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DNA glycosylases

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https://www.readbyqxmd.com/read/28747435/search-for-dna-damage-by-human-alkyladenine-dna-glycosylase-involves-early-intercalation-by-an-aromatic-residue
#1
Jenna M Hendershot, Patrick J O'Brien
DNA repair enzymes recognize and remove damaged bases that are embedded in the duplex. To gain access, most enzymes use nucleotide flipping , whereby the target nucleotide is rotated 180 degree into the active site. In human alkyladenine DNA glycosylase (AAG), the enzyme that initiates base excision repair of alkylated bases, the flipped-out nucleotide is stabilized by intercalation of the side chain of tyrosine 162 that replaces the lesion nucleobase. Previous kinetic studies provided evidence for the formation of a transient complex that precedes the stable flipped-out complex, but it is not clear how this complex differs from nonspecific complexes...
July 26, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28746850/investigation-of-n-terminal-phospho-regulation-of%C3%A2-uracil-dna-glycosylase-using-protein-semisynthesis
#2
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/28727777/8-oxoguanine-dna-glycosylase-ogg1-deficiency-elicits-coordinated-changes-in-lipid-and-mitochondrial-metabolism-in-muscle
#3
Vladimir Vartanian, Jana Tumova, Pawel Dobrzyn, Agnieszka Dobrzyn, Yusaku Nakabeppu, R Stephen Lloyd, Harini Sampath
Oxidative stress resulting from endogenous and exogenous sources causes damage to cellular components, including genomic and mitochondrial DNA. Oxidative DNA damage is primarily repaired via the base excision repair pathway that is initiated by DNA glycosylases. 8-oxoguanine DNA glycosylase (OGG1) recognizes and cleaves oxidized and ring-fragmented purines, including 8-oxoguanine, the most commonly formed oxidative DNA lesion. Mice lacking the OGG1 gene product are prone to multiple features of the metabolic syndrome, including high-fat diet-induced obesity, hepatic steatosis, and insulin resistance...
2017: PloS One
https://www.readbyqxmd.com/read/28727736/persistent-damaged-bases-in-dna-allow-mutagenic-break-repair-in-escherichia-coli
#4
Jessica M Moore, Raul Correa, Susan M Rosenberg, P J Hastings
Bacteria, yeast and human cancer cells possess mechanisms of mutagenesis upregulated by stress responses. Stress-inducible mutagenesis potentially accelerates adaptation, and may provide important models for mutagenesis that drives cancers, host pathogen interactions, antibiotic resistance and possibly much of evolution generally. In Escherichia coli repair of double-strand breaks (DSBs) becomes mutagenic, using low-fidelity DNA polymerases under the control of the SOS DNA-damage response and RpoS general stress response, which upregulate and allow the action of error-prone DNA polymerases IV (DinB), II and V to make mutations during repair...
July 20, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28723094/structure-activity-relationships-reveal-key-features-of-8-oxoguanine-adenine-mismatch-detection-by-the-muty-dna-glycosylase
#5
Amelia H Manlove, Paige L McKibbin, Emily L Doyle, Chandrima Majumdar, Michelle L Hamm, Sheila S David
Base excision repair glycosylases locate and remove damaged based in DNA with remarkable specificity. The MutY glycosylases, unusual for their excision of undamaged adenines mispaired to the oxidized base 8-oxoguanine (OG), must recognize both bases of the mispair in order to prevent promutagenic activity. Moreover, MutY must effectively find OG:A mismatches within the context of highly abundant and structurally similar T:A base-pairs. Very little is known about the factors that initiate MutY's interaction with the substrate when it first encounters an intrahelical OG:A mispair, or about the order of recognition checkpoints...
July 19, 2017: ACS Chemical Biology
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
#6
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...
July 18, 2017: Clinical Chemistry
https://www.readbyqxmd.com/read/28719838/identification-of-a-prototypical-single-stranded-uracil-dna-glycosylase-from-listeria-innocua
#7
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...
July 8, 2017: DNA Repair
https://www.readbyqxmd.com/read/28715893/5-formyl-and-5-carboxydeoxycytidines-do-not-cause-accumulation-of-harmful-repair-intermediates-in-stem-cells
#8
René Rahimoff, Olesea Kosmatchev, Angie Kirchner, Toni Pfaffeneder, Fabio Spada, Victor Brantl, Markus Müller, Thomas Carell
5-Formyl-dC (fdC) and 5-carboxy-dC (cadC) are newly discovered bases in the mammalian genome that are supposed to be substrates for base excision repair (BER) in the framework of active demethylation. The bases are recognized by the monofunctional thymine DNA glycosylase (Tdg), which cleaves the glycosidic bond of the bases to give potentially harmful abasic sites (AP-sites). Because of the turnover of fdC and cadC during cell state transitions, it is an open question to what extent such harmful AP-sites may accumulate during these processes...
