1
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Kasai H, Kawasaki Y, Kawai K. Pyrimidine Ring-Opened Product from Oxidative DNA Damage of 5-Formyl-2'-deoxyuridine. Chem Res Toxicol 2019; 32:737-744. [PMID: 30785277 DOI: 10.1021/acs.chemrestox.8b00401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
After thymidine (dT) was treated with a Fenton-type reagent and further incubated for a long period (6 days) under physiological conditions (37 °C, pH 7.4), a new product, named dT*, was detected by HPLC in addition to the free thymine base and the known oxidative dT damage, 5-formyl-2'-deoxyuridine (f5dU). dT* was found to be formed from f5dU. The structure of dT* was determined to be 3-amino-2-carbamoyl-2-propenal-N3-2'-deoxyriboside, a pyrimidine ring-opened product from f5dU, on the basis of 1H- and 13C NMR analyses and mass spectra. From the model compound 1-methyl-5-formyluracil, a similar ring-opened product was formed after the incubation. dT* was also detected in DNA treated with a Fenton-type reagent or γ-rays, followed by the prolonged incubation. dT* will be a new promising marker of oxidative DNA damage. The possible role of this product in oxy-radical-induced mutagenesis is discussed.
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Affiliation(s)
- Hiroshi Kasai
- Department of Environmental Oncology, Institute of Industrial Ecological Sciences , University of Occupational and Environmental Health , 807-8555 Kitakyushu , Japan
| | - Yuya Kawasaki
- Department of Environmental Oncology, Institute of Industrial Ecological Sciences , University of Occupational and Environmental Health , 807-8555 Kitakyushu , Japan
| | - Kazuaki Kawai
- Department of Environmental Oncology, Institute of Industrial Ecological Sciences , University of Occupational and Environmental Health , 807-8555 Kitakyushu , Japan
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2
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Kuznetsova AA, Iakovlev DA, Misovets IV, Ishchenko AA, Saparbaev MK, Kuznetsov NA, Fedorova OS. Pre-steady-state kinetic analysis of damage recognition by human single-strand selective monofunctional uracil-DNA glycosylase SMUG1. MOLECULAR BIOSYSTEMS 2018; 13:2638-2649. [PMID: 29051947 DOI: 10.1039/c7mb00457e] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
In all organisms, DNA glycosylases initiate base excision repair pathways resulting in removal of aberrant bases from DNA. Human SMUG1 belongs to the superfamily of uracil-DNA glycosylases catalyzing the hydrolysis of the N-glycosidic bond of uridine and uridine lesions bearing oxidized groups at C5: 5-hydroxymethyluridine (5hmU), 5-formyluridine (5fU), and 5-hydroxyuridine (5hoU). An apurinic/apyrimidinic (AP) site formed as the product of an N-glycosylase reaction is tightly bound to hSMUG1, thus inhibiting the downstream action of AP-endonuclease APE1. The steady-state kinetic parameters (kcat and KM; obtained from the literature) correspond to the enzyme turnover process limited by the release of hSMUG1 from the complex with the AP-site. In the present study, our objective was to carry out a stopped-flow fluorescence analysis of the interaction of hSMUG1 with a DNA substrate containing a dU:dG base pair to follow the pre-steady-state kinetics of conformational changes in both molecules. A comparison of kinetic data obtained by means of Trp and 2-aminopurine fluorescence and Förster resonance energy transfer (FRET) detection allowed us to elucidate the stages of specific and nonspecific DNA binding, to propose the mechanism of damaged base recognition by hSMUG1, and to determine the true rate of the catalytic step. Our results shed light on the kinetic mechanism underlying the initiation of base excision repair by hSMUG1 using the "wedge" strategy for DNA lesion search.
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Affiliation(s)
- Alexandra A Kuznetsova
- Institute of Chemical Biology and Fundamental Medicine (ICBFM), Siberian Branch of Russian Academy of Sciences, 8 Lavrentyev Ave., Novosibirsk 630090, Russia.
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3
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Aparici-Espert I, Garcia-Lainez G, Andreu I, Miranda MA, Lhiaubet-Vallet V. Oxidatively Generated Lesions as Internal Photosensitizers for Pyrimidine Dimerization in DNA. ACS Chem Biol 2018; 13:542-547. [PMID: 29300457 DOI: 10.1021/acschembio.7b01097] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
In this work, the attention is focused on UVA-photosensitized reactions triggered by a DNA chromophore-containing lesion, namely 5-formyluracil. This is a major oxidatively generated lesion that exhibits an enhanced light absorption in the UVB-UVA region. The mechanistic study combining photochemical and photobiological techniques shows that irradiation of 5-formyluracil leads to a triplet excited state capable of sensitizing formation of cyclobutane pyrimidine dimers in DNA via a triplet-triplet energy transfer. This demonstrates for the first time that oxidatively generated DNA damage can behave as an intrinsic sensitizer and result in an important extension of the active fraction of the solar spectrum with photocarcinogenic potential. Overall, this raises the question of an aggravated photomutagenicity of the 5-formyluracil lesion.
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Affiliation(s)
- Isabel Aparici-Espert
- Instituto Universitario Mixto de Tecnología Química (UPV-CSIC), Universitat Politècnica de València, Consejo Superior de Investigaciones Científicas, Avenida de los Naranjos, s/n, 46022, Valencia (Spain)
| | - Guillermo Garcia-Lainez
- Instituto de Investigación Sanitaria La Fe, Hospital Universitari i Politècnic La Fe, Avenida de Fernando Abril Martorell 106, 46026 Valencia (Spain)
| | - Inmaculada Andreu
- Instituto de Investigación Sanitaria La Fe, Hospital Universitari i Politècnic La Fe, Avenida de Fernando Abril Martorell 106, 46026 Valencia (Spain)
| | - Miguel Angel Miranda
- Instituto Universitario Mixto de Tecnología Química (UPV-CSIC), Universitat Politècnica de València, Consejo Superior de Investigaciones Científicas, Avenida de los Naranjos, s/n, 46022, Valencia (Spain)
| | - Virginie Lhiaubet-Vallet
- Instituto Universitario Mixto de Tecnología Química (UPV-CSIC), Universitat Politècnica de València, Consejo Superior de Investigaciones Científicas, Avenida de los Naranjos, s/n, 46022, Valencia (Spain)
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4
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Alsøe L, Sarno A, Carracedo S, Domanska D, Dingler F, Lirussi L, SenGupta T, Tekin NB, Jobert L, Alexandrov LB, Galashevskaya A, Rada C, Sandve GK, Rognes T, Krokan HE, Nilsen H. Uracil Accumulation and Mutagenesis Dominated by Cytosine Deamination in CpG Dinucleotides in Mice Lacking UNG and SMUG1. Sci Rep 2017; 7:7199. [PMID: 28775312 PMCID: PMC5543110 DOI: 10.1038/s41598-017-07314-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 06/23/2017] [Indexed: 12/30/2022] Open
Abstract
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. The highest increase was found in brain, which contained about 26-fold higher genomic 5-hydroxymethyluracil levels than the wild type. Smug1−/− mice did not accumulate uracil in their genome and Ung−/− mice showed slightly elevated uracil levels. Contrastingly, Ung−/−Smug1−/− mice showed a synergistic increase in uracil levels with up to 25-fold higher uracil levels than wild type. Whole genome sequencing of UNG/SMUG1-deficient tumours revealed that combined UNG and SMUG1 deficiency leads to the accumulation of mutations, primarily C to T transitions within CpG sequences. This unexpected sequence bias suggests that CpG dinucleotides are intrinsically more mutation prone. In conclusion, we showed that SMUG1 efficiently prevent genomic uracil accumulation, even in the presence of UNG, and identified mutational signatures associated with combined UNG and SMUG1 deficiency.
