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Uracil dna glycosylase

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https://www.readbyqxmd.com/read/29785056/genome-wide-mapping-reveals-that-deoxyuridine-is-enriched-in-the-human-centromeric-dna
#1
Xiaoting Shu, Menghao Liu, Zhike Lu, Chenxu Zhu, Haowei Meng, Sihao Huang, Xiaoxue Zhang, Chengqi Yi
Uracil in DNA can be generated by cytosine deamination or dUMP misincorporation; however, its distribution in the human genome is poorly understood. Here we present a selective labeling and pull-down technology for genome-wide uracil profiling and identify thousands of uracil peaks in three different human cell lines. Surprisingly, uracil is highly enriched at the centromere of the human genome. Using mass spectrometry, we demonstrate that human centromeric DNA contains a higher level of uracil. We also directly verify the presence of uracil within two centromeric uracil peaks on chromosomes 6 and 11...
May 21, 2018: Nature Chemical Biology
https://www.readbyqxmd.com/read/29746667/a-fluorescent-reporter-for-quantification-and-enrichment-of-dna-editing-by-apobec-cas9-or-cleavage-by-cas9-in-living-cells
#2
Amber St Martin, Daniel Salamango, Artur Serebrenik, Nadine Shaban, William L Brown, Francesco Donati, Uday Munagala, Silvestro G Conticello, Reuben S Harris
Base editing is an exciting new genome engineering technology. C-to-T mutations in genomic DNA have been achieved using ribonucleoprotein complexes comprised of rat APOBEC1 single-stranded DNA deaminase, Cas9 nickase (Cas9n), uracil DNA glycosylase inhibitor (UGI), and guide (g)RNA. Here, we report the first real-time reporter system for quantification of APOBEC-mediated base editing activity in living mammalian cells. The reporter expresses eGFP constitutively as a marker for transfection or transduction, and editing restores functionality of an upstream mCherry cassette through the simultaneous processing of two gRNA binding regions that each contain an APOBEC-preferred 5'TCA target site...
May 9, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29735979/uracil-dna-glycosylase-is-not-implicated-in-the-choice-of-the-dna-repair-pathway-during-b-cell-class-switch-recombination
#3
Nour Ghazzaui, Hussein Issaoui, Alexis Saintamand, Yves Denizot, François Boyer
No abstract text is available yet for this article.
May 7, 2018: Cellular & Molecular Immunology
https://www.readbyqxmd.com/read/29730325/rapid-sensitive-and-reliable-detection-of-klebsiella-pneumoniae-by-label-free-multiple-cross-displacement-amplification-coupled-with-nanoparticles-based-biosensor
#4
Yi Wang, Weiqiang Yan, Yan Wang, Jianguo Xu, Changyun Ye
Klebsiella pneumoniae (K. pneumoniae), as an important hospital-acquired bacterium, is responsible for severe morbidity and mortality among the elderly, newborn and immune-compromised people. We established a rcsA gene-based label-free multiple cross displacement amplification (MCDA) assay for rapid, simple and sensitive detection of K. pneumoniae by using lateral flow biosensor (LFB). MCDA reaction was conducted at a fixed temperature (65 °C) for only 30 min, and amplification results were directly indicated using LFB...
May 3, 2018: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/29717169/ung-1-and-apn-1-are-the-major-enzymes-to-efficiently-repair-5-hydroxymethyluracil-dna-lesions-in-c-elegans
#5
Arturo Papaluca, J Richard Wagner, H Uri Saragovi, Dindial Ramotar
In Caenorhabditis elegans, two DNA glycosylases, UNG-1 and NTH-1, and two AP endonucleases, APN-1 and EXO-3, have been characterized from the base-excision repair (BER) pathway that repairs oxidatively modified DNA bases. UNG-1 removes uracil, while NTH-1 can remove 5-hydroxymethyluracil (5-hmU), an oxidation product of thymine, as well as other lesions. Both APN-1 and EXO-3 can incise AP sites and remove 3'-blocking lesions at DNA single strand breaks, and only APN-1 possesses 3'- to 5'-exonulease and nucleotide incision repair activities...
May 1, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29707704/integration-of-single-molecule-detection-with-magnetic-separation-for-multiplexed-detection-of-dna-glycosylases
#6
Chen-Chen Li, Yan Zhang, Bo Tang, Chun-Yang Zhang
We combine single-molecule detection with magnetic separation for simultaneous measurement of human 8-oxoG DNA glycosylase 1 (hOGG1) and uracil DNA glycosylase (UDG) based on excision repair-initiated endonuclease IV (Endo IV)-assisted signal amplification. This method can sensitively detect multiple DNA glycosylases, and it can be further applied for the simultaneous measurement of enzyme kinetic parameters and screening of both hOGG1 and UDG inhibitors.
