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DNA glycosylases

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https://www.readbyqxmd.com/read/28517932/mechanism-of-discrimination-of-8-oxoguanosine-versus-guanosine-by-e-coli-fpg
#1
Namrata Jayanth, Mrinalini Puranik
The mutagenic 8-oxoguanosine monophosphate 1, the predominant product of DNA oxidation, is excised by formamidopyrimidine glycosylase (Fpg) in bacteria. The mechanism of recognition of 8-oxodG, which differs subtly from its normal counterpart, guanosine monophosphate (dG), by E. coli Fpg remains elusive due to the lack of structural data of E. coli Fpg bound to 8-oxodG. Here, we present solution-state structure of 8-oxodG oligomer bound to E. coli E3Q Fpg using UV resonance Raman (UVRR) spectroscopy. The vibrational spectra report on the π-stacking and hydrogen bonding interactions established by 8-oxodG with E...
May 18, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28514671/evaluation-of-improved-is6110-lamp-assay-for-diagnosis-of-pulmonary-and-extra-pulmonary-tuberculosis
#2
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/28514164/the-non-bulky-dna-lesions-spiroiminodihydantoin-and-5-guanidinohydantoin-significantly-block-human-rna-polymerase-ii-elongation-in-vitro
#3
Marina Kolbanovskiy, Moinuddin A Chowdhury, Aditi Nadkarni, Suse Broyde, Nicholas E Geacintov, David A Scicchitano, Vladimir Shafirovich
The most common, oxidatively generated lesion in cellular DNA is 8-oxo-7,8-dihydroguanine, which can be oxidized further to yield highly mutagenic spiroiminodihydantoin (Sp) and 5-guanidinohydantoin (Gh) in DNA. In human cell-free extracts, both lesions can be excised by base excision repair and global genomic nucleotide excision repair. However, it is not known if these lesions can be removed by transcription-coupled DNA repair (TCR), a pathway that clears lesions from DNA that impede RNA synthesis. To determine if Sp or Gh impede transcription, which could make them viable substrates for TCR, either an Sp or a Gh lesion was positioned on the transcribed strand of DNA under the control of a promoter that supports transcription by human RNA polymerase II...
May 17, 2017: Biochemistry
https://www.readbyqxmd.com/read/28507144/critical-roles-of-dna-demethylation-in-the-activation-of-ripening-induced-genes-and-inhibition-of-ripening-repressed-genes-in-tomato-fruit
#4
Zhaobo Lang, Yihai Wang, Kai Tang, Dengguo Tang, Tatsiana Datsenka, Jingfei Cheng, Yijing Zhang, Avtar K Handa, Jian-Kang Zhu
DNA methylation is a conserved epigenetic mark important for genome integrity, development, and environmental responses in plants and mammals. Active DNA demethylation in plants is initiated by a family of 5-mC DNA glycosylases/lyases (i.e., DNA demethylases). Recent reports suggested a role of active DNA demethylation in fruit ripening in tomato. In this study, we generated loss-of-function mutant alleles of a tomato gene, SlDML2, which is a close homolog of the Arabidopsis DNA demethylase gene ROS1 In the fruits of the tomato mutants, increased DNA methylation was found in thousands of genes...
May 15, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28505099/mutational-and-kinetic-analysis-of-lesion-recognition-by-escherichia-coli-endonuclease-viii
#5
Olga A Kladova, Alexandra A Kuznetsova, Olga S Fedorova, Nikita A Kuznetsov
Escherichia coli endonuclease VIII (Endo VIII) is a DNA glycosylase with substrate specificity for a wide range of oxidatively damaged pyrimidine bases. Endo VIII catalyzes hydrolysis of the N-glycosidic bond and β, δ-elimination of 3'- and 5'-phosphate groups of an apurinic/apyrimidinic site. Single mutants of Endo VIII L70S, L70W, Y71W, F121W, F230W, and P253W were analyzed here with the aim to elucidate the kinetic mechanism of protein conformational adjustment during damaged-nucleotide recognition and catalytic-complex formation...
May 13, 2017: Genes
https://www.readbyqxmd.com/read/28503778/a-topical-zinc-ionophore-blocks-tumorigenic-progression-in-uv-exposed-skh-1-high-risk-mouse-skin
#6
Rebecca Justiniano, Jessica Perer, Anh Hua, Mohammad Fazel, Andrea Krajisnik, Christopher M Cabello, Georg T Wondrak
Nonmelanoma skin cancer (NMSC) is the most common malignancy in the United States representing a considerable public health burden. Pharmacological suppression of skin photo-carcinogenesis has shown promise in preclinical and clinical studies, but more efficacious photochemopreventive agents are needed. Here, we tested feasibility of harnessing pharmacological disruption of intracellular zinc-homeostasis for photochemoprevention in vitro and in vivo. Employing the zinc-ionophore and FDA-approved microbicidal agent zinc pyrithione (ZnPT), used worldwide in over-the-counter (OTC) topical consumer products, we first demonstrated feasibility of achieving ZnPT-based intracellular Zn(2+) -overload in cultured malignant keratinocytes (HaCaT-ras II-4; SCC-25) employing membrane-permeable fluorescent probes...
