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DNA glycosylases

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https://www.readbyqxmd.com/read/29773766/impact-of-the-ser326cys-polymorphism-of-the-ogg1-gene-on-the-level-of-oxidative-dna-damage-in-patients-with-colorectal-cancer
#1
Jacek Kabzinski, Anna Walczak, Adam Dziki, Michał Mik, Ireneusz Majsterek
As a result of reactive oxygen species operation, cell damage occurs in both cellular organelles and molecules, including DNA. Oxidative damage within the genetic material can lead to accumulation of mutations and consequently to cancer transformation. OGG1 glycosylase, a component of the Base Excision Repair (BER) system, is one of the enzymes that prevents excessive accumulation of 8-oxoguanine (8-oxG), the most common compound formed by oxidative DNA damage. In case of structural changes of OGG1 resulting from polymorphic variants, we can observe a significant increase in the concentration of 8-oxG...
April 30, 2018: Polski Przeglad Chirurgiczny
https://www.readbyqxmd.com/read/29768722/genoprotective-effect-of-phyllanthus-orbicularis-extract-against-uva-uvb-and-solar-radiation
#2
Marioly Vernhes Tamayo, André Passaglia Schuch, Teiti Yagura, Luis Baly Gil, Carlos Frederico Martins Menck, Angel Sánchez-Lamar
One approach to protect the human skin against harmful effects of solar ultraviolet (UV) radiation is to use natural products as photoprotectors. In this work, the extract from specie Phyllanthus orbicularis K was evaluated as a protective agent against the photodamage by UVB, UVA artificial lamps and environmental sunlight exposure. The plasmid DNA solutions were exposed to radiations using the DNA-dosimeter system in presence of plant extract. The DNA repair enzymes, E. coli Formamidopyrimidine-DNA glycosylase (Fpg) and T4 bacteriophage endonuclease V (T4-endo V), were employed to discriminate oxidized DNA damage and cyclobutane pyrimidine dimers (CPD) respectively...
May 16, 2018: Photochemistry and Photobiology
https://www.readbyqxmd.com/read/29767793/inhalation-of-house-dust-and-ozone-alters-systemic-levels-of-endothelial-progenitor-cells-oxidative-stress-and-inflammation-in-elderly-subjects
#3
Kim Jantzen, Annie Jensen, Ali Kermanizadeh, Grethe Elholm, Torben Sigsgaard, Peter Møller, Martin Roursgaard, Steffen Loft
Ambient air pollution including ozone and especially particulate matter represents important causes of cardiovascular disease. However, there is limited knowledge on indoor air dust with respect to this risk and the potential interactions between dust and ozone. Here, we exposed 23 healthy elderly subjects for 5.5 h, to either clean air, house dust at 275 µg/m3 (diameter < 2.5 µm), ozone at 100 ppb or combined house dust and ozone in a double-blinded randomized cross-over study. The combined house dust and ozone exposure was associated with a 48% (95% CI 24%-65%) decrease as compared with the clean air exposure, in CD34+KDR+ late endothelial progenitor cells (EPCs) per leukocyte in the blood shortly after exposure, whereas none of the single exposures resulted in a significant effect...
May 14, 2018: Toxicological Sciences: An Official Journal of the Society of Toxicology
https://www.readbyqxmd.com/read/29762710/base-flipping-dynamics-from-an-intrahelical-to-an-extrahelical-state-exerted-by-thymine-dna-glycosylase-during-dna-repair-process
#4
Lin-Tai Da, Jin Yu
Thymine DNA glycosylase (TDG) is a DNA repair enzyme that excises a variety of mismatched or damaged nucleotides (nts), e.g. dU, dT, 5fC and 5caC. TDG is shown to play essential roles in maintaining genome integrity and correctly programming epigenetic modifications through DNA demethylation. After locating the lesions, TDG employs a base-flipping strategy to recognize the damaged nucleobases, whereby the interrogated nt is extruded from the DNA helical stack and binds into the TDG active site. The dynamic mechanism of the base-flipping process at an atomistic resolution, however, remains elusive...
May 14, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29747151/role-of-pon1-sod2-ogg1-xrcc1-and-xrcc4-polymorphisms-on-modulation-of-dna-damage-in-workers-occupationally-exposed-to-pesticides
#5
Vivian F Silva Kahl, Fernanda Rabaioli da Silva, Jodel da Silva Alves, Gabrieli Flesch da Silva, Juliana Picinini, Varinderpal Singh Dhillon, Michael Fenech, Melissa Rosa de Souza, Johnny F Dias, Claudia Telles de Souza, Mirian Salvador, Cátia Dos Santos Branco, Flávia Valadão Thiesen, Daniel Simon, Juliana da Silva
Tobacco farming has been proving to induce poor health outcomes in agricultural workers, genomic instability being the triggering one. This study evaluated influence of PON1 (paraoxonase 1), SOD2 (superoxide dismutase), OGG1 (8-oxoguanine glycosylase), XRCC1 (X-ray repair cross-complementing protein 1), and XRCC4 (X-ray repair cross-complementing protein 4) genes polymorphisms on DNA damage in 121 subjects occupationally exposed to pesticides mixtures and nicotine at tobacco fields and 121 non-exposed individuals...