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Affiliation(s)
- Lene Alsøe
- Department of Clinical Molecular Biology, Ahus Campus, University of Oslo, Oslo, Norway.,Akershus University Hospital, Lørenskog, Norway
| | - Antonio Sarno
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway.,The Liaison Committee for Education, Research and Innovation in Central Norway, Trondheim, Norway
| | - Sergio Carracedo
- Department of Clinical Molecular Biology, Ahus Campus, University of Oslo, Oslo, Norway.,Akershus University Hospital, Lørenskog, Norway
| | - Diana Domanska
- Department of Informatics, University of Oslo, PO Box 1080 Blindern, NO-0316, Oslo, Norway
| | | | - Lisa Lirussi
- Department of Clinical Molecular Biology, Ahus Campus, University of Oslo, Oslo, Norway.,Akershus University Hospital, Lørenskog, Norway
| | - Tanima SenGupta
- Department of Clinical Molecular Biology, Ahus Campus, University of Oslo, Oslo, Norway.,Akershus University Hospital, Lørenskog, Norway
| | - Nuriye Basdag Tekin
- Department of Clinical Molecular Biology, Ahus Campus, University of Oslo, Oslo, Norway.,Akershus University Hospital, Lørenskog, Norway
| | - Laure Jobert
- Department of Clinical Molecular Biology, Ahus Campus, University of Oslo, Oslo, Norway.,Akershus University Hospital, Lørenskog, Norway.,LifeTechnologies AS, Ullernschauseen 52, 0379, Oslo, Norway
| | - Ludmil B Alexandrov
- Theoretical Biology and Biophysics (T-6), Los Alamos National Laboratory, Los Alamos, NM, 87545, USA.,Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA.,University of New Mexico Comprehensive Cancer Center, Albuquerque, NM, 87102, USA
| | - Anastasia Galashevskaya
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | | | - Geir Kjetil Sandve
- Department of Informatics, University of Oslo, PO Box 1080 Blindern, NO-0316, Oslo, Norway
| | - Torbjørn Rognes
- Department of Informatics, University of Oslo, PO Box 1080 Blindern, NO-0316, Oslo, Norway.,Department of Microbiology, Oslo University Hospital, Rikshospitalet, PO Box 4950 Nydalen, NO-0424, Oslo, Norway
| | - Hans E Krokan
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Hilde Nilsen
- Department of Clinical Molecular Biology, Ahus Campus, University of Oslo, Oslo, Norway. .,Akershus University Hospital, Lørenskog, Norway.
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5
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Kawasaki F, Murat P, Li Z, Santner T, Balasubramanian S. Synthesis and biophysical analysis of modified thymine-containing DNA oligonucleotides. Chem Commun (Camb) 2017; 53:1389-1392. [PMID: 28074944 PMCID: PMC5759927 DOI: 10.1039/c6cc08670e] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We report the synthesis of a 5-formyl-2'-deoxyuridine (5fU) phosphoramidite and the preparation of oligonucleotides comprising all known, naturally observed eukaryotic thymidine modifications. Biophysical characterization of the synthetic oligonucleotides indicates that 5fU, but not the other T-derivatives, can alter DNA structures.
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Affiliation(s)
- F Kawasaki
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
| | - P Murat
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
| | - Z Li
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
| | - T Santner
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
| | - S Balasubramanian
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK. and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK and School of Clinical Medicine, University of Cambridge, Cambridge CB2 0SP, UK
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6
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Valente WJ, Ericson NG, Long AS, White PA, Marchetti F, Bielas JH. Mitochondrial DNA exhibits resistance to induced point and deletion mutations. Nucleic Acids Res 2016; 44:8513-8524. [PMID: 27550180 PMCID: PMC5062989 DOI: 10.1093/nar/gkw716] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 08/04/2016] [Indexed: 12/17/2022] Open
Abstract
The accumulation of somatic mitochondrial DNA (mtDNA) mutations contributes to the pathogenesis of human disease. Currently, mitochondrial mutations are largely considered results of inaccurate processing of its heavily damaged genome. However, mainly from a lack of methods to monitor mtDNA mutations with sufficient sensitivity and accuracy, a link between mtDNA damage and mutation has not been established. To test the hypothesis that mtDNA-damaging agents induce mtDNA mutations, we exposed MutaTMMouse mice to benzo[a]pyrene (B[a]P) or N-ethyl-N-nitrosourea (ENU), daily for 28 consecutive days, and quantified mtDNA point and deletion mutations in bone marrow and liver using our newly developed Digital Random Mutation Capture (dRMC) and Digital Deletion Detection (3D) assays. Surprisingly, our results demonstrate mutagen treatment did not increase mitochondrial point or deletion mutation frequencies, despite evidence both compounds increase nuclear DNA mutations and demonstrated B[a]P adduct formation in mtDNA. These findings contradict models of mtDNA mutagenesis that assert the elevated rate of mtDNA mutation stems from damage sensitivity and abridged repair capacity. Rather, our results demonstrate induced mtDNA damage does not readily convert into mutation. These findings suggest robust mitochondrial damage responses repress induced mutations after mutagen exposure.
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Affiliation(s)
- William J Valente
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA Medical Scientist Training Program, University of Washington School of Medicine, Seattle, WA 98195, USA Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA 98195, USA
| | - Nolan G Ericson
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Alexandra S Long
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON K1A 0K9, Canada
| | - Paul A White
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON K1A 0K9, Canada
| | - Francesco Marchetti
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON K1A 0K9, Canada
| | - Jason H Bielas
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA 98195, USA Department of Pathology, University of Washington, Seattle, WA 98195, USA Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
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7
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Guo P, Xu X, Qiu X, Zhou Y, Yan S, Wang C, Lu C, Ma W, Weng X, Zhang X, Zhou X. Synthesis and spectroscopic properties of fluorescent 5-benzimidazolyl-2′-deoxyuridines 5-fdU probes obtained from o-phenylenediamine derivatives. Org Biomol Chem 2013; 11:1610-3. [DOI: 10.1039/c3ob27519a] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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8
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Khrustalev VV, Barkovsky EV. A blueprint for a mutationist theory of replicative strand asymmetries formation. Curr Genomics 2012; 13:55-64. [PMID: 22942675 PMCID: PMC3269017 DOI: 10.2174/138920212799034730] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2011] [Revised: 09/15/2011] [Accepted: 09/29/2011] [Indexed: 11/26/2022] Open
Abstract
In the present review, we summarized current knowledge on replicative strand asymmetries in prokaryotic genomes. A cornerstone for the creation of a theory of their formation has been overviewed. According to our recent works, the probability of nonsense mutation caused by replication-associated mutational pressure is higher for genes from lagging strands than for genes from leading strands of both bacterial and archaeal genomes. Lower density of open reading frames in lagging strands can be explained by faster rates of nonsense mutations in genes situated on them. According to the asymmetries in nucleotide usage in fourfold and twofold degenerate sites, the direction of replication-associated mutational pressure for genes from lagging strands is usually the same as the direction of transcription-associated mutational pressure. It means that lagging strands should accumulate more 8-oxo-G, uracil and 5-formyl-uracil, respectively. In our opinion, consequences of cytosine deamination (C to T transitions) do not lead to the decrease of cytosine usage in genes from lagging strands because of the consequences of thymine oxidation (T to C transitions), while guanine oxidation (causing G to T transversions) makes the main contribution into the decrease of guanine usage in fourfold degenerate sites of genes from lagging strands. Nucleotide usage asymmetries and bias in density of coding regions can be found in archaeal genomes, although, the percent of "inversed" asymmetries is much higher for them than for bacterial genomes. "Homogenized" and "inversed" replicative strand asymmetries in archaeal genomes can be used as retrospective indexes for detection of OriC translocations and large inversions.