April 30, 2018: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/29698444/formalin-fixation-increases-deamination-mutation-signature-but-should-not-lead-to-false-positive-mutations-in-clinical-practice
#7
Leah M Prentice, Ruth R Miller, Jeff Knaggs, Alborz Mazloomian, Rosalia Aguirre Hernandez, Patrick Franchini, Kourosh Parsa, Basile Tessier-Cloutier, Anna Lapuk, David Huntsman, David F Schaeffer, Brandon S Sheffield
Genomic analysis of cancer tissues is an essential aspect of personalized oncology treatment. Though it has been suggested that formalin fixation of patient tissues may be suboptimal for molecular studies, this tissue processing approach remains the industry standard. Therefore clinical molecular laboratories must be able to work with formalin fixed, paraffin embedded (FFPE) material. This study examines the effects of pre-analytic variables introduced by routine pathology processing on specimens used for clinical reports produced by next-generation sequencing technology...
2018: PloS One
https://www.readbyqxmd.com/read/29608170/multiplexed-isothermal-amplification-based-diagnostic-platform-to-detect-zika-chikungunya-and-dengue-1
#8
Ozlem Yaren, Barry W Alto, Kevin M Bradley, Patricia Moussatche, Lyudmyla Glushakova, Steven A Benner
Zika, dengue, and chikungunya viruses are transmitted by mosquitoes, causing diseases with similar patient symptoms. However, they have different downstream patient-to-patient transmission potentials, and require very different patient treatments. Thus, recent Zika outbreaks make it urgent to develop tools that rapidly discriminate these viruses in patients and trapped mosquitoes, to select the correct patient treatment, and to understand and manage their epidemiology in real time. Unfortunately, current diagnostic tests, including those receiving 2016 emergency use authorizations and fast-track status, detect viral RNA by reverse transcription polymerase chain reaction (RT-PCR), which requires instrumentation, trained users, and considerable sample preparation...
March 13, 2018: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29596604/a-structurally-conserved-motif-in-%C3%AE-herpesvirus-uracil-dna-glycosylases-elicits-duplex-nucleotide-flipping
#9
Christopher Earl, Claire Bagnéris, Kara Zeman, Ambrose Cole, Tracey Barrett, Renos Savva
Efficient γ-herpesvirus lytic phase replication requires a virally encoded UNG-type uracil-DNA glycosylase as a structural element of the viral replisome. Uniquely, γ-herpesvirus UNGs carry a seven or eight residue insertion of variable sequence in the otherwise highly conserved minor-groove DNA binding loop. In Epstein-Barr Virus [HHV-4] UNG, this motif forms a disc-shaped loop structure of unclear significance. To ascertain the biological role of the loop insertion, we determined the crystal structure of Kaposi's sarcoma-associated herpesvirus [HHV-8] UNG (kUNG) in its product complex with a uracil-containing dsDNA, as well as two structures of kUNG in its apo state...
March 27, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29594577/detection-of-nucleic-acids-and-elimination-of-carryover-contamination-by-using-loop-mediated-isothermal-amplification-and-antarctic-thermal-sensitive-uracil-dna-glycosylase-in-a-lateral-flow-biosensor-application-to-the-detection-of-streptococcus-pneumoniae
#10
Yi Wang, Yan Wang, Dongxun Li, Jianguo Xu, Changyun Ye
The authors report on a loop-mediated isothermal amplification (LAMP) scheme that uses antarctic thermally sensitive uracil-DNA-glycosylase (AUDG) for simultaneous detection of nucleic acids and elimination of carryover contamination. It was applied in a lateral flow assay (LFA) format. The assay has attractive features in that it does not require the use of labeled primers or probes, and can eliminate false-positive results generated by unwanted hybridization between two labeled primers or between a labeled primer and probe...
