Base-pairing properties of the oxidized cytosine derivative, 5-hydroxy uracil

Biochemical and Biophysical Research Communications

Volumn 366, Issue 3, 2008, Pages 752-757

  Thiviyanathan, Varatharasa ^a   Somasunderam, Anoma ^a   Volk, David E ^a   Hazra, Tapas K ^a   Mitra, Sankar ^a   Gorenstein, David G ^a  

^a University of Texas Medical Branch School of Medicine   (United States)

Author keywords

Base pair mismatch; DNA repair; Hydroxy uracil; Oxidative DNA damage

Indexed keywords

5 HYDROXYURACIL; ALANINE; CYSTEINE; CYTOSINE; CYTOSINE DERIVATIVE; DNA POLYMERASE; DOUBLE STRANDED DNA; GLYCINE; HYDROXYL GROUP; THREONINE; UNCLASSIFIED DRUG;

ARTICLE; BASE PAIRING; CIRCULAR DICHROISM; DEAMINATION; DNA DAMAGE; DNA REPLICATION; GENE MUTATION; MELTING POINT; MOLECULAR STABILITY; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; OXIDATION; OXIDATIVE STRESS; PRIORITY JOURNAL; ULTRAVIOLET RADIATION;

BASE PAIRING; COMPUTER SIMULATION; CYTOSINE; DNA; MODELS, CHEMICAL; MODELS, MOLECULAR; OXIDATION-REDUCTION; URACIL;

EID: 37549060396     PISSN: 0006291X     EISSN: 10902104     Source Type: Journal    
DOI: 10.1016/j.bbrc.2007.12.010     Document Type: Article

References (21)

1. Ames B.N., Shigenaga M.K., and Hagen T.M. Oxidants, antioxidants, and the degenerative diseases of aging. Proc. Natl. Acad. Sci. USA 90 (1993) 7915-7922
2. Ward J.F. The complexity of DNA damage: relevance to biological consequences. Int. J Radiat. Biol. 66 (1994) 427-432
3. Schaaper R.M., Danforth B.N., and Glickman B.W. Mechanisms of spontaneous mutagenesis: an analysis of the spectrum of spontaneous mutation in the Escherichia coli lacI gene. J. Mol. Biol. 189 (1986) 273-284
4. Moraes E.C., Keyse S.M., and Tyrrell R.M. Mutagenesis by hydrogen peroxide treatment of mammalian cells: a molecular analysis. Carcinogenesis 11 (1990) 283-293
5. Feig D.I., Sowers L.C., and Loeb L.C.L.A. Reverse chemical mutagenesis: identification of the mutagenic lesions resulting from reactive oxygen species-mediated damage to DNA. Proc. Natl. Acad. Sci. USA 91 (1994) 6609-6613
6. Dizdaroglu M., Holwitt E., Hagan M.P., and Blakely W.F. Formation of cytosine glycol and 5,6-dihydroxycytosine in deoxyribonucleic acid on treatment with osmium tetroxide. Biochem. J. 235 (1986) 531-536
7. Kreutzer D.A., and Essigman J.M. Oxidized, deaminated cytosines are a source of C→T transitions in vivo. Proc. Natl. Acad. Sci. USA 95 (1998) 3578-3582
8. Rappoport Z. The Chemistry of Enols. The Chemistry of Functional Groups (1990), Wiley, Chichester
9. Moschel R.C., and Behrman E.J. Oxidation of nucleic acid bases by potassium peroxodisulfate in alkaline aqueous solution. J. Org. Chem. 39 (1974) 1983-1989
10. Purmal A.A., Lampman G.W., Bond J.P., Hatahet Z., and Wallace S.S. Enzymatic processing of uracil, a major oxidative product of DNA cytosine. J. Biol. Chem. 273 (1998) 10026-10035
11. Prumal A.A., Kow Y.W., and Wallace S.S. 5-Hydroxypyrimidine deoxynucleoside triphosphates are more efficiently incorporated into DNA by exonuclease-free Klenow fragment than 8-oxopurine deoxynucleoside triphosphates. Nucleic Acids Res. 22 (1994) 3930-3935
12. Vaisman A., and Woodgate R. Unique misinsertion specificity of poliota may decrease the mutagenic potential of deaminated cytosines. EMBO J. 20 (2001) 6520-6529
13. Cheng K.C., Cahill D.S., Kasai H., Nishimura S., and Loeb L.A. 8-Hydroxyguanine, an abundant form of oxidative DNA damage, causes G→T and A→C substitutions. J. Biol. Chem. 267 (1992) 166-172
14. Volk D.E., Thiviyanathan V., Somasunderam A., and Gorenstein D.G. Ab initio base-pairing energies of uracil and 5-hydroxyuracil with standard DNA bases at the BSSE-free DFT and MP2 theory levels. Org. Biomol. Chem. 4 (2006) 1741-1745
15. Zhang S., Yang X., and Gorenstein D.G. Enhanced suppression of residual water in a "270" WET sequence. J. Magn. Reson. 143 (2000) 382-386
16. C.R. Canton, P.R. Schimmel, Techniques for the Study of Biological Structure and Function, in: Biophysical Chemistry, Part II. W.H. Freeman, New York, 1980.
17. Devoe H., and Tinoco I. The hypochromism of helical polynucleotides. J. Mol. Biol. 4 (1962) 518-527
18. Gray D.M., Hung S.H., and Johnson K.H. Absorption and circular dichroism spectroscopy of nucleic acid duplexes and triplexes. Methods Enzymol. 246 (1995) 19-34
19. Gary D.M., Ratliff R.L., and Vaughan M.R. Circular dichroism spectroscopy of DNA. Methods Enzymol. 211 (1992) 389-406
20. LaFrancois C.J., Jang Y.H., Cagin T., Goddard W.A., and Sowers L.C. Conformation and proton configuration of pyrimidine deoxynucleoside oxidation damage products in water. Chem. Res. Toxicol. 13 (2000) 462-470
21. Kino K., Shimizu Y., Sugasawa K., Sugiyama H., and Hanaoka F. Nucleotide excision repair of 5-formyluracil in vivo is enhanced by the presence of mismatched bases. Biochemistry 43 (2004) 2682-2687