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Affiliation(s)
- Vladislav V Khrustalev
- Department of General Chemistry, Belarussian State Medical University, Belarus, Minsk, Dzerzinskogo, 83, Russia
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9
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Abstract
LC with atmospheric pressure ionization MS is essential to a large number of quantitative bioanalyses for a variety of compounds, especially nonvolatile or highly polar compounds. However, in many instances, weak ionization, poor LC retention and instability of certain analytes hinder the development of the LC–MS/MS method. Chemical derivatization has been used for different classes of analytes to improve their ionization efficiency, chromatographic separation and chemical stability. This work presents an overview of chemical derivatization methods that have been applied to the quantitative LC–MS/MS analyses of nine classes of molecules, including aldehydes, amino acids, bisphosphonate drugs, carbohydrates, carboxylic acids, nucleosides and their associated analogs, steroids, thiol-containing compounds and vitamin D metabolites, in biological matrices.
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10
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Hirose W, Sato K, Matsuda A. Fluorescence Properties of 5-(5,6-Dimethoxybenzothiazol-2-yl)-2′-deoxyuridine (dbtU) and Oligodeoxyribonucleotides Containing dbtU. European J Org Chem 2011. [DOI: 10.1002/ejoc.201100818] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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11
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Hirose W, Sato K, Matsuda A. Selective detection of 5-formyl-2'-deoxyuridine, an oxidative lesion of thymidine, in DNA by a fluorogenic reagent. Angew Chem Int Ed Engl 2011; 49:8392-4. [PMID: 20862761 DOI: 10.1002/anie.201004087] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Wataru Hirose
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
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12
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Hirose W, Sato K, Matsuda A. Selective Detection of 5-Formyl-2′-deoxyuridine, an Oxidative Lesion of Thymidine, in DNA by a Fluorogenic Reagent. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201004087] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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13
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Sato K, Hirose W, Matsuda A. Synthesis of 5-formyl-2'-deoxyuridine and its incorporation into oligodeoxynucleotides. ACTA ACUST UNITED AC 2009; Chapter 1:Unit 1.21. [PMID: 19085981 DOI: 10.1002/0471142700.nc0121s35] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A straightforward, efficient method for the synthesis of 5-formyl-2'-deoxyuridine (dfU) and solid-phase synthesis of oligodeoxynucleotides containing dfU using a phosphoramidite method are described. The synthesis of dfU is achieved by oxidation of the 5-methyl group in thymidine derivatives. However, incorporation of the dfU 3'-O-phosphoramidite into oligodeoxynucleotides proceeds in low yield, due to instability of the 5-formyl group under conditions used for automated DNA synthesis. Therefore, oligodeoxynucleotides containing a 5-(1,2-dihydroxyethyl)uracil derivative are first prepared and finally oxidized by periodate to give the desired oligodeoxynucleotides containing 5-formyluracil.
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Affiliation(s)
- Kousuke Sato
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
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14
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Guidoni L, Gontrani L, Bencivenni L, Sadun C, Ballirano P. Overcoming the Inadequacy of X-ray Powder Diffraction in Reliable Hydrogen Location with the Aid of First Principles Calculations: Crystal Structure Determination of Orotaldehyde Monohydrate. J Phys Chem A 2008; 113:353-9. [DOI: 10.1021/jp809076t] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Leonardo Guidoni
- Dipartimento di Fisica, Sapienza Università di Roma, P. le A. Moro 5, I-00185 Roma, Italy, CASPUR, Consorzio interuniversitario per le Applicazioni di Supercalcolo Per Università e Ricerca, Via dei Tizii 6, I-00185 Roma, Italy, Dipartimento di Chimica, Sapienza Università di Roma, P. le A. Moro 5, I-00185 Roma, Italy, and Dipartimento di Scienze della Terra, Sapienza Università di Roma, P. le A. Moro, 5 I-00185 Roma, Italy
| | - Lorenzo Gontrani
- Dipartimento di Fisica, Sapienza Università di Roma, P. le A. Moro 5, I-00185 Roma, Italy, CASPUR, Consorzio interuniversitario per le Applicazioni di Supercalcolo Per Università e Ricerca, Via dei Tizii 6, I-00185 Roma, Italy, Dipartimento di Chimica, Sapienza Università di Roma, P. le A. Moro 5, I-00185 Roma, Italy, and Dipartimento di Scienze della Terra, Sapienza Università di Roma, P. le A. Moro, 5 I-00185 Roma, Italy
| | - Luigi Bencivenni
- Dipartimento di Fisica, Sapienza Università di Roma, P. le A. Moro 5, I-00185 Roma, Italy, CASPUR, Consorzio interuniversitario per le Applicazioni di Supercalcolo Per Università e Ricerca, Via dei Tizii 6, I-00185 Roma, Italy, Dipartimento di Chimica, Sapienza Università di Roma, P. le A. Moro 5, I-00185 Roma, Italy, and Dipartimento di Scienze della Terra, Sapienza Università di Roma, P. le A. Moro, 5 I-00185 Roma, Italy
| | - Claudia Sadun
- Dipartimento di Fisica, Sapienza Università di Roma, P. le A. Moro 5, I-00185 Roma, Italy, CASPUR, Consorzio interuniversitario per le Applicazioni di Supercalcolo Per Università e Ricerca, Via dei Tizii 6, I-00185 Roma, Italy, Dipartimento di Chimica, Sapienza Università di Roma, P. le A. Moro 5, I-00185 Roma, Italy, and Dipartimento di Scienze della Terra, Sapienza Università di Roma, P. le A. Moro, 5 I-00185 Roma, Italy
| | - Paolo Ballirano
- Dipartimento di Fisica, Sapienza Università di Roma, P. le A. Moro 5, I-00185 Roma, Italy, CASPUR, Consorzio interuniversitario per le Applicazioni di Supercalcolo Per Università e Ricerca, Via dei Tizii 6, I-00185 Roma, Italy, Dipartimento di Chimica, Sapienza Università di Roma, P. le A. Moro 5, I-00185 Roma, Italy, and Dipartimento di Scienze della Terra, Sapienza Università di Roma, P. le A. Moro, 5 I-00185 Roma, Italy
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15
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Yonekura SI, Nakamura N, Doi T, Sugiyama H, Yamamoto K, Yonei S, Zhang QM. Recombinant Schizosaccharomyces pombe Nth1 protein exhibits DNA glycosylase activities for 8-oxo-7,8-dihydroguanine and thymine residues oxidized in the methyl group. JOURNAL OF RADIATION RESEARCH 2007; 48:417-24. [PMID: 17641464 DOI: 10.1269/jrr.07042] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Bacteria and eukaryotes possess redundant enzymes that recognize and remove oxidatively damaged bases from DNA through base excision repair. DNA glycosylases remove damaged bases to initiate the base excision repair. The exocyclic methyl group of thymine does not escape oxidative damage to produce 5-formyluracil (5-foU) and 5-hydroxymethyluracil (5-hmU). 5-foU is a potentially mutagenic lesion. A homolog of E. coli endonuclease III (SpNth1) had been identified and characterized in Schizosaccharomyces pombe. In this study, we found that SpNth1 recognizes and removes 5-foU and 5-hmU from DNA with similar efficiency. The specific activities for the removal of 5-foU and 5-hmU were comparable with that for thymine glycol. The expression of SpNth1 reduced the hydrogen peroxide toxicity and the frequency of spontaneous mutations in E. coli nth nei mutant. It was also revealed that SpNth1 had DNA glycosylase activity for removing 8-oxo-7,8-dihydroguanine (8-oxoG) from 8-oxoG/G and 8-oxoG/A mispairs. These results indicated that SpNth1 has a broad substrate specificity and is involved in the base excision repair of 8-oxoG and thymine residues oxidized in the methyl group in S. pombe.