March 7, 2018: Mikrochimica Acta
https://www.readbyqxmd.com/read/29547780/monitoring-base-excision-repair-in-chlamydomonas-reinhardtii-cell-extracts
#11
Teresa Morales-Ruiz, Álvaro C Romero-Valenzuela, Vanessa M Vázquez-Grande, Teresa Roldán-Arjona, Rafael R Ariza, Dolores Córdoba-Cañero
Base excision repair (BER) is a major defense pathway against spontaneous DNA damage. This multistep process is initiated by DNA glycosylases that recognise and excise the damaged base, and proceeds by the concerted action of additional proteins that perform incision of the abasic site, gap filling and ligation. BER has been extensively studied in bacteria, yeasts and animals. Although knowledge of this pathway in land plants is increasing, there are no reports detecting BER in algae. We describe here an experimental in vitro system allowing the specific analysis of BER in the model alga Chlamydomonas reinhardtii...
May 2018: DNA Repair
https://www.readbyqxmd.com/read/29436623/development-of-uracil-dna-glycosylase-supplemented-loop-mediated-isothermal-amplification-coupled-with-nanogold-probe-udg-lamp-aunp-for-specific-detection-of-pseudomonas-aeruginosa
#12
Orapan Manajit, Siwaporn Longyant, Paisarn Sithigorngul, Parin Chaivisuthangkura
Pseudomonas aeruginosa (P. aeruginosa) is an important opportunistic pathogen that causes serious infections in humans, including keratitis in contact lens wearers. Therefore, establishing a rapid, specific and sensitive method for the identification of P. aeruginosa is imperative. In the present study, the uracil-DNA-glycosylase-supplemented loop-mediated isothermal amplification combined with nanogold labeled hybridization probe (UDG-LAMP-AuNP) was developed for the detection of P. aeruginosa. UDG-LAMP was performed to prevent carry over contamination and the LAMP reactions can be readily observed using the nanogold probe...
April 2018: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29403014/deaminase-mediated-multiplex-genome-editing-in-escherichia-coli
#13
Satomi Banno, Keiji Nishida, Takayuki Arazoe, Hitoshi Mitsunobu, Akihiko Kondo
In eukaryotes, the CRISPR-Cas9 system has now been widely used as a revolutionary genome engineering tool1, 2 . However, in prokaryotes, the use of nuclease-mediated genome editing tools has been limited to negative selection for the already modified cells because of its lethality3, 4 . Here, we report on deaminase-mediated targeted nucleotide editing (Target-AID) 5 adopted in Escherichia coli. Cytidine deaminase PmCDA1 fused to the nuclease-deficient CRISPR-Cas9 system achieved specific point mutagenesis at the target sites in E...
April 2018: Nature Microbiology
https://www.readbyqxmd.com/read/29366630/an-advanced-uracil-dna-glycosylase-supplemented-loop-mediated-isothermal-amplification-udg-lamp-technique-used-in-the-sensitive-and-specific-detection-of-cryptosporidium-parvum-cryptosporidium-hominis-and-cryptosporidium-meleagridis-in-aids-patients
#14
Shirzad Fallahi, Seyedeh Fatemeh Moosavi, Azadeh Karimi, Ali Sharafi Chegeni, Mohammad Saki, Parsa Namdari, Mohammad Menati Rashno, Ali Mohamad Varzi, Mohammad Javad Tarrahi, Mohammad Almasian
The rapid and accurate detection of Cryptosporidium spp. is critically important for the prevention and timely treatment of cryptosporidiosis in AIDS patients (APs). This study was conducted to examine a UDG-LAMP technique for the first time to diagnose cryptosporidiosis in APs. After collecting demographic and clinical data, three stool samples were collected from the participants (120 volunteering APs). The microscopic examination of stained smears using the acid-fast method and the UDG-LAMP assay were performed for each sample...
May 2018: Diagnostic Microbiology and Infectious Disease
https://www.readbyqxmd.com/read/29336305/inferring-joint-sequence-structural-determinants-of-protein-functional-specificity
#15
Andrew F Neuwald, L Aravind, Stephen F Altschul
Residues responsible for allostery, cooperativity, and other subtle but functionally important interactions remain difficult to detect. To aid such detection, we employ statistical inference based on the assumption that residues distinguishing a protein subgroup from evolutionarily divergent subgroups often constitute an interacting functional network. We identify such networks with the aid of two measures of statistical significance. One measure aids identification of divergent subgroups based on distinguishing residue patterns...
