du-stem-loop-primer-is-efficient-for-the-detection-of-bacterial-small-rnas
#20
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
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