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Affiliation(s)
- Shin-Ichiro Yonekura
- Laboratory of Radiation Biology, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto, Japan
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16
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Hong H, Wang Y. Derivatization with Girard reagent T combined with LC-MS/MS for the sensitive detection of 5-formyl-2'-deoxyuridine in cellular DNA. Anal Chem 2007; 79:322-6. [PMID: 17194156 PMCID: PMC2531228 DOI: 10.1021/ac061465w] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nucleoside 5-formyl-2'-deoxyuridine (FodU) is a major thymidine lesion generated by reactive oxygen species. In vitro and in vivo replication studies revealed that FodU can be mutagenic. A reliable and sensitive quantification method is, therefore, important for assessing the biological implications of this lesion. However, the detection limit of FodU by liquid chromatography-tandem mass spectrometry (LC-MS/MS) was relatively poor compared with those of other oxidative DNA base damages. In this paper we described a new approach for the highly sensitive detection of FodU. We derivatized FodU with Girard reagent T to form a hydrazone conjugate harboring a precharged quaternary ammonium moiety, which enabled the facile detection of the resulting conjugate by positive-ion electrospray ionization MS. We also showed that the combination of derivatization with LC-MS/MS on a linear-ion-trap mass spectrometer could allow for the quantification of FodU at a detection limit of 3-4 fmol, which is approximately 20-fold better than that for the direct analysis of the underivatized compound. By using isotope-labeled FodU as the internal standard and this derivatization method, we further quantified, by using LC-MS/MS, the yield of FodU formed in cellular DNA.
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Affiliation(s)
- Haizheng Hong
- Environmental Toxicology Graduate Program and Department of Chemistry, University of California at Riverside, Riverside, California 92521, USA
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17
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Volk DE, Thiviyanathan V, Somasunderam A, Gorenstein DG. Ab initio base-pairing energies of an oxidized thymine product, 5-formyluracil, with standard DNA bases at the BSSE-free DFT and MP2 theory levels. Org Biomol Chem 2007; 5:1554-8. [PMID: 17571183 DOI: 10.1039/b702755a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Oxidation of the thymine methyl group produces two stable products, non-mutagenic 5-hydroxymethyluracil and highly mutagenic 5-formyluracil. We have calculated the interaction energy of base-pair formation involving 5-formyluracil bound to the natural DNA bases adenine (A), cytosine (C), guanine (G), and thymine (T), and discuss the effects of the 5-formyl group with respect to similar base-pairs containing uracil, 5-hydroxyuracil, thymine (5-methyluracil), and 5-hydroxycytosine. The interaction geometries and energies were calculated four ways: (a) using density functional theory (DFT) without basis set super-position error (BSSE) corrections, (b) using DFT with BSSE correction of geometries and energies, (c) using Møller-Plesset second order perturbation theory (MP2) without BSSE correction, and (d) using MP2 with BSSE geometry and energy correction. All calculations used the 6-311G(d,p) basis set. Notably, we find that the A:5-formyluracil base-pair is more stable than the precursor A:T base-pair. The relative order of base-pair stabilities is A:5-Fo-U > G:5-Fo-U > C:5-Fo-U > T:5-Fo-U.
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Affiliation(s)
- David E Volk
- Sealy Center for Structural Biology and Molecular Biophysics, Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX 77555-1157, USA
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18
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Irie D, Ono A, Izuta S. Recognition of oxidized thymine base on the single-stranded DNA by replication protein A. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2006; 25:439-51. [PMID: 16838837 DOI: 10.1080/01457630600684138] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Replication protein A (RAP) is a eukaryotic single-stranded DNA binding protein involved in DNA replication, repair, and recombination. Recent studies indicate that RPA preferentially binds the damaged sites rather than the undamaged sites. Therefore, RPA is thought to be a member ofrepair factories or a sensor of lesion on DNA. To obtain further information of behavior of RPA against the oxidized lesion, we studied the binding affinity of RPA for the single-stranded DNA containing 5-formyluracil, a major lesion of thymine base yielded by the oxidation, using several synthetic oligonucleotides. The affinity of RPA for oligonucleotides was determined by gel shift assay. Results suggest that the surrounding sequence of 5-formyluracil may affect the affinity for RPA, and that the 5-formyluracil on the purine stretch but not the pyrimidine stretch increases the affinity for RPA. Results of affinity labeling experiment of RPA with the oligonucleotides containing 5-formyluracil indicate that RPA1 subunit may directly recognize and bind to the 5-formyluracil on the single-stranded DNA.
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Affiliation(s)
- Daisuke Irie
- Graduate School of Science and Technology, Kumamoto University, Kumamoto, Japan
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19
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Xylanolytic and Alkaliphilic Dietzia sp. Isolated from Larvae of the Japanese Horned Beetle, Trypoxylus dichotomus. ACTA ACUST UNITED AC 2006. [DOI: 10.3209/saj.20.49] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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20
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Dohno C, Okamoto A, Saito I. Stable, Specific, and Reversible Base Pairing via Schiff Base. J Am Chem Soc 2005; 127:16681-4. [PMID: 16305258 DOI: 10.1021/ja054618q] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We here present a novel covalently linked base pair via Schiff base formation between 5-formyluracil (fU) and 5-aminocytosine (AmC). Formation of the Schiff base linkage proceeds reversibly and does not require any additives. The cross-linked DNA is very stable under denaturing conditions, whereas it completely dissociates upon heating at 90 degrees C. The pairing ability of AmC and fU is very specific and is applicable to the detection of fU, which is the major oxidative lesion of T in DNA. We propose the Schiff base linkage as a new artificial base pairing scheme to create functional DNAs.