January 16, 2018: ELife
https://www.readbyqxmd.com/read/29310268/integrating-dna-structure-switch-with-branched-hairpins-for-the-detection-of-uracil-dna-glycosylase-activity-and-inhibitor-screening
#16
Jing Zhu, Qijie Hao, Yi Liu, Zhaohui Guo, Buayxigul Rustam, Wei Jiang
The detection of uracil-DNA glycosylase (UDG) activity is pivotal for its biochemical studies and the development of drugs for UDG-related diseases. Here, we explored an integrated DNA structure switch for high sensitive detection of UDG activity. The DNA structure switch containing two branched hairpins was employed to recognize UDG enzyme and generate fluorescent signal. Under the action of UDG, one branched hairpin was impelled folding into a close conformation after the excision of the single uracil. This reconfigured hairpin could immediately initiate the polymerization/nicking amplification reaction of another branched hairpin accompanying with the release of numerous G-quadruplexes (G4s)...
March 1, 2018: Talanta
https://www.readbyqxmd.com/read/29178619/abasic-site-assisted-inhibition-of-nicking-endonuclease-activity-for-the-sensitive-determination-of-uracil-dna-glycosylase
#17
Jun Ki Ahn, Chang Yeol Lee, Ki Soo Park, Hyun Gyu Park
We herein describe A novel strategy to accurately determine uracil DNA glycosylase (UDG) activity is described based on the finding that nicking endonuclease-assisted cleavage reaction can be regulated by the presence of abasic site. This strategy utilizes DNA probes rationally designed to contain uracil base at the cleavage site for nicking endonuclease, which is coupled to the isothermal nicking endonuclease amplification reaction (NEAR) method. In the absence of UDG, intact DNA probes generate a large number of double-stranded (ds) DNA products through the NEAR, but the presence of UDG that converts uracil base into abasic site suppresses nicking endonuclease activity and the subsequent NEAR...
November 27, 2017: Biotechnology Journal
https://www.readbyqxmd.com/read/29171849/uracil-removal-inhibited-ligase-reaction-in-combination-with-catalytic-hairpin-assembly-for-the-sensitive-and-specific-detection-of-uracil-dna-glycosylase-activity
#18
Xiaowen Xu, Lei Wang, Yushu Wu, Wei Jiang
Sensitive and specific detection of uracil-DNA glycosylase (UDG) activity is crucial in biomedical study and disease diagnosis. Here, we developed a uracil removal-inhibited ligase reaction in combination with catalytic hairpin assembly (CHA) for the sensitive and specific detection of UDG activity. A hairpin probe is specially designed, which contains two uracil bases in the loop and is extended with toehold and branch-migration domains at the ends of the stem. Two short oligonucleotides are separately hybridized to one-half of the loop of the hairpin probe to form a DNA complex with a nick...
December 4, 2017: Analyst
https://www.readbyqxmd.com/read/29163805/-thymine-dna-glycosylase-tdg-is-involved-in-the-pathogenesis-of-intestinal-tumors-with-reduced-apc-expression
#19
Jinfei Xu, Salvatore Cortellino, Rossella Tricarico, Wen-Chi Chang, Gabrielle Scher, Karthik Devarajan, Michael Slifker, Robert Moore, Maria Rosaria Bassi, Elena Caretti, Margie Clapper, Harry Cooper, Alfonso Bellacosa
Thymine DNA Glycosylase (TDG) is a base excision repair enzyme that acts as a thymine and uracil DNA N-glycosylase on G:T and G:U mismatches, thus protecting CpG sites in the genome from mutagenesis by deamination. In addition, TDG has an epigenomic function by removing the novel cytosine derivatives 5-formylcytosine and 5-carboxylcytosine (5caC) generated by Ten-Eleven Translocation (TET) enzymes during active DNA demethylation. We and others previously reported that TDG is essential for mammalian development...
October 27, 2017: Oncotarget
https://www.readbyqxmd.com/read/29137710/loop-mediated-isothermal-amplification-using-self-avoiding-molecular-recognition-systems-and-antarctic-thermal-sensitive-uracil-dna-glycosylase-for-detection-of-nucleic-acid-with-prevention-of-carryover-contamination
#20
Yi Wang, Dongxin Liu, Jianping Deng, Yan Wang, Jianguo Xu, Changyun Ye
Loop-mediated isothermal amplification (LAMP) is the most popular technique to amplify nucleic acid sequence without the use of temperature cycling. However, LAMP is often confounded by false-positive results, arising from interactions between (hetero-dimer) or within (self-dimerization) primers, off-target hybrids and carryover contaminants. Here, we devised a new LAMP technique that is self-avoiding molecular recognition system (SAMRS) components and antarctic thermal sensitive uracil-DNA-glycosylase (AUDG) enzyme-assisted, termed AUDG-SAMRS-LAMP...
December 15, 2017: Analytica Chimica Acta
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