A specific partner for abasic damage in DNA

Nature

Volumn 399, Issue 6737, 1999, Pages 704-708

  Matray, Tracy J ^a   Kool, Eric T ^a  

^a UNIVERSITY OF ROCHESTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENINE; DNA; DNA POLYMERASE; DOUBLE STRANDED DNA; NUCLEOTIDE; THYMINE;

ARTICLE; BASE PAIRING; DNA DAMAGE; DNA HELIX; DNA REPLICATION; DNA SYNTHESIS; HYDROGEN BOND; MOLECULAR MODEL; PRIORITY JOURNAL; STRUCTURE ANALYSIS;

BASE PAIRING; DNA; DNA DAMAGE; DNA POLYMERASE I; DNA PRIMERS; DNA REPLICATION; ESCHERICHIA COLI; HYDROGEN BONDING; KINETICS; NUCLEIC ACID CONFORMATION; NUCLEOTIDES; PYRENES; STRUCTURE-ACTIVITY RELATIONSHIP;

ABIES;

EID: 0033578081     PISSN: 00280836     EISSN: None     Source Type: Journal    
DOI: 10.1038/21453     Document Type: Article

References (29)

1. Moran, S., Ren, R. X.-F. & Kool, E. T. A thymidine triphosphate shape mimic lacking Watson-Crick pairing ability is replicated with high specificity. Proc. Natl Acad. Sci. USA 94, 10506-10511 (1997).
2. Goodman, M. F. Hydrogen bonding revisited: geometric selection as a principal determinant of DNA replication fidelity. Proc. Natl Acad. Sci. USA 94, 10493-10495 (1997).
3. Morales, J. C. & Kool, E. T. Efficient replication of a DNA base pair between non-hydrogen-bonded nucleoside analogues. Nature Struct. Biol. 5, 950-954 (1998).
4. Moran, S., Ben, R. X.-F., Rumney, S. & Kool, E. T. Difluorotoluene, a nonpolar isostere of thymine, codes specifically and efficiently for adenine in DNA replication. J. Am. Chem. Soc. 119, 2056-2057 (1997).
5. Goodman, M. F., Creighton, S., Bloom, L. B. & Petruska, J. Biochemical basis of DNA replication fidelity. Crit Rev. Biochem. Mol. Biol. 28, 83-126 (1993).
6. Kool, E. T. Replication of non-hydrogen bonded bases by DNA polymerases: a mechanism for steric matching. Biopolymers (Nucleic Acid Sciences) 48, 3-17 (1998).
7. Loeb, L. A. & Preston, B. D. Mutagenesis by apurinic/apyrimidinic sites. Annu. Rev. Genet. 20, 201-230 (1986).
8. Ren, R. X-F., Chaudhuri, N. C., Paris, P. L., Rumney, S. & Kool, E. T. Naphthalene, phenanthrene, and pyrene as DNA base analogues: synthesis, structure, and fluorescence in DNA. J. Am. Chem. Soc. 118, 7671-7678 (1996).
9. Matray, T. J. & Kool, E. T. Selective and stable DNA base pairing without hydrogen bonds. J. Am. Chem. Soc. 120, 6191-6192 (1998).
10. Mishra, M. C. & Broom, A. D. A novel synthesis of nucleoside 5′ triphosphates. J. Chem. Soc., Chem. Commun. 1276-1277 (1991).
11. Hoard, D. E. & Ott, D. G. Conversion of mono- and oligodeoxyribonucleotides to 5′-triphosphates. J. Am. Chem. Soc. 87, 1785-1788 (1965).
12. Millicon, T. A. et al. Synthesis and biophysical studies of short oligodeoxynucleotides with novel modifications. Nucleic Acids Res. 12, 7435-7453 (1984).
13. Takeshita, M., Chang., C., Johnson, F., Will, S. & Grollman, A. P. Oligodeoxy-nucleotides containing synthetic abasic sites. Model substrates for DNA polymerases and apurinic/apyrimidinic endonucleases. J. Biol. Chem. 262, 10171-10179 (1987).
14. Randall, S. K., Eritja, R., Kaplan, B. E., Petruska, J. & Goodman, M. F. Nucleotide insertion kinetics opposite abasic lesions in DNA. J. Biol. Chem. 262, 6864-6870 (1987).
15. Sagher, D. & Strauss, B. Insertion of nucleotides opposite apurinic/apyrimidinic sites in deoxyribonucleic acid during in vitro synthesis: uniqueness of adenine nucleotides. Biochemistry 22, 4518-4526 (1983).
16. Schaaper, R. M., Kunkel, T. A. & Loeb, L. A. Infidelity of DNA synthesis associated with bypass of apurinic sites. Proc. Natl Acad. Sci. USA 80, 487-491 (1983).
17. Lawrence, C. W., Borden, A., Banerjee, S. K. & LeClerc, J. E. Mutation frequency and spectrum resulting from a single abasic site in a single-stranded vector. Nucleic Acids Res. 18, 2153-2157 (1990).
18. Paz-Elizur, T., Takishita, M. & Livneh, Z. Mechanism of bypass synthesis through an abasic site analog by DNA polymerase I. Biochemistry 36, 1766-1773 (1997).
19. Doublié, S., Tabor, S., Long, A. M., Richardson, C. C. & Ellenberger, T. Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 Å resolution. Nature 391, 251-258 (1998).
20. Kiefer, J. R., Mao, C., Braman, J. C. & Beese, L. S. Visualizing DNA replication in a catalytically active Bacillus DNA polymerase crystal. Nature 391, 304-307 (1998).
21. Huang, H., Chopra, R., Verdine, G. L. & Harrison, S. C. Structure of a covalently trapped catalytic complex of HIV-1 reverse transcriptase: implications for drug resistance. Science 282, 1669-1675 (1998).
22. Diederichsen, U. Selectivity of DNA replication: the importance of geometry over hydrogen bonding. Angew. Chem. 37, 1655-1657 (1998).
23. Fygenson, D. K. & Goodman, M. F. Appendix. Gel kinetic analysis of polymerase fidelity in the presence of multiple enzyme DNA encounters. J. Biol. Chem. 272, 27931-27935 (1997).
24. Shibutani, S., Takeshita, M. & Grollman, A. P. Translesional synthesis on DNA templates containing a single abasic site. A mechanistic study of the "A rule". J. Biol. Chem. 272, 13916-13921 (1997).
25. Lindahl, T. & Nyberg, B. Rate of depurination of native deoxyribonucleic acid. Biochemistry 11, 3610-3618 (1972).
26. Weiss, B. & Grossman, L. Phosphodiesterases involved in DNA repair. Adv. Enzymol. Rel. Areas Mol. Biol. 60, 1-34 (1972).
27. Ide, H. et al. Synthesis and damage specificity of a novel probe for the detection of abasic sites in DNA. Biochemistry 32, 8276-8283 (1993).
28. Maulik, G. et al. Novel non-isotopic detection of MutY enzyme-recognized mismatches in DNA via ultrasensitive detection of aldehydes. Nucleic Acids Res. 27, 1316-1322 (1999).
29. Denissenko, M. F., Pao, A., Tang, M. & Pfeifer, G. P. Preferential formation of benzo[a]pyrene adducts at lung cancer mutational hotspots in p53. Science 274, 430-432 (1996).