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Affiliation(s)
- Chikara Dohno
- Department of Synthetic Chemistry and Biological Chemistry, Faculty of Engineering, Kyoto University, Kyoto 615-8510, Japan
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21
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An Q, Robins P, Lindahl T, Barnes DE. C --> T mutagenesis and gamma-radiation sensitivity due to deficiency in the Smug1 and Ung DNA glycosylases. EMBO J 2005; 24:2205-13. [PMID: 15902269 PMCID: PMC1150883 DOI: 10.1038/sj.emboj.7600689] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2005] [Accepted: 04/29/2005] [Indexed: 01/03/2023] Open
Abstract
The most common genetic change in aerobic organisms is a C:G to T:A mutation. C --> T transitions can arise through spontaneous hydrolytic deamination of cytosine to give a miscoding uracil residue. This is also a frequent DNA lesion induced by oxidative damage, through exposure to agents such as ionizing radiation, or from endogenous sources that are implicated in the aetiology of degenerative diseases, ageing and cancer. The Ung and Smug1 enzymes excise uracil from DNA to effect repair in mammalian cells, and gene-targeted Ung(-/-) mice exhibit a moderate increase in genome-wide spontaneous mutagenesis. Here, we report that stable siRNA-mediated silencing of Smug1 in mouse embryo fibroblasts also generates a mutator phenotype. However, an additive 10-fold increase in spontaneous C:G to T:A transitions in cells deficient in both Smug1 and Ung demonstrates that these enzymes have distinct and nonredundant roles in suppressing C --> T mutability at non-CpG sites. Such cells are also hypersensitive to ionizing radiation, and reveal a role of Smug1 in the repair of lesions generated by oxidation of cytosine.
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Affiliation(s)
- Qian An
- Cancer Research UK London Research Institute, Clare Hall Laboratories, South Mimms, UK
| | - Peter Robins
- Cancer Research UK London Research Institute, Clare Hall Laboratories, South Mimms, UK
| | - Tomas Lindahl
- Cancer Research UK London Research Institute, Clare Hall Laboratories, South Mimms, UK
- Cancer Research UK London Research Institute, Clare Hall Laboratories, South Mimms EN6 3LD, UK. Tel.: +44 207 269 3983/3985; Fax: +44 207 269 3819; E-mail:
| | - Deborah E Barnes
- Cancer Research UK London Research Institute, Clare Hall Laboratories, South Mimms, UK
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22
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Guerniou V, Rapin D, Millau JF, Bufflier E, Favier A, Cadet J, Sauvaigo S. Repair of oxidative damage of thymine by HeLa whole-cell extracts: simultaneous analysis using a microsupport and comparison with traditional PAGE analysis. Biochimie 2005; 87:151-9. [PMID: 15760707 DOI: 10.1016/j.biochi.2004.12.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2004] [Accepted: 12/05/2004] [Indexed: 10/26/2022]
Abstract
In mammalian cells, the base excision repair (BER) pathway allows the remove of small DNA base lesions such as oxidized bases. It is initiated by glycosylases that removed the modified base leaving an abasic site that is subsequently processed by AP endonuclease activities. Measurement of BER activities in cell extracts is time consuming and hazardous when radioactive material is used. We report in this study, the parallelized fluorescent analysis of excision of several oxidation products of thymine by cell extracts. To conduct the study, 5-(hydroxymethyl)uracil, 5-formyluracil, 5-carboxyuracil and formylamine together with uracil and the control thymine, were incorporated into oligonucleotides of identical sequences and paired either with adenine or with guanine containing DNA fragments. The oligonucleotides were fixed by sandwich hybridization in wells of a microplate (OLISA technology). Excision by HeLa extracts of the six different DNA base lesions could be followed simultaneously in the same well. Our results showed that the extent of excision of the lesions was the same on support and in solution using classical PAGE analysis approach with modified (32)P-labeled oligonucleotides. We demonstrated that the simultaneous analysis on support is a successful approach to facilitate high-throughput screening of BER activities present in cell extracts. Moreover, extended study of 5-carboxyuracil revealed that this lesion displays similar biological properties as 5-formyluracil.
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Affiliation(s)
- Valérie Guerniou
- Laboratoire Lésions des Acides Nucléiques, Service de Chimie Inorganique et Biologique, CEA/DSM/Département de Recherche Fondamentale sur la Matière Condensée, CEA-Grenoble, 17, rue des Martyrs, 38054 Grenoble cedex 9, France
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23
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Ide H, Kotera M. Human DNA glycosylases involved in the repair of oxidatively damaged DNA. Biol Pharm Bull 2004; 27:480-5. [PMID: 15056851 DOI: 10.1248/bpb.27.480] [Citation(s) in RCA: 98] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Reactive oxygen species from endogenous and environmental sources induce oxidative damage to DNA, and hence pose an enormous threat to the genetic integrity of cells. Such oxidative DNA damage is restored by the base excision repair (BER) pathway that is conserved from bacteria to humans and is initiated by DNA glycosylases, which simply remove the aberrant base from the DNA backbone by hydrolyzing the N-glycosidic bond (monofunctional DNA glycosylase), or further catalyze the incision of a resulting abasic site (bifunctional DNA glycosylase). In human cells, oxidative pyrimidine lesions are generally removed by hNTH1, hNEIL1, or hNEIL2, whereas oxidative purine lesions are removed by hOGG1. hSMUG1 excises a subset of oxidative base damage that is poorly recognized by the above enzymes. Unlike these enzymes, hMYH removes intact A misincorporated opposite template 8-oxoguanine during DNA replication. Although hNTH1, hOGG1, and hMYH account for major cellular glycosylase activity for inherent substrate lesions, mouse models deficient in the enzymes exhibit no overt phenotypes such as the development of cancer, implying backup mechanisms. Contrary to the mouse model, hMYH mutations have been shown to lead to a multiple colorectal adenoma syndrome and high colorectal cancer risk. For cleavage of the N-glycosidic bond, bifunctional DNA glycosylases (hNTH1, hNEIL1, hNEIL2, and hOGG1) use Lys or Pro for direct attack on sugar C1', whereas monofunctional DNA glycosylases (hSMUG1 and hMYH) use an activated water molecule. DNA glycosylases for oxidative damage, if not all, are covalently trapped by DNA containing 2-deoxyribonolactone or oxanine. Thus, the depletion of functional DNA glycosylases using covalent trapping may reduce the BER capacity of cancer cells, hence potentiating the efficacy of anticancer drugs or radiation therapy.
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Affiliation(s)
- Hiroshi Ide
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashi-Hiroshima 739-8526, Japan.
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24
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Matsubara M, Tanaka T, Terato H, Ohmae E, Izumi S, Katayanagi K, Ide H. Mutational analysis of the damage-recognition and catalytic mechanism of human SMUG1 DNA glycosylase. Nucleic Acids Res 2004; 32:5291-302. [PMID: 15466595 PMCID: PMC521670 DOI: 10.1093/nar/gkh859] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Single-strand selective monofunctional uracil-DNA glycosylase (SMUG1), previously thought to be a backup enzyme for uracil-DNA glycosylase, has recently been shown to excise 5-hydroxyuracil (hoU), 5-hydroxymethyluracil (hmU) and 5-formyluracil (fU) bearing an oxidized group at ring C5 as well as an uracil. In the present study, we used site-directed mutagenesis to construct a series of mutants of human SMUG1 (hSMUG1), and tested their activity for uracil, hoU, hmU, fU and other bases to elucidate the catalytic and damage-recognition mechanism of hSMUG1. The functional analysis of the mutants, together with the homology modeling of the hSMUG1 structure based on that determined recently for Xenopus laevis SMUG1, revealed the crucial residues for the rupture of the N-glycosidic bond (Asn85 and His239), discrimination of pyrimidine rings through pi-pi stacking to the base (Phe98) and specific hydrogen bonds to the Watson-Crick face of the base (Asn163) and exquisite recognition of the C5 substituent through water-bridged (uracil) or direct (hoU, hmU and fU) hydrogen bonds (Gly87-Met91). Integration of the present results and the structural data elucidates how hSMUG1 accepts uracil, hoU, hmU and fU as substrates, but not other oxidized pyrimidines such as 5-hydroxycytosine, 5-formylcytosine and thymine glycol, and intact pyrimidines such as thymine and cytosine.