May 15, 2017: Photochemistry and Photobiology
https://www.readbyqxmd.com/read/28482831/molecular-dynamics-simulation-of-the-opposite-base-preference-and-interactions-in-the-active-site-of-formamidopyrimidine-dna-glycosylase
#7
Alexander V Popov, Anton V Endutkin, Yuri N Vorobjev, Dmitry O Zharkov
BACKGROUND: Formamidopyrimidine-DNA glycosylase (Fpg) removes abundant pre-mutagenic 8-oxoguanine (oxoG) bases from DNA through nucleophilic attack of its N-terminal proline at C1' of the damaged nucleotide. Since oxoG efficiently pairs with both C and A, Fpg must excise oxoG from pairs with C but not with A, otherwise a mutation occurs. The crystal structures of several Fpg-DNA complexes have been solved, yet no structure with A opposite the lesion is available. RESULTS: Here we use molecular dynamic simulation to model interactions in the pre-catalytic complex of Lactococcus lactis Fpg with DNA containing oxoG opposite C or A, the latter in either syn or anti conformation...
May 8, 2017: BMC Structural Biology
https://www.readbyqxmd.com/read/28475923/evaluation-of-imazethapyr-induced-dna-oxidative-damage-by-alkaline-endo-iii-and-fpg-modified-single-cell-gel-electrophoresis-assay-in-hypsiboas-pulchellus-tadpoles-anura-hylidae
#8
Juan Manuel Pérez-Iglesias, Celeste Ruiz de Arcaute, Guillermo S Natale, S Soloneski, Marcelo L Larramendy
Imazethapyr (IMZT) is a selective postemergent herbicide with residual action. Available data analyzing its effects in aquatic vertebrates are scarce. In previous studies, we demonstrated that IMZT induces lesions into the DNA of Hypsiboas pulchellus tadpoles using the single-cell gel electrophoresis (SCGE) assay as a biomarker for genotoxicity. Currently, this assay can be modified by including incubation with lesion-specific endonucleases, e.g., endonuclease III (Endo III) and formamidopyrimidine-DNA glycosylase (Fpg), which detect oxidized pyrimidine and purine bases, respectively...
August 2017: Ecotoxicology and Environmental Safety
https://www.readbyqxmd.com/read/28465192/lung-inflammation-and-genotoxicity-in-mice-lungs-after-pulmonary-exposure-to-candle-light-combustion-particles
#9
Astrid Skovmand, Ana Cecilia Damiao Gouveia, Ismo Kalevi Koponen, Peter Møller, Steffen Loft, Martin Roursgaard
Candle burning produces a large amount of particles that contribute substantially to the exposure to indoor particulate matter. The exposures to various types of combustion particles, such as diesel exhaust particles, have been associated with increased risk of lung cancer by mechanisms that involve oxidative stress, inflammation and genotoxicity. The aim of this study was to compare pulmonary effects of candle light combustion particles (CP) with two benchmark diesel exhaust particles (A-DEP and SRM2975). Intratracheal (i...
April 29, 2017: Toxicology Letters
https://www.readbyqxmd.com/read/28464993/genotoxicity-of-two-new-carbazole-derivatives-with-antifungal-activity
#10
Aliy K Zhanataev, Natalya V Eremina, Zlata V Chayka, Vasily I Kazey, Ekaterina L Andrianova, Andrei A Purmal, Elena B Rydkina, Andrey D Durnev
The class of carbazoles includes compounds with high biological activities and broad spectra of action. PLX01107 and PLX01008 are xenomycins, a new subclass of antimicrobial carbazole derivatives demonstrating strong antifungal activity in vitro. We performed three tests, a bacterial reverse mutation assay (Ames test), in vitro cytokinesis-block micronucleus assay, and chromosome aberration test in mouse bone marrow cells, to investigate the possible genotoxicity of these compounds. Despite their structural similarity, the two compounds had different genotoxicity profiles...
April 2017: Mutation Research
https://www.readbyqxmd.com/read/28464992/2-nitroanisole-induced-oxidative-dna-damage-in-salmonella-typhimurium-and-in-rat-urinary-bladder-cells
#11
Kunio Wada, Yoshitaka Katoh, Aya Ohnuma-Koyama, Naofumi Takahashi, Masami Yamada, Kyomu Matsumoto
2-Nitroanisole (2-NA) is used in the manufacturing of azo dyes and causes cancer, mainly in the urinary bladder. Previous in vivo genotoxic data seems to be insufficient to explain the mechanism through which 2-NA induces carcinogenesis, and several bladder carcinogens were reported to induce oxidative DNA damage. Thus, we examined the potential induction of oxidative DNA damage by 2-NA using bacterial strain YG3008, a mutMST-deficient derivative of strain TA100. Consequently, strain YG3008, when compared with strain TA100, was found to be more sensitive to 2-NA, indicating oxidative DNA damage in bacterial cells...