July 21, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28715891/s-k-edge-xas-studies-of-the-effect-of-dna-binding-on-the-fe4s4-site-in-endoiii-and-muty
#9
Yang Ha, Anna R Arnold, Nicole N Nuñez, Phillip L Bartels, Andy Zhou, Sheila S David, Jacqueline K Barton, Britt Hedman, Keith O Hodgson, Edward I Solomon
S K-edge X-ray Absorption Spectroscopy (XAS) was used to study the [Fe4S4] clusters in the DNA repair glycosylases EndoIII and MutY to evaluate the effects of DNA binding and solvation on Fe-S bond covalencies (ie. the amount of S 3p character mixed into the Fe 3d valence orbitals). Increased covalencies in both iron-thiolate and iron-sulfide bonds would stabilize the oxidized state of the [Fe4S4] clusters. The results are compared to those on previously studied [Fe4S4] model complexes, ferredoxin (Fd), and to new data on high potential iron-sulfur protein (HiPIP)...
July 18, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28709140/spectroelectrochemical-insights-into-structural-and-redox-properties-of-immobilized-endonuclease-iii-and-its-catalytically-inactive-mutant
#10
Elin Moe, Filipe Rollo, Célia M Silveira, Murat Sezer, Peter Hildebrandt, Smilja Todorovic
Endonuclease III is a Fe-S containing bifunctional DNA glycosylase which is involved in the repair of oxidation damaged DNA. Here we employ surface enhanced IR spectroelectrochemistry and electrochemistry to study the enzyme from the highly radiation- and desiccation-resistant bacterium Deinococcus radiodurans (DrEndoIII2). The experiments are designed to shed more light onto specific parameters that are currently proposed to govern damage search and recognition by endonucleases III. We demonstrate that electrostatic interactions required for the redox activation of DrEndoIII2 may result in high electric fields that alter its structural and thermodynamic properties...
July 5, 2017: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
https://www.readbyqxmd.com/read/28709015/human-cells-contain-a-factor-that-facilitates-the-dna-glycosylase-mediated-excision-of-oxidized-bases-from-occluded-sites-in-nucleosomes
#11
R L Maher, C G Marsden, A M Averill, S S Wallace, J B Sweasy, D S Pederson
Reactive oxygen species generate some 20,000 base lesions per human cell per day. The vast majority of these potentially mutagenic or cytotoxic lesions are subject to base excision repair (BER). Although chromatin remodelers have been shown to enhance the excision of oxidized bases from nucleosomes in vitro, it is not clear that they are recruited to and act at sites of BER in vivo. To test the hypothesis that cells possess factors that enhance BER in chromatin, we assessed the capacity of nuclear extracts from human cells to excise thymine glycol (Tg) lesions from exogenously added, model nucleosomes...
July 5, 2017: DNA Repair
https://www.readbyqxmd.com/read/28696896/assessment-of-dna-damage-in-a-group-of-professional-dancers-during-a-10-month-dancing-season
#12
Filipa Esteves, Eduardo Teixeira, Tânia Amorim, Carla Costa, Cristiana Pereira, Sónia Fraga, Vanessa Moraes De Andrade, João Paulo Teixeira, Solange Costa
Despite the numerous health benefits of physical activity, some studies reported that increased intensity and duration may induce oxidative stress in several cellular components including DNA. The aim of this study was to assess the level of basal DNA damage as well as oxidative DNA damage in a group of professional dancers before and after a 10-month dancing season. A group of individuals from general population was also assessed as a control. The alkaline version of the comet assay was the method selected to measure both basal DNA damage and oxidative stress, since this method quantifies both endpoints...
July 11, 2017: Journal of Toxicology and Environmental Health. Part A
https://www.readbyqxmd.com/read/28684912/the-effects-of-grafted-mesenchymal-stem-cells-labeled-with-iron-oxide-or-cobalt-zinc-iron-nanoparticles-on-the-biological-macromolecules-of-rat-brain-tissue-extracts
#13
Bozena Novotna, Vit Herynek, Pavel Rossner, Karolina Turnovcova, Pavla Jendelova
INTRODUCTION: Rat mesenchymal stem cells (rMSCs) labeled with 1) poly-l-lysine-coated superparamagnetic iron oxide nanoparticles or 2) silica-coated cobalt-zinc-iron nanoparticles were implanted into the left brain hemisphere of rats, to assess their effects on the levels of oxidative damage to biological macromolecules in brain tissue. METHODS: Controls were implanted with unlabeled rMSCs. Animals were sacrificed 24 hours or 4 weeks after the treatment, and the implantation site along with the surrounding tissue was isolated from the brain...
2017: International Journal of Nanomedicine
https://www.readbyqxmd.com/read/28683413/pyrrolo-dc-modified-duplex-dna-as-a-novel-probe-for-the-sensitive-assay-of-base-excision-repair-enzyme-activity
#14
Chang Yeol Lee, Ki Soo Park, Hyun Gyu Park
We develop a novel approach to determine formamidopyrimidine DNA glycosylase (Fpg) activity by taking advantage of the unique fluorescence property of pyrrolo-dC (PdC) positioned opposite to 8-oxoguanine (8-oxoG) in duplex DNA. In its initial state, PdC in duplex DNA undergoes the efficient stacking and collisional quenching interactions, showing the low fluorescence signal. In contrast, the presence of Fpg, which specifically removes 8-oxoG and incises resulting apurinic (AP) site, transforms duplex DNA into single-stranded (ss) DNAs...