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Affiliation(s)
- Mayumi Matsubara
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
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25
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Evans MD, Dizdaroglu M, Cooke MS. Oxidative DNA damage and disease: induction, repair and significance. MUTATION RESEARCH/REVIEWS IN MUTATION RESEARCH 2004; 567:1-61. [PMID: 15341901 DOI: 10.1016/j.mrrev.2003.11.001] [Citation(s) in RCA: 877] [Impact Index Per Article: 43.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2003] [Revised: 11/12/2003] [Accepted: 11/12/2003] [Indexed: 04/08/2023]
Abstract
The generation of reactive oxygen species may be both beneficial to cells, performing a function in inter- and intracellular signalling, and detrimental, modifying cellular biomolecules, accumulation of which has been associated with numerous diseases. Of the molecules subject to oxidative modification, DNA has received the greatest attention, with biomarkers of exposure and effect closest to validation. Despite nearly a quarter of a century of study, and a large number of base- and sugar-derived DNA lesions having been identified, the majority of studies have focussed upon the guanine modification, 7,8-dihydro-8-oxo-2'-deoxyguanosine (8-OH-dG). For the most part, the biological significance of other lesions has not, as yet, been investigated. In contrast, the description and characterisation of enzyme systems responsible for repairing oxidative DNA base damage is growing rapidly, being the subject of intense study. However, there remain notable gaps in our knowledge of which repair proteins remove which lesions, plus, as more lesions identified, new processes/substrates need to be determined. There are many reports describing elevated levels of oxidatively modified DNA lesions, in various biological matrices, in a plethora of diseases; however, for the majority of these the association could merely be coincidental, and more detailed studies are required. Nevertheless, even based simply upon reports of studies investigating the potential role of 8-OH-dG in disease, the weight of evidence strongly suggests a link between such damage and the pathogenesis of disease. However, exact roles remain to be elucidated.
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Affiliation(s)
- Mark D Evans
- Oxidative Stress Group, Department of Clinical Biochemistry, University of Leicester, Leicester Royal Infirmary, University Hospitals of Leicester NHS Trust, LE2 7LX, UK
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26
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Kino K, Shimizu Y, Sugasawa K, Sugiyama H, Hanaoka F. Nucleotide excision repair of 5-formyluracil in vitro is enhanced by the presence of mismatched bases. Biochemistry 2004; 43:2682-7. [PMID: 15005603 DOI: 10.1021/bi0361416] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
5-Formyluracil (fU) is a major thymine lesion produced by reactive oxygen radicals and photosensitized oxidation. Although this residue is a potentially mutagenic lesion and is removed by several base excision repair enzymes, it is unknown whether fU is the substrate of nucleotide excision repair (NER). Here, we analyzed the binding specificity of XPC-HR23B, which initiates NER, and cell-free NER activity on fU opposite four different bases. The result of the gel mobility shift assay showed that XPC-HR23B binds the fU-containing substrates in the following order: fU:C >> fU:T > fU:G > fU:A. Furthermore, in the presence of XPC-HR23B, the dual incision activity was the same as the order of the binding affinity of XPC-HR23B to fU. Therefore, it is concluded that even fU, regarded as a shape mimic of thymine, can be recognized as a substrate of NER incision, and the efficiency depends on instability of the base pair.
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Affiliation(s)
- Katsuhito Kino
- Cellular Physiology Laboratory, RIKEN, Japan Science and Technology Corporation, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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27
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Katafuchi A, Nakano T, Masaoka A, Terato H, Iwai S, Hanaoka F, Ide H. Differential Specificity of Human and Escherichia coli Endonuclease III and VIII Homologues for Oxidative Base Lesions. J Biol Chem 2004; 279:14464-71. [PMID: 14734554 DOI: 10.1074/jbc.m400393200] [Citation(s) in RCA: 104] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
In human cells, oxidative pyrimidine lesions are restored by the base excision repair pathway initiated by homologues of Endo III (hNTH1) and Endo VIII (hNEIL1 and hNEIL2). In this study we have quantitatively analyzed and compared their activity toward nine oxidative base lesions and an apurinic/apyrimidinic (AP) site using defined oligonucleotide substrates. hNTH1 and hNEIL1 but not hNEIL2 excised the two stereoisomers of thymine glycol (5R-Tg and 5S-Tg), but their isomer specificity was markedly different: the relative activity for 5R-Tg:5S-Tg was 13:1 for hNTH1 and 1.5:1 for hNEIL1. This was also the case for their Escherichia coli homologues: the relative activity for 5R-Tg:5S-Tg was 1:2.5 for Endo III and 3.2:1 for Endo VIII. Among other tested lesions for hNTH1, an AP site was a significantly better substrate than urea, 5-hydroxyuracil (hoU), and guanine-derived formamidopyrimidine (mFapyG), whereas for hNEIL1 these base lesions and an AP site were comparable substrates. In contrast, hNEIL2 recognized an AP site exclusively, and the activity for hoU and mFapyG was marginal. hNEIL1, hNEIL2, and Endo VIII but not hNTH1 and Endo III formed cross-links to oxanine, suggesting conservation of the -fold of the active site of the Endo VIII homologues. The profiles of the excision of the Tg isomers with HeLa and E. coli cell extracts closely resembled those of hNTH1 and Endo III, confirming their major contribution to the repair of Tg isomers in cells. However, detailed analysis of the cellular activity suggests that hNEIL1 has a significant role in the repair of 5S-Tg in human cells.
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Affiliation(s)
- Atsushi Katafuchi
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
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28
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Avila-Adame C, Olaya G, Köller W. Characterization of Colletotrichum graminicola Isolates Resistant to Strobilurin-Related QoI Fungicides. PLANT DISEASE 2003; 87:1426-1432. [PMID: 30812383 DOI: 10.1094/pdis.2003.87.12.1426] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Isolates of Colletotrichum graminicola were collected from annual bluegrass or bent grass turf in Japan and the United States, and their sensitivities to QoI fungicides (QoIs) as well as their cytochrome b sequences were characterized. Five isolates sampled from turf treated repeatedly with azoxystrobin were highly QoI resistant under both in vivo and in vitro test conditions. The nucleotide sequences of a large cytochrome b gene segment involving the binding site of QoIs were fully homologous for all resistant isolates and contained the G143A target site mutation known to confer QoI resistance in other pathogens. QoI-sensitive isolates collected prior to treatments with QoIs were more diverse with regard to their cytochrome b gene sequences and their phenotype responses to QoIs. All wild-type isolates retained a glycine in position 143 of cytochrome b. Three of the four QoI-sensitive isolates were, in addition, distinguished by leucines in positions 95, 130, and 141, which were exchanged to threonine in all resistant but also in one of the sensitive isolates. In addition to a more pronounced divergence of cytochrome b sequences, the sensitive wild-type isolates also were diverse with regard to the induction of alternative respiration in response to QoI action, as indicated by comparisons of QoI sensitivities displayed in the absence or presence of the alternative oxidase inhibitor salicylhydroxamic acid. These different phenotype responses expressed under in vitro test conditions had no or only a slight impact on anthracnose control in protective applications of azoxystrobin. Isolate responses in vitro were very similar for trifloxystrobin, indicating cross-resistance among the class of QoIs. Our results imply that C. graminicola falls into the class of pathogens with a potential for rapid selection of highly QoI-resistant phenotypes. Frequent monitoring of population sensitivities will be required to determine the status of population responses toward practical QoI resistance.
