Solution structure of duplex DNA containing an extrahelical abasic site analog determined by NMR spectroscopy and molecular dynamics

Nucleic Acids Research

Volumn 26, Issue 10, 1998, Pages 2385-2391

  Lin, Zhen ^a   Hung, Kwong Ngai ^a   Grollman, Arthur P ^a   De Los Santos, Carlos ^a  

^a STONY BROOK UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DOUBLE STRANDED DNA;

ARTICLE; DELETION MUTANT; DNA HELIX; DNA SYNTHESIS; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL; SIMULATION;

COMPUTER SIMULATION; DNA; FURANS; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; NUCLEIC ACID CONFORMATION; NUCLEIC ACID HETERODUPLEXES; OLIGODEOXYRIBONUCLEOTIDES;

EID: 0032524724     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/26.10.2385     Document Type: Article

References (45)

1. Lindahl, T. (1982) Annu. Rev. Biochem. 51, 61-87.
2. Loeb, L. A. and Preston, B. D. (1986) Annu. Rev. Genet. 20, 201-230.
3. Weiss, B. and Grossman, L. (1978) Adv. Enzymol. Relat. Areas Mol. Biol. 60, 1-34.
4. Millican, T. A., Mock, G. A., Chauncey, M. A., Patel, T. P., Eaton, M. A., Gunning, J., Cutbush, S. D., Niedele, S. and Mann, J. (1984) Nucleic Acids Res. 12, 7435-7453.
5. Takeshita, M., Chang, C.-N., Johnson, F., Will, S. and Grollman, A. P. (1987) J. Biol. Chem. 262, 10171-10179.
6. Randall, S. K., Eritja, R., Kaplan, B., Petruska, J. and Goodman, M. F. (1987) J. Biol. Chem. 262, 6864-6870.
7. Takeuchi, M., Lillis, R., Demple, B. and Takeshita, M. (1994) J. Biol. Chem. 269, 21907-21914.
8. Paz-Elizur, T., Takeshita, M., Goodman, M., O'Donnell, M. and Livneh, Z. (1996) J. Biol. Chem. 271, 24662-24669.
9. Paz-Elizur, T., Takeshita, M. and Livneh, Z. (1997) Biochemistry 36, