Structural and dynamic effects of single 7-hydro-8-oxoguanine bases located in a frameshift target DNA sequence

Biophysical Chemistry

Volumn 118, Issue 1, 2005, Pages 31-41

  Barone, Flavia ^a   Lankas, Filip ^b   Spackova, Nada ^c   Sponer, Jiri ^c   Karran, Peter ^d   Bignami, Margherita ^a   Mazzei, Filomena ^a  

^a ISTITUTO SUPERIORE DI SANITÀ   (Italy)

^b EPFL   (Switzerland)

^c INSTITUTE OF BIOPHYSICS   (Czech Republic)

^d IMPERIAL CANCER RESEARCH FUND   (United Kingdom)

Author keywords

7 hydro 8 oxoguanine; DNA conformation; DNA dynamics; Frameshift; Molecular dynamics

Indexed keywords

7 HYDRO 8 OXOGUANINE; DNA BASE; DNA POLYMERASE; DOUBLE STRANDED DNA; OLIGONUCLEOTIDE; PRIMER DNA; SINGLE STRANDED DNA; UNCLASSIFIED DRUG;

ANISOTROPY; ARTICLE; COMPRESSION; DNA MODIFICATION; DNA REPLICATION; DNA SEQUENCE; DNA TEMPLATE; FLUORESCENCE POLARIZATION; GENE TARGETING; MOLECULAR DYNAMICS; MOVEMENT (PHYSIOLOGY); PHYSICAL CHEMISTRY; PRIORITY JOURNAL; RIGIDITY; SIMULATION; TORSION;

BASE PAIR MISMATCH; BASE SEQUENCE; DNA; DNA REPAIR; DNA REPLICATION; DNA-DIRECTED DNA POLYMERASE; FLUORESCENCE POLARIZATION; GUANINE; HYPOXANTHINE PHOSPHORIBOSYLTRANSFERASE; NUCLEIC ACID CONFORMATION; TEMPLATES, GENETIC;

EID: 24344466194     PISSN: 03014622     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bpc.2005.06.003     Document Type: Article

References (37)

