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2007 | 5 | 1 | 49-61
Tytuł artykułu

Structural analysis of base mispairing in DNA containing oxidative guanine lesion

Treść / Zawartość
Warianty tytułu
Języki publikacji
EN
Abstrakty
EN
Classical molecular dynamics methods were used to analyze the importance of 8-oxoguanine (8-oxoG) pairing with other DNA bases in order to determine the impact of oxidative guanine lesions on DNA structure. Six lesioned molecules, each containing 8-oxoG mispaired with one of the four normal bases on the the opposite strand at the center of 40-mer DNA, and one non-damaged DNA molecule, were simulated for 2 nanoseconds of real time. The 8-oxoG lesioned bases were found to incorporate opposite all normal bases. There are observed conformational and energetical differences among these parings. 8-oxoG in anti-form creates firm hydrogen bonds with cytosine and this bonding has a strong attractive electrostatic interaction energy similar to that of a native base pair-guanine to cytosine. Meanwhile, it does not form a stable base pair with purine bases (adenine and guanine) nor with the pyrimidine base thymine. On the other hand, the 8-oxoG in syn-form was found to pair with adenine.
Słowa kluczowe
Wydawca

Czasopismo
Rocznik
Tom
5
Numer
1
Strony
49-61
Opis fizyczny
Daty
wydano
2007-03-01
online
2007-03-01
Twórcy
  • Division of Radiological Protection and Biology, National Institute of Infectious Diseases, Toyama 1-23-1, Shinjuku-ku, Tokyo, 162-8640, Japan, fuj@nih.go.jp
  • Japan Atomic Energy Agency, Shirakata, Shirane 2-4, Tokai-mura, Ibaraki, 319-1195, Japan
  • Research Organization for Information Science and Technology, Shirakata, Shirane 2-4, Tokai-mura, Ibaraki, 319-1195, Japan
autor
  • Japan Atomic Energy Agency, Shirakata, Shirane 2-4, Tokai-mura, Ibaraki, 319-1195, Japan
Bibliografia
  • [1] H. Kasai, P.F. Crain, Y. Kuchino, S. Nishimura, A. Ootsuyama and H. Tanooka: “Formation of 8-ydroxyguanine moiety in cellular DNA by agents producing oxygen radicals and evidence for its repair”, Carcinogenesis, Vol. 7, (1986), pp. 1849–1851. http://dx.doi.org/10.1093/carcin/7.11.1849[Crossref]
  • [2] M.L. Wood, A. Esteve, M.L. Morningstar, G.M. Kuziemko and J.M. Essigmann: “Genetic effects of oxidative DNA damage: comparative mutagenesis of 7,8-dihydro-8-oxoguanine and 7,8-dihydro-8-oxoadenine in Escherichia coli“, Nucleic Acids Res., Vol. 20, (1992), pp. 6023–6032. http://dx.doi.org/10.1093/nar/20.22.6023[Crossref]
  • [3] X. Tan, A.P. Grollman and S. Shibutani: “Comparison of the mutagenic properties of 8-oxo-7,8-dihydro-2’-deoxyadenosine and 8-oxo-7-8-dihydro-2’-deoxyguanosine DNA lesions in mammalian cells”, Carcinogenesis, Vol. 20, (1999), pp. 2287–2292. http://dx.doi.org/10.1093/carcin/20.12.2287[Crossref]
  • [4] H. Kamiya: “Mutagenic potentials of damaged nucleic acids produced by reactive oxygen/nitrogen species: approaches using synthetic oligonucleotides and nucleotides”, Nucleic Acids Res., Vol. 31, (2003), pp. 517–531. http://dx.doi.org/10.1093/nar/gkg137[Crossref]
  • [5] G.W. Hsu, M. Ober, T. Carell and L.S. Beese: “Error-prone replication of oxidatively damaged DNA by a high-fidelity DNA polymerase“, Nature, Vol. 431, (2004), pp. 217–221. http://dx.doi.org/10.1038/nature02908[Crossref]
  • [6] S. Shibutani, M. Takeshita and A.P. Grollman: “Insertion of specific bases during DNA synthesis past the oxidation-damaged base 8-oxodG“, Nature, Vol. 349, (1991), pp. 431–434. http://dx.doi.org/10.1038/349431a0[Crossref]
  • [7] A.P. Grollman and M. Moriya: “Mutagenesis by 8-oxoguanine: an enemy within“, Trends Genetic., Vol. 9, (1993), pp. 246–249. http://dx.doi.org/10.1016/0168-9525(93)90089-Z[Crossref]
  • [8] H. Ling, F. Boudsocq, R. Woodgate and W. Yang: “Crystal Structure of a Y-Family DNA Polymerase in Action: A Mechanism for Error-Prone and Lesion-Bypass Replication“, Cell, Vol. 107, (2001), pp. 91–102. http://dx.doi.org/10.1016/S0092-8674(01)00515-3[Crossref]
  • [9] H.E. Krokan, R. Standal and G. Slupphaug: “DNA glycosylases in the base excision repair of DNA“, Biochem. J., Vol. 325, (1997), pp. 1–16.