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Affiliation(s)
- Cruz Avila-Adame
- Department of Plant Pathology, Cornell University, New York State Agricultural Experiment Station, Geneva 14456
| | | | - Wolfram Köller
- Department of Plant Pathology, Cornell University, New York State Agricultural Experiment Station
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29
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Matsubara M, Masaoka A, Tanaka T, Miyano T, Kato N, Terato H, Ohyama Y, Iwai S, Ide H. Mammalian 5-formyluracil-DNA glycosylase. 1. Identification and characterization of a novel activity that releases 5-formyluracil from DNA. Biochemistry 2003; 42:4993-5002. [PMID: 12718542 DOI: 10.1021/bi027322v] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
5-Formyluracil (fU) is a major oxidative thymine lesion produced by reactive oxygen species and exhibits genotoxic and cytotoxic effects via several mechanisms. In the present study, we have searched for and characterized mammalian fU-DNA glycosylase (FDG) using two approaches. In the first approach, the FDG activity was examined using purified base excision repair enzymes. Human and mouse endonuclease III homologues (NTH1) showed a very weak FDG activity, but the parameter analysis and NaBH(4) trapping assays of the Schiff base intermediate revealed that NTH1 was kinetically incompetent for repair of fU. In the second approach, FDG was partially purified (160-fold) from rat liver. The enzyme was a monofunctional DNA glycosylase and recognized fU in single-stranded (ss) and double-stranded (ds) DNA. The most purified FDG fraction also exhibited monofunctional DNA glycosylase activities for uracil (U), 5-hydroxyuracil (hoU), and 5-hydroxymethyluracil (hmU) in ssDNA and dsDNA. The fU-excising activity of FDG was competitively inhibited by dsDNA containing U.G, hoU.G, and hmU.A but not by intact dsDNA containing T.A. Furthermore, the activities of FDG for fU, hmU, hoU, and U in ssDNA and dsDNA were neutralized by the antibody raised against SMUG1 uracil-DNA glycosylase, showing that FDG is a rat homologue of SMUG1.
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Affiliation(s)
- Mayumi Matsubara
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
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30
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Masaoka A, Matsubara M, Hasegawa R, Tanaka T, Kurisu S, Terato H, Ohyama Y, Karino N, Matsuda A, Ide H. Mammalian 5-formyluracil-DNA glycosylase. 2. Role of SMUG1 uracil-DNA glycosylase in repair of 5-formyluracil and other oxidized and deaminated base lesions. Biochemistry 2003; 42:5003-12. [PMID: 12718543 DOI: 10.1021/bi0273213] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In the accompanying paper [Matsubara, M., et al. (2003) Biochemistry 42, 4993-5002], we have partially purified and characterized rat 5-formyluracil (fU)-DNA glycosylase (FDG). Several lines of evidence have indicated that FDG is a rat homologue of single-strand-selective monofunctional uracil-DNA glycosylase (SMUG1). We report here that rat and human SMUG1 (rSMUG1 and hSMUG1) expressed from the corresponding cDNAs indeed excise fU in single-stranded (ss) and double-stranded (ds) DNA. The enzymes also excised uracil (U) and uracil derivatives bearing an oxidized group at C5 [5-hydroxyuracil (hoU) and 5-hydroxymethyluracil (hmU)] in ssDNA and dsDNA but not analogous cytosine derivatives (5-hydroxycytosine and 5-formylcytosine) and other oxidized damage. The damage specificity and the salt concentration dependence of rSMUG1 (and hSMUG1) agreed well with those of FDG, confirming that FDG is rSMUG1. Consistent with the damage specificity above, hSMUG1 removed damaged bases from Fenton-oxidized calf thymus DNA, generating abasic sites. The amount of resulting abasic sites was about 10% of that generated by endonuclease III or 8-oxoguanine glycosylase in the same substrate. The HeLa cell extract and hSMUG1 exhibited a similar damage preference (hoU.G > hmU.A, fU.A), and the activities for fU, hmU, and hoU in the cell extract were effectively neutralized with hSMUG1 antibodies. These data indicate a dual role of hSMUG1 as a backup enzyme for UNG and a primary repair enzyme for a subset of oxidized pyrimidines such as fU, hmU, and hoU.
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Affiliation(s)
- Aya Masaoka
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
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31
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Wen Cheng Y, Lee H. Environmental exposure and lung cancer among nonsmokers: an example of Taiwanese female lung cancer. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART C, ENVIRONMENTAL CARCINOGENESIS & ECOTOXICOLOGY REVIEWS 2003; 21:1-28. [PMID: 12826030 DOI: 10.1081/gnc-120021371] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Lung cancer is the leading cause of cancer death worldwide and in Taiwan. Cigarette smoking is considered to be the most important risk factor, since about 90% of lung cancer can be related to cigarette smoking. Despite the recent decrease of cigarette smoking, lung cancer is still the leading cause of cancer death in the United States. In Taiwan, only around 50% of lung cancer incidence could be associated with cigarette smoking, particularly less than 10% of Taiwanese women are smokers. Thus, the aetiology of lung cancer for nonsmokers remains unknown. DNA damages including bulky and oxidative damage may be related with mutation of tumor suppressor genes, such as p53 gene. The high DNA adduct levels in female may be associated with frequent exposure to indoor cooking oil fumes (COF) and outdoor heavy air pollution. Oxidative stress induced by COF was also discussed. Different p53 mutation spectra and mutation frequency between genders reflected that different environmental factors may be involved in nonsmoking male and female lung cancer development. Most importantly, our recent report has demonstrated that human papillomavirus (HPV) infection was associated with nonsmoking female lung cancer. Based on our studies with Taiwanese nonsmoking lung cancer as the model, the possible aetiological factors of lung cancer incidence in Taiwanese nonsmokers were elucidated.
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Affiliation(s)
- Ya Wen Cheng
- Institute of Medicine and Toxicology, Lung Cancer Research Center, Chung Shan Medical University, Taiwan, ROC
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Abstract
The oxidation of the thymine methyl group can generate 5-formyluracil (FoU). Template FoU residues are known to miscode, generating base substitution mutations. The repair of the FoU lesion is therefore important in minimizing mutations induced by DNA oxidation. We have studied the repair of FoU in synthetic oligonucleotides when paired with A and G. In E. coli cell extract, the repair of FoU is four orders of magnitude lower than the repair of U and is similar for both FoU:A and FoU:G base pairs. In HeLa nuclear extract, the repair of FoU:A is similarly four orders of magnitude lower than the repair of uracil, although the FoU:G lesion is repaired 10 times more efficiently than FoU:A. The FoU:G lesion is shown to be repaired by E. coli mismatch uracil DNA glycosylase (Mug), thermophile mismatch thymine DNA glycosylase (Tdg), mouse mismatch thymine DNA glycosylase (mTDG) and human methyl-CpG-binding thymine DNA glycosylase (MBD4), whereas the FoU:A lesion is repaired only by Mug and mTDG. The repair of FoU relative to the other pyrimidines examined here in human cell extract differs from the substrate preferences of the known glycosylases, suggesting that additional, and as yet unidentified glycosylases exist in human cells to repair the FoU lesion. Indeed, as observed in HeLa nuclear extract, the repair of mispaired FoU derived from misincorporation of dGMP across from template FoU could promote rather than minimize mutagenesis. The pathways by which this important lesion is repaired in human cells are as yet unexplained, and are likely to be complex.
