Molecular dynamics simulation of 7, 8-dihydro-8-oxoguanine DNA

Journal of Biomolecular Structure & Dynamics
Hisashi Ishida

Abstract

To elucidate the effect of guanine lesion produced by the oxidative damage on DNA, 1 nanosecond molecular dynamics simulations of native and oxidized DNA were performed. The target DNA molecules are dodecamer duplex d(CGCGAATTCGCG)(2) and its derivative duplex d(C(1)G(2)C(3)(8-oxoG)(4)A(5)A(6)T(7)T(8)C(9)G(10)C(11)G(12).d(C(13)G(14)C(15)G(16)A(17)A(18)T(19)T(20)C(21)G(22)C(23)G(24), which has one oxidized guanine, 7, 8-dihydro-8-oxoguanine (8-oxoG), at the fourth position. The local structural change due to the lesion of 8-oxoG and the global dynamic structure of the 8-oxoG DNA were studied. It was found that the 8-oxoG DNA remained structurally stable during the simulation due to newly produced hydrogen bonds around the (8-oxoG)(4) residue. However, there were distinguishable differences in structural parameters and dynamic property in the 8-oxoG DNA. The conformation around the (8-oxoG)(4) residue departed from the usual conformation of native DNA and took an unique conformation of epsilon-zeta in B(II) conformation and chi in high anti orientation at the (8-oxoG)(4) residue, and adopted a very low helical twist angle at the C(3):G(22)-(8-oxoG)(4):C21) step. Further analysis by principal component analysis indicated that the ...Continue Reading

References

Sep 1, 1992·Mutation Research·G E HolmesH Bernstein
Sep 1, 1992·Mutation Research·M Dizdaroglu
Jan 1, 1992·Methods in Enzymology·R E Dickerson
Nov 17, 1992·Biochemistry·M L MichaelsJ H Miller
Aug 1, 1992·Proceedings of the National Academy of Sciences of the United States of America·M L MichaelsJ H Miller
Jan 15, 1991·Proceedings of the National Academy of Sciences of the United States of America·V P ChuprinaW Saenger
Apr 11, 1991·Nucleic Acids Research·Y OdaE Ohtsuka
Jun 1, 1991·Proceedings of the National Academy of Sciences of the United States of America·J TchouS Nishimura
Jan 25, 1985·Science·P A Cerutti
Apr 1, 1988·Proceedings of the National Academy of Sciences of the United States of America·Y NghiemJ H Miller
Oct 23, 1980·Nature·R WingR E Dickerson
Jan 31, 1995·Proceedings of the National Academy of Sciences of the United States of America·L A LipscombL D Williams
Jan 1, 1994·Annual Review of Biochemistry·B Demple, L Harrison
Dec 1, 1993·Proteins·A AmadeiH J Berendsen
Sep 1, 1993·Proceedings of the National Academy of Sciences of the United States of America·B N AmesT M Hagen
Jul 1, 1993·Trends in Genetics : TIG·A P Grollman, M Moriya
Oct 1, 1993·Proceedings of the National Academy of Sciences of the United States of America·T BesshoS Mitra
Aug 8, 1997·The Journal of Biological Chemistry·K B Beckman, B N Ames
Jun 6, 1998·Nucleic Acids Research·H YamaguchiR Osman
Feb 12, 1999·Nucleic Acids Research·G DianovV A Bohr
Apr 27, 1999·Journal of Biomolecular Structure & Dynamics·T E CheathamP A Kollman
May 14, 1999·Current Opinion in Structural Biology·A Kitao, N Go
Jul 20, 1999·Annual Review of Biophysics and Biomolecular Structure·C Sagui, T A Darden
Nov 11, 1999·Proceedings of the National Academy of Sciences of the United States of America·A KlunglandD E Barnes
Dec 3, 1999·Science·T Lindahl, R D Wood
Jun 29, 2000·Annual Review of Biochemistry·A K McCulloughR S Lloyd
Jul 13, 2000·Journal of Molecular Biology·X J LuW K Olson

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Citations

Mar 7, 2007·Journal of Molecular Modeling·Piotr Cysewski, Przemysław Czeleń
May 14, 2010·Journal of Molecular Modeling·Piotr Cysewski, Przemysław Czeleń
Jan 24, 2009·Biochemistry·Diana V MaltsevaElizaveta S Gromova
Jun 6, 2003·Journal of the American Chemical Society·John H MillerMichael A Kennedy
Oct 6, 2005·Journal of the American Chemical Society·Xiaolin ChengCarlos Simmerling

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