June 27, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28675037/sensitive-detection-of-dna-lesions-by-bulge-enhanced-highly-specific-coamplification-at-lower-denaturation-temperature-polymerase-chain-reaction
#15
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/28668128/transient-kinetic-methods-for-mechanistic-characterization-of-dna-binding-and-nucleotide-flipping
#16
Jenna M Hendershot, Patrick J O'Brien
Enzymes that modify nucleobases in double-stranded genomic DNA, either as part of a DNA repair pathway or as an epigenetic modifying pathway, adopt a multistep pathway to locate target sites and reconfigure the DNA to gain access. Work on several different enzymes has shown that in almost all cases base flipping, also known as nucleotide flipping, is a key feature of specific site recognition. In this chapter, we discuss some of the strategies that can be used to perform a kinetic characterization for DNA binding and nucleotide flipping...
2017: Methods in Enzymology
https://www.readbyqxmd.com/read/28668127/kinetic-methods-for-studying-dna-glycosylases-functioning-in-base-excision-repair
#17
Christopher T Coey, Alexander C Drohat
Base excision repair (BER) is a conserved and ubiquitous pathway that is initiated by DNA glycosylases, which recognize and remove damaged or mismatched nucleobases, setting the stage for restoration of the correct DNA sequence by follow-on BER enzymes. DNA glycosylases employ a nucleotide-flipping step prior to cleavage of the N-glycosyl bond, and most exhibit slow release of the abasic DNA product and/or strong product inhibition. As such, studying the catalytic mechanism of these enzymes requires care in the design, execution, and interpretation of single- and multiple-turnover kinetics experiments, which is the topic of this chapter...
2017: Methods in Enzymology
https://www.readbyqxmd.com/read/28665322/pre-replicative-repair-of-oxidized-bases-maintains-fidelity-in-mammalian-genomes-the-cowcatcher-role-of-neil1-dna-glycosylase
#18
Suganya Rangaswamy, Arvind Pandey, Sankar Mitra, Muralidhar L Hegde
Genomic fidelity in the humans is continuously challenged by genotoxic reactive oxygen species (ROS) generated both endogenously during metabolic processes, and by exogenous agents. Mispairing of most ROS-induced oxidized base lesions during DNA replication induces mutations. Although bulky base adducts induced by ultraviolet light and other environmental mutagens block replicative DNA polymerases, most oxidized base lesions do not block DNA synthesis. In 8-oxo-G:A mispairs generated by the incorporation of A opposite unrepaired 8-oxo-G, A is removed by MutYH (MYH) for post-replicative repair, and other oxidized base lesions must be repaired prior to replication in order to prevent mutation fixation...
June 30, 2017: Genes
https://www.readbyqxmd.com/read/28663564/no-cancer-predisposition-or-increased-spontaneous-mutation-frequencies-in-neil-dna-glycosylases-deficient-mice
#19
Veslemøy Rolseth, Luisa Luna, Ann Karin Olsen, Rajikala Suganthan, Katja Scheffler, Christine G Neurauter, Ying Esbensen, Anna Kuśnierczyk, Gunn A Hildrestrand, Anne Graupner, Jill M Andersen, Geir Slupphaug, Arne Klungland, Hilde Nilsen, Magnar Bjørås
Base excision repair (BER) is a major pathway for removal of DNA base lesions and maintenance of genomic stability, which is essential in cancer prevention. DNA glycosylases recognize and remove specific lesions in the first step of BER. The existence of a number of these enzymes with overlapping substrate specificities has been thought to be the reason why single knock-out models of individual DNA glycosylases are not cancer prone. In this work we have characterized DNA glycosylases NEIL1 and NEIL2 (Neil1 (-/-) /Neil2 (-/-)) double and NEIL1, NEIL2 and NEIL3 (Neil1 (-/-) /Neil2 (-/-) /Neil3 (-/-)) triple knock-out mouse models...
June 29, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28662073/apng-as-a-prognostic-marker-in-patients-with-glioblastoma
#20
Sigurd Fosmark, Sofie Hellwege, Rikke H Dahlrot, Kristian L Jensen, Helene Derand, Jesper Lohse, Mia D Sørensen, Steinbjørn Hansen, Bjarne W Kristensen
AIM: Expression of the base excision repair enzyme alkylpurine-DNA-N-glycosylase (APNG) has been correlated to temozolomide resistance. Our aim was to evaluate the prognostic value of APNG in a population-based cohort with 242 gliomas including 185 glioblastomas (GBMs). Cellular heterogeneity of GBMs was taken into account by excluding APNG expression in non-tumor cells from the analysis. METHODS: APNG expression was evaluated using automated image analysis and a novel quantitative immunohistochemical (IHC) assay (qIHC), where APNG protein expression was evaluated through countable dots...
2017: PloS One
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