April 2017: Mutation Research
https://www.readbyqxmd.com/read/28461979/search-for-modified-dna-sites-with-the-human-methyl-cpg-binding-enzyme-mbd4
#12
D A Yakovlev, A A Kuznetsova, O S Fedorova, N A Kuznetsov
The MBD4 enzyme initiates the process of DNA demethylation by the excision of modified DNA bases, resulting in the formation of apurinic/apyrimidinic sites. MBD4 contains a methyl-CpG-binding domain which provides the localization of the enzyme at the CpG sites, and a DNA glycosylase domain that is responsible for the catalytic activity. The aim of this work was to clarify the mechanisms of specific site recognition and formation of catalytically active complexes between model DNA substrates and the catalytic N-glycosylase domain MBD4cat...
January 2017: Acta Naturae
https://www.readbyqxmd.com/read/28448977/is-human-oxoguanine-glycosylase-1-genetic-variant-successful-even-on-oral-squamous-cell-carcinoma
#13
Levent Aydemir, Elif Sinem Bireller, Hakan Avci, Zeynep Boy Metin, Kemal Deger, Meral Unur, Bedia Cakmakoglu
BACKGROUND: Oral squamous cell carcinoma (OSCC) is one of the most widespread cancer types that arise from different sites of oral cavity and has a 5-year survival rate. This study is aimed at investigating the human oxoguanine glycosylase 1 (hOGG1)-Ser326Cys and APE-Asp148Glu polymorphisms of DNA repair genes in OSCC. MATERIALS AND METHODS: We investigated the hOGG1-Ser326Cys and APE-Asp148Glu polymorphisms of DNA repair genes in the oral cavity. Genotyping was conducted using polymerase chain reaction-restriction fragment length polymorphism analysis based on 132 patients who were diagnosed as having OSCC and 160 healthy subjects...
April 28, 2017: Pathobiology: Journal of Immunopathology, Molecular and Cellular Biology
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/28426967/an-intrinsic-epigenetic-barrier-for-functional-axon-regeneration
#16
Yi-Lan Weng, Ran An, Jessica Cassin, Jessica Joseph, Ruifa Mi, Chen Wang, Chun Zhong, Seung-Gi Jin, Gerd P Pfeifer, Alfonso Bellacosa, Xinzhong Dong, Ahmet Hoke, Zhigang He, Hongjun Song, Guo-Li Ming
Mature neurons in the adult peripheral nervous system can effectively switch from a dormant state with little axonal growth to robust axon regeneration upon injury. The mechanisms by which injury unlocks mature neurons' intrinsic axonal growth competence are not well understood. Here, we show that peripheral sciatic nerve lesion in adult mice leads to elevated levels of Tet3 and 5-hydroxylmethylcytosine in dorsal root ganglion (DRG) neurons. Functionally, Tet3 is required for robust axon regeneration of DRG neurons and behavioral recovery...
April 19, 2017: Neuron
https://www.readbyqxmd.com/read/28415770/human-8-oxoguanine-dna-glycosylase-gene-polymorphism-ser326cys-and-cancer-risk-updated-meta-analysis
#17
Sang Wook Kang, Su Kang Kim, Hae Jeong Park, Joo-Ho Chung, Ju Yeon Ban
Genetic polymorphism of human 8-oxoguanine glycosylase 1 (hOGG1) has been reported to have a relationship with the risk of the development of various cancers. Many studies have described the influence of Ser326Cys polymorphism of the hOGG1 gene on cancer susceptibility. However, the results have remained inconclusive and controversial. Therefore, we performed a meta-analysis to more precisely determine the relationship between the hOGG1 polymorphism and the development of cancer.Electronic databases including PubMed, Embase, Google Scholar, and the Korean Studies Information Service System (KISS) were searched...
March 15, 2017: Oncotarget
https://www.readbyqxmd.com/read/28397787/correlated-mutation-in-the-evolution-of-catalysis-in-uracil-dna-glycosylase-superfamily
#18
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/28396405/structure-of-a-dna-glycosylase-that-unhooks-interstrand-cross-links
#19
Elwood A Mullins, Garrett M Warren, Noah P Bradley, Brandt F Eichman
DNA glycosylases are important editing enzymes that protect genomic stability by excising chemically modified nucleobases that alter normal DNA metabolism. These enzymes have been known only to initiate base excision repair of small adducts by extrusion from the DNA helix. However, recent reports have described both vertebrate and microbial DNA glycosylases capable of unhooking highly toxic interstrand cross-links (ICLs) and bulky minor groove adducts normally recognized by Fanconi anemia and nucleotide excision repair machinery, although the mechanisms of these activities are unknown...
April 25, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28395718/-over-expression-of-uracil-dna-glycosylase-2-ung2-enhances-the-resistance-to-oxidative-damage-in-hepg2-cells
#20
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
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