May 7, 2018: Ecotoxicology and Environmental Safety
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
#6
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/29746250/cellular-assays-for-studying-the-fe-s-cluster-containing-base-excision-repair-glycosylase-mutyh-and-homologs
#7
Chandrima Majumdar, Nicole N Nuñez, Alan G Raetz, Cindy Khuu, Sheila S David
Many DNA repair enzymes, including the human adenine glycosylase MUTYH, require iron-sulfur (Fe-S) cluster cofactors for DNA damage recognition and subsequent repair. MUTYH prokaryotic and eukaryotic homologs are a family of adenine (A) glycosylases that cleave A when mispaired with the oxidatively damaged guanine lesion, 8-oxo-7,8-dihydroguanine (OG). Faulty OG:A repair has been linked to the inheritance of missense mutations in the MUTYH gene. These inherited mutations can result in the onset of a familial colorectal cancer disorder known as MUTYH-associated polyposis (MAP)...
2018: Methods in Enzymology
https://www.readbyqxmd.com/read/29746241/fe-s-clusters-and-muty-base-excision-repair-glycosylases-purification-kinetics-and-dna-affinity-measurements
#8
Nicole N Nuñez, Chandrima Majumdar, Kori T Lay, Sheila S David
A growing number of iron-sulfur (Fe-S) cluster cofactors have been identified in DNA repair proteins. MutY and its homologs are base excision repair (BER) glycosylases that prevent mutations associated with the common oxidation product of guanine (G), 8-oxo-7,8-dihydroguanine (OG) by catalyzing adenine (A) base excision from inappropriately formed OG:A mispairs. The finding of an [4Fe-4S]2+ cluster cofactor in MutY, Endonuclease III, and structurally similar BER enzymes was surprising and initially thought to represent an example of a purely structural role for the cofactor...
2018: Methods in Enzymology
https://www.readbyqxmd.com/read/29739980/systematic-analysis-of-demeter-like-dna-glycosylase-genes-shows-lineage-specific-smi-mir7972-involved-in-smdml1-regulation-in-salvia-miltiorrhiza
#9
Jiang Li, Caili Li, Shanfa Lu
DEMETER-like DNA glycosylases (DMLs) initiate the base excision repair-dependent DNA demethylation to regulate a wide range of biological processes in plants. Six putative SmDML genes, termed SmDML1-SmDML6, were identified from the genome of S. miltiorrhiza, an emerging model plant for Traditional Chinese Medicine (TCM) studies. Integrated analysis of gene structures, sequence features, conserved domains and motifs, phylogenetic analysis and differential expression showed the conservation and divergence of SmDMLs...
May 8, 2018: Scientific Reports
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
#10
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
#11
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/29722448/titanium-dioxide-nanoparticles-translocate-through-differentiated-caco-2-cell-monolayers-without-disrupting-the-barrier-functionality-or-inducing-genotoxic-damage
#12
Laura Vila, Alba García-Rodríguez, Ricard Marcos, Alba Hernández
The widespread use of titanium dioxide nanoparticles (TiO2 NPs) in commercial food products makes intestinal cells a suitable target. Accordingly, we have used the human colon adenocarcinoma Caco-2 cells to detect their potential harmful effects. Caco-2 cells can differentiate in to enterocytic-like cells, forming consistent cell monolayers and are used as a model of the intestinal barrier. Using both undifferentiated and differentiated Caco-2 cells, we have explored a set of biomarkers, aiming to evaluate undesirable effects associated to TiO2 NP exposure...
May 3, 2018: Journal of Applied Toxicology: JAT
https://www.readbyqxmd.com/read/29718661/the-fifth-domain-in-the-g-quadruplex-forming-sequence-of-the-human-neil3-promoter-locks-dna-folding-in-response-to-oxidative-damage
#13
Carla Alvarez Omaga, Aaron M Fleming, Cynthia J Burrows
DNA oxidation is an inevitable and usually detrimental process but the cell is capable of reversing this state due to possessing a highly developed set of DNA repair machineries, including the DNA glycosylase NEIL3 that is encoded by the NEIL3 gene. In this work, the G-rich promoter region of the human NEIL3 gene was shown to fold into a dynamic G-quadruplex (G4) structure under near physiological conditions using spectroscopic techniques (e.g., NMR, circular dichroism, fluorescence, and UV-vis) and DNA polymerase stop assays...