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Affiliation(s)
- Pingfang Liu
- Department of Biochemistry and Microbiology, School of Medicine, Loma Linda University, Loma Linda, CA 92350, USA
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33
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Kamiya H. Mutagenic potentials of damaged nucleic acids produced by reactive oxygen/nitrogen species: approaches using synthetic oligonucleotides and nucleotides: survey and summary. Nucleic Acids Res 2003; 31:517-31. [PMID: 12527759 PMCID: PMC140503 DOI: 10.1093/nar/gkg137] [Citation(s) in RCA: 215] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
DNA and DNA precursors (deoxyribonucleotides) suffer damage by reactive oxygen/nitrogen species. They are important mutagens for organisms, due to their endogenous formation. Damaged DNA and nucleotides cause alterations of the genetic information by the mispairing properties of the damaged bases, such as 8-hydroxyguanine (7,8-dihydro-8-oxoguanine) and 2-hydroxyadenine. Here, the author reviews the mutagenic potentials of damaged bases in DNA and of damaged DNA precursors formed by reactive oxygen/nitrogen species, focusing on the results obtained with synthetic oligonucleotides and 2'-deoxyribonucleoside 5'-triphosphates.
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Affiliation(s)
- Hiroyuki Kamiya
- Graduate School of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan.
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Shin CY, Turker MS. A:T --> G:C base pair substitutions occur at a higher rate than other substitution events in Pms2 deficient mouse cells. DNA Repair (Amst) 2002; 1:995-1001. [PMID: 12531009 DOI: 10.1016/s1568-7864(02)00149-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The mismatch repair pathway involves multiple proteins that are required to correct DNA polymerase generated mismatches before they become mutations. It has been shown recently, that the predominant base-pair substitution events leading to loss of endogenous Aprt activity in Pms2 null mouse cells are A:T --> G:C mutations (Oncogene 21 (2002) 1768, Oncogene 21 (2002) 2840). To determine if this observation could be explained by an increased rate of A:T --> G:C mutations relative to other base-pair substitutions, we developed a reversion assay to examine G:C --> A:T, C:G --> A:T, and A:T --> G:C mutations within mouse Aprt in a Pms2 null mouse kidney cell line. The results demonstrated a 6-50-fold increase in the rate of the A:T --> G:C mutations relative to the other base-pair substitutions. Additional work demonstrated that growth of the Pms2 null cells in antioxidant containing medium reduced the rate of the A:T --> G:C mutations. The results are discussed with regards to the role of mismatch repair proteins in preventing base-pair substitutions, including those induced by oxidative stress.
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Affiliation(s)
- Chi Y Shin
- Center for Research on Occupational and Environmental Toxicology, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA
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35
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Burdzy A, Noyes KT, Valinluck V, Sowers LC. Synthesis of stable-isotope enriched 5-methylpyrimidines and their use as probes of base reactivity in DNA. Nucleic Acids Res 2002; 30:4068-74. [PMID: 12235391 PMCID: PMC137105 DOI: 10.1093/nar/gkf520] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2002] [Revised: 07/24/2002] [Accepted: 07/24/2002] [Indexed: 11/13/2022] Open
Abstract
A specific and efficient method is presented for the conversion of 2'-deoxyuridine to thymidine via formation and reduction of the intermediate 5-hydroxymethyl derivative. The method has been used to generate both thymidine and 5-methyl-2'-deoxycytidine containing the stable isotopes 2H, 13C and 15N. Oligodeoxyribonucleotides have been constructed with these mass-tagged bases to investigate sequence-selectivity in hydroxyl radical reactions of pyrimidine methyl groups monitored by mass spectrometry. Studying the reactivity of 5-methylcytosine (5mC) is difficult as the reaction products can deaminate to the corresponding thymine derivatives, making the origin of the reaction products ambiguous. The method reported here can distinguish products derived from 5mC and thymine as well as investigate differences in reactivity for either base in different sequence contexts. The efficiency of formation of 5-hydroxymethyluracil from thymine is observed to be similar in magnitude in two different sequence contexts and when present in a mispair with guanine. The oxidation of 5mC proceeds slightly more efficiently than that of thymine and generates both 5-hydroxymethylcytosine and 5-formylcytosine but not the deaminated products. Thymine glycol is generated by both thymine and 5mC, although with reduced efficiency for 5mC. The method presented here should be widely applicable, enabling the examination of the reactivity of selected bases in DNA.
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Affiliation(s)
- Artur Burdzy
- Department of Biochemistry and Microbiology, Loma Linda University School of Medicine, Loma Linda, CA 92350, USA
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36
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Abstract
The principal oxidized cytosine bases, uracil glycol, 5-hydroxycytosine, and 5-hydroxyuracil, are readily bypassed, miscode, and are thus important premutagenic lesions. Similarly the principal oxidation product of guanine, 8-oxoguanine, miscodes with A and is a premutagenic lesion. Most of the thymine and adenine products that retain their ring structure primarily pair with their cognate bases and are not potent premutagenic lesions. Although thymine glycol pairs with its cognate base and is not mutagenic it significantly distorts the DNA molecule and is a lethal lesion. Ring fragmentation, ring contraction, and ring open products of both pyrimidines and purines block DNA polymerases and are potentially lethal lesions. Although these breakdown products have the potential to mispair during translesion synthesis, the mutational spectra of prokaryotic mutants defective in the pyrimidine-specific and/or purine-specific DNA glycosylases do not reflect that expected of the breakdown products. Taken together, the data suggest that the principal biological consequences of endogenously produced and unrepaired free radical-damaged DNA bases are mutations.
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Affiliation(s)
- Susan S Wallace
- Department of Microbiology and Molecular Genetics, The Markey Center for Molecular Genetics, The University of Vermont, Burlington, VT 05405-0068, USA.
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Kamiya H, Murata-Kamiya N, Karino N, Ueno Y, Matsuda A, Kasai H. Induction of T --> G and T --> A transversions by 5-formyluracil in mammalian cells. Mutat Res 2002; 513:213-22. [PMID: 11719107 DOI: 10.1016/s1383-5718(01)00312-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Oxidatively damaged thymine, 5-formyluracil (5-fU), was incorporated into a predetermined site of double-stranded shuttle vectors. The nucleotide sequences in which the modified base was incorporated were 5'-CFTAAG-3' and 5'-CTFAAG-3' (F represents 5-fU), the recognition site for the restriction enzyme AflII (5'-CTTAAG-3'). The 5-fU was incorporated into a template strand of either the leading or lagging strand of DNA replication. The modified DNAs were transfected into simian COS-7 cells, and the DNAs replicated in the cells were recovered and were analyzed after the second transfection into Escherichia coli. The 5-fU did not block DNA replication in mammalian cells. The 5-fU residues were weakly mutagenic, and their mutation frequencies in double-stranded vectors were 0.01-0.04%. The T --> G and T --> A transversions were the mutations found most frequently, suggesting the formation of 5-fU.C and 5-fU.T base pairs, respectively. This is the first report that clearly shows the induction of transversion mutations by an oxidized pyrimidine base in DNA in mammalian cells.
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Affiliation(s)
- Hiroyuki Kamiya
- Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, 1-1 Iseigaoka, Yahatanishi-ku, Kitakyushu 807-8555, Japan.
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