  • [10] P.A. van der Kemp, D. Thomas, R. Barbey, R. de Oliviera and S. Boiteux: “Cloning and expression in Escherichia coli of the OGG1 gene of Saccharomyces cerevisiae, which codes for a DNA glycosylase that excises 7,8-dihydro-8-oxoguanine and 2,6-diamino-4-hydroxy-5-N-methylformamidopyrimidine“, Proc. Natl. Acad. Sci. USA, Vol. 93(11), (1996), 5197–5202. http://dx.doi.org/10.1073/pnas.93.11.5197[Crossref]
  • [11] M. Bjoras, L. Luna, B. Johnsen, E. Hoff, T. Haug, T. Rognes and E. Seeberg: “Opposite base-dependent reactions of a human base excision enzyme on DNA containing 7,8-dihydro-8-oxoguanine and abasic sites“, EMBO J., Vol. 16, (1997), pp. 6314–6322. http://dx.doi.org/10.1093/emboj/16.20.6314[Crossref]
  • [12] V. Duarte, J.G. Muller and C.J. Burrows: “Insertion of dGMP and dAMP during in vitro DNA synthesis opposite an oxidized form of 7,8-dihydro-8-oxoguanine“, Nucleic Acids Res., Vol. 27, (1999), pp. 496–502. http://dx.doi.org/10.1093/nar/27.2.496[Crossref]
  • [13] Q.M. Zhang, N. Ishikawa, T. Nakahara and S. Yonei: “Escherichia coli MutY protein has a guanine-DNA glycosylase that acts on 7,8-dihydro-8-oxoguanine:guanine mispair to prevent spontaneous G:C → C:G transversions“, Nucleic Acids Res., Vol. 26, (1998), pp. 4669–4675. http://dx.doi.org/10.1093/nar/26.20.4669[Crossref]
  • [14] J.C. Fromme, A. Banerjee, S.J. Huang and G.L. Verdine: “Structural basis for removal of adenine mispaired with 8-oxoguanine by MutY adenine DNA glycosylase“, Nature, Vol. 427, (2004), pp. 652–656. http://dx.doi.org/10.1038/nature02306[Crossref]
  • [15] D.A. Case, D.A. Pearlman, J.W. Caldwell, T.E. Cheatham III, J. Wang, W.S. Ross, C.L. Simmerling, T.A. Darden, K.M. Merz, R.V. Stanton, A.L. Cheng, J.J. Vincent, M. Crowley, V. Tsui, H. Gohlke, R.J. Radmer, Y. Duan, J. Pitera, I. Massova, G.L. Seibel, U.C. Singh, P.K. Weiner and P.A. Kollman: AMBER 7.0, University of California San Francisco, 2002, http://amber.scripps.edu/.
  • [16] H. Fujimoto, M. Pinak, T. Nemoto, P. O’Neill, E. Kume, K. Saito and H. Maekawa: “Molecular dynamics simulation of clustered DNA damage sites containing 8-oxoguanine and abasic site“, J. Comput. Chem., Vol. 26, (2005), pp. 788–798. http://dx.doi.org/10.1002/jcc.20184[Crossref]
  • [17] M.J. Frisch, G.W. Trucks, H.B. Schlegel, G.E. Scuseria, M.A. Robb, J.R. Cheeseman, J.A. Montgomery, Jr., T. Vreven, K.N. Kudin, J.C. Burant, J.M. Millam, S.S. Iyengar, J. Tomasi, V. Barone, B. Mennucci, M. Cossi, G. Scalmani, N. Rega, G.A. Petersson, H. Nakatsuji, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, M. Klene, X. Li, J.E. Knox, H.P. Hratchian, J.B. Cross, V. Bakken, C. Adamo, J. Jaramillo, R. Gomperts, R.E. Stratmann, O. Yazyev, A.J. Austin, R. Cammi, C. Pomelli, J.W. Ochterski, P.Y. Ayala, K. Morokuma, G.A. Voth, P. Salvador, J.J. Dannenberg, V.G. Zakrzewski, S. Dapprich, A.D. Daniels, M.C. Strain, O. Farkas, D.K. Malick, A.D. Rabuck, K. Raghavachari, J.B. Foresman, J.V. Ortiz, Q. Cui, A.G. Baboul, S. Clifford, J. Cioslowski, B.B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, I. Komaromi, R.L. Martin, D.J. Fox, T. Keith, M.A. Al-Laham, C.Y. Peng, A. Nanayakkara, M. Challacombe, P.M.W. Gill, B. Johnson, W. Chen, M.W. Wong, C. Gonzalez and J.A. Pople: GAUSSIAN 03, Revision C.02, Gaussian, Inc., Wallingford CT, 2004, http://www.gaussian.com/.
  • [18] X. Cheng, C. Kelso, V. Hornak, C. de los Santos, A.P. Grollman and C. Simmerling: “Dynamic behavior of DNA base pairs containing 8-oxoguanine“, J. Am. Chem. Soc., Vol. 127, (2005), pp. 13906–13918. http://dx.doi.org/10.1021/ja052542s[Crossref]
  • [19] K.A. Olszewski, M. Gutowski and L. Piela: “Interpretation of the hydrogen-bond energy at the Hartree-Fock level for pairs of the HF, H2O and NH3 molecules“, J. Phys. Chem., Vol. 94, (1990), pp. 5710–5714. http://dx.doi.org/10.1021/j100378a020[Crossref]
  • [20] Y. Mo: “Probing the nature of hydrogen bonds in DNA base pairs“, J. Mol. Modeling, Vol. 12, (2006), pp. 665–672. http://dx.doi.org/10.1007/s00894-005-0021-y[Crossref]
  • [21] R.J. Brooker: Genetics: Analysis and Principles, 2nd ed., McGraw-Hill Higher Education, Singapore, 2004
Typ dokumentu
Bibliografia
Identyfikatory
Identyfikator YADDA
bwmeta1.element.-psjd-doi-10_2478_s11534-006-0044-8
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