May 2, 2018: Biochemistry
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
#14
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/29712855/fact-complex-is-required-for-dna-demethylation-at-heterochromatin-during-reproduction-in-arabidopsis
#15
Jennifer M Frost, M Yvonne Kim, Guen Tae Park, Ping-Hung Hsieh, Miyuki Nakamura, Samuel J H Lin, Hyunjin Yoo, Jaemyung Choi, Yoko Ikeda, Tetsu Kinoshita, Yeonhee Choi, Daniel Zilberman, Robert L Fischer
The DEMETER (DME) DNA glycosylase catalyzes genome-wide DNA demethylation and is required for endosperm genomic imprinting and embryo viability. Targets of DME-mediated DNA demethylation reside in small, euchromatic, AT-rich transposons and at the boundaries of large transposons, but how DME interacts with these diverse chromatin states is unknown. The STRUCTURE SPECIFIC RECOGNITION PROTEIN 1 (SSRP1) subunit of the chromatin remodeler FACT (facilitates chromatin transactions), was previously shown to be involved in the DME-dependent regulation of genomic imprinting in Arabidopsis endosperm...
April 30, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29707704/integration-of-single-molecule-detection-with-magnetic-separation-for-multiplexed-detection-of-dna-glycosylases
#16
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/29698889/acetylation-of-oxidized-base-repair-initiating-neil1-dna-glycosylase-required-for-chromatin-bound-repair-complex-formation-in-the-human-genome-increases-cellular-resistance-to-oxidative-stress
#17
Shiladitya Sengupta, Chunying Yang, Muralidhar L Hegde, Pavana M Hegde, Joy Mitra, Arvind Pandey, Arijit Dutta, Abdul Tayyeb Datarwala, Kishor K Bhakat, Sankar Mitra
Posttranslational modifications of DNA repair proteins have been linked to their function. However, it is not clear if posttranslational acetylation affects subcellular localization of these enzymes. Here, we show that the human DNA glycosylase NEIL1, which is involved in repair of both endo- and exogenously generated oxidized bases via the base excision repair (BER) pathway, is acetylated by histone acetyltransferase p300. Acetylation occurs predominantly at Lys residues 296, 297 and 298 located in NEIL1's disordered C-terminal domain...
April 17, 2018: DNA Repair
https://www.readbyqxmd.com/read/29698444/formalin-fixation-increases-deamination-mutation-signature-but-should-not-lead-to-false-positive-mutations-in-clinical-practice
#18
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/29689355/is-oxidative-stress-involved-in-the-sex-dependent-response-to-ochratoxin-a-renal-toxicity
#19
José Manuel Enciso, Adela López de Cerain, Laura Pastor, Amaya Azqueta, Ariane Vettorazzi
Ochratoxin A (OTA) is a mycotoxin considered the most powerful renal carcinogen in rodents and classified as a possible human carcinogen. Though its mechanism of action is still unknown, indirect DNA reactivity mediated by oxidative stress has been hypothesized to play an important role. Moreover, large sex-differences have been observed in carcinogenicity studies, male rats being more sensitive than females. Male and female F344 rats were administered (p.o.) with bicarbonate or 0.5 mg OTA/kg b.w. for 7 days; or with bicarbonate, 0...
April 21, 2018: Food and Chemical Toxicology
https://www.readbyqxmd.com/read/29685966/excision-of-the-doubly-methylated-base-n-4-5-dimethylcytosine-from-dna-by-escherichia-coli-nei-and-fpg-proteins
#20
Marina Alexeeva, Prashanna Guragain, Almaz N Tesfahun, Miglė Tomkuvienė, Aysha Arshad, Rūta Gerasimaitė, Audronė Rukšėnaitė, Giedrė Urbanavičiūtė, Magnar Bjørås, Jon K Laerdahl, Arne Klungland, Saulius Klimašauskas, Svein Bjelland
Cytosine (C) in DNA is often modified to 5-methylcytosine (m5 C) to execute important cellular functions. Despite the significance of m5 C for epigenetic regulation in mammals, damage to m5 C has received little attention. For instance, almost no studies exist on erroneous methylation of m5 C by alkylating agents to doubly or triply methylated bases. Owing to chemical evidence, and because many prokaryotes express methyltransferases able to convert m5 C into N 4 ,5-dimethylcytosine (m N 4,5 C) in DNA, m N 4,5 C is probably present in vivo We screened a series of glycosylases from prokaryotic to human and found significant DNA incision activity of the Escherichia coli Nei and Fpg proteins at m N 4,5 C residues in vitro The activity of Nei was highest opposite cognate guanine followed by adenine, thymine (T) and C...
June 5, 2018: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
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