1. S. Shibutani, M. Takeshita, and A.P. Grollman Insertion of specific bases during DNA synthesis past the oxidation-damaged base 8-oxodG Nature 349 1991 431 434
2. K.C. Cheng, D.S. Cahill, H. Kasai, S. Nishimura, and L.A. Loeb 8-Hydroxyguanine, an abundant form of oxidative DNA damage, causes G-T and A-C substitutions J. Biol. Chem. 267 1992 166 172
3. G. Slupphaug, B. Kavli, and H.E. Krokan The interacting pathways for prevention and repair of oxidative DNA damage Mutat. Res. 531 2003 231 251
4. P. Fortini, B. Pascucci, E. Parlanti, M. D'Errico, V. Simonelli, and E. Dogliotti The base excision repair: mechanisms and its relevance for cancer susceptibility Biochimie 85 2003 1053 1071
5. M. Sekiguchi Cloning and expression of cDNA for a human enzyme that hydrolyzes 8-oxo-dGTP, a mutagenic substrate for DNA synthesis J. Biol. Chem. 268 1993 23524 23530
6. C. Colussi, E. Parlanti, P. Degan, G. Aquilina, D. Barnes, P. Macpherson, P. Karran, M. Crescenzi, E. Dogliotti, and M. Bignami The mammalian mismatch repair pathway removes DNA 8-oxodGMP incorporated from the oxidized dNTP pool Curr. Biol. 12 2002 912 918
7. M.T. Russo, M.F. Blasi, F. Chiera, P. Fortini, P. Degan, P. Macpherson, M. Furuichi, Y. Nakabeppu, P. Karran, G. Aquilina, and M. Bignami The oxidized deoxynucleoside triphosphate pool is a significant contributor to genetic instability in mismatch repair-deficient cells Mol. Cell. Biol. 24 2004 465 474
8. G.E. Plum, A.P. Grollman, F. Johnson, and K.J. Breslauer Influence of the oxidatively damaged adduct 8-deoxyguanosine on the conformation, energetics and thermodynamic stability of a DNA duplex Biochemistry 34 1995 16148 16160
9. L.A. Lipscomb, M.E. Peek, M.L. Morningstar, S.M. Verghis, E.M. Miller, A. Rich, J.M. Essigmann, and L.D. Williams X-ray structure of a DNA decamer containing 7,8-dihydro-8-oxoguanine Proc. Natl. Acad. Sci. U. S. A. 92 1995 719 723
10. Y. Oda, S. Uesugi, M. Ikehara, S. Nishimura, Y. Kawase, H. Ishikawa, H. Inoue, and E. Ohtsuka NMR studies of a DNA containing 8-hydroxydeoxyguanosine Nucleic Acids Res. 19 1991 1407 1412
11. F. Barone, L. Cellai, C. Giordano, M. Matzeu, F. Mazzei, and F. Pedone Gamma-ray footprinting and fluorescence polarization anisotropy of a 30-mer synthetic DNA fragment with one 2′-deoxy-7-hydro-8-oxoguanosine lesion Eur. Biophys. J. 28 2000 621 628
12. F. Barone, E. Dogliotti, L. Cellai, C. Giordano, M. Bjoras, and F. Mazzei Influence of DNA torsional rigidity on excision of 7,8-dihydro-8-oxo-2′ deoxyguanosine in the presence of opposing abasic sites by human OGG1 protein Nucleic Acids Res. 31 2003 1897 1903
13. J. Sambrook, E.F. Fritsch, and T. Maniatis Molecular cloning A Laboratory Manual 1989 Cold Spring Harbor NY
14. K.J. Breslauer Extracting thermodynamic data from equilibrium melting curves for oligonucleotide order-disorder transition S. Agraval Methods in Molecular Biology vol. 26 1994 Humana Press Totowa, NJ 347 372
15. F. Barone, G. Chirico, M. Matzeu, F. Mazzei, and F. Pedone Triple helix DNA oligomer melting measured by fluorescence polarization anisotropy Eur. Biophys. J. 27 1998 137 146
16. M. Collini, G. Chirico, G. Baldini, and M.E. Bianchi Conformation of short DNA fragments by modulated fluorescence polarization anisotropy Biopolymers 36 1995 211 225
17. S.A. Allison, and M. Schurr Torsion dynamics and depolarization of fluorescence of linear molecules. I. Theory and application to DNA Chem. Phys. 41 1979 35 39
18. D.P. Millar, R.J. Robbins, and A.H. Zewail Torsion and bending of nucleic acids studied by subnanosecond time resolved fluorescence depolarization of intercalated dyes J. Chem. Phys. 76 1982 2080 2094
19. J.H. Miller, C.-C.P. Fan-Chiang, T.P. Straatsma, and M.A. Kennedy 8-oxoguanine enhances bending of DNA that favors binding to glycosylases J. Am. Chem. Soc. 125 2003 6331 6336
20. X.J. Lu, and W. Olson 3DNA: a software package for analysis, rebuilding and visualization of three-dimensional nucleic acids structures Nucleic Acids Res. 31 2003 5108 5121
21. F. Lankas, J. Sponer, J. Langowski, and T.E. Cheatham III DNA basepair step deformability inferred from molecular dynamics simulations Biophys. J. 85 2003 2872 2883
22. P. Varnai, and K. Zakrzewska DNA and its counterions: a molecular dynamics study Nucleic Acids Res. 32 2004 4269 4280
23. D.L. Beveridge, G. Barreiro, K.S. Byun, D.A. Case, T.E. Cheatham III, S.B. Dixit, E. Giudice, F. Lankas, R. Lavery, J.H. Maddocks, J.H. Osman, E. Seibert, H. Sklenar, G. Stoll, K.M. Thayer, P. Varnai, and M.A. Young Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. I. Research design and results on d(CpG) steps Biophys. J. 87 2004 3799 3813
24. K. Reblova, N. Spackova, R. Stefl, K. Csaszar, J. Koca, N.B. Leontis, and J. Sponer Non-Watson-Crick base pairing and hydration in RNA motifs: molecular dynamics of 5S rRNA loop Eur. Biophys. J. 84 2003 3564 3582
25. N. Spackova, I. Berger, and J. Sponer Nanosecond molecular dynamics of zipper-like DNA duplex structures containing sheared G.A mismatch pairs J. Am. Chem. Soc. 122 2000 7564 7572
26. P. Auffinger, and E. Westhof Water and ion binding around r(UpA)12 and d(TpA) 12 oligomers - comparison with RNA and DNA (CpG)12 duplexes J. Mol. Biol. 305 2001 1057 1072
27. F. Pedone, F. Mazzei, M. Matzeu, and F. Barone Torsional constant of 27-mer DNA oligomers of different sequences Biophys. Chemist. 94 2001 175 184
28. E.F. Gale, E. Cundliffe, P.E. Reynolds, M.H. Richmond, and M.J. Waring The Molecular Basis of Antibiotic Action 1981 Wiley London
29. M.L. Dodson, and R.S. Lloyd Backbone dynamics of DNA containing 8-oxoguanine: importance for substrate recognition by base excision repair glycosylases Mutat. Res. 487 2001 93 108
30. H. Ishida Molecular dynamics simulation of 7,8-dihydro-8-oxoguanine DNA J. Biol. Struct. Dyn. 19 2002 839 851
31. P. Varnai, D. Djuranovic, R. Lavery, and B. Hartmann Alpha/gamma transitions in the B-DNA duplex structures Nucleic Acids Res. 30 2002 5398 5406
32. D.C. Malins, N.L. Polissar, G.K. Ostrander, and M.A. Vinson Single 8-oxo-guanine and 8-oxo-adenine lesions induce marked changes in the backbone structure of a 25-base DNA strand Proc. Natl. Acad. Sci. U. S. A. 97 2000 12442 12445
33. G. Chirico, M. Collini, K. Toth, N. Brun, and J. Langowski Rotational dynamics of curved DNA fragments studied by fluorescence polarization anisotropy Eur. Biophys. J. 29 2001 597 606
34. S.J. Johnson, J.S. Taylor, and L.S. Beese Processive DNA synthesis observed in a polymerase crystal suggests a mechanism for the prevention of frameshift mutations Proc. Natl. Acad. Sci, U. S. A. 100 2003 3895 3900
35. T.A. Kunkel, and K. Bebenek DNA replication fidelity Ann. Rev. Biochem. 69 2000 497 529
36. A.L. Jackson, R. Chen, and L.A. Loeb Induction of microsatellite instability by oxidative DNA damage Proc. Natl. Acad. Sci. U. S. A. 95 1998 12468 12473
37. M.C. Earley, and G.F. Crouse The role of mismatch repair in the prevention of base pair mutations in Saccharomyces cerevisiae Proc. Natl. Acad. Sci. U. S. A. 95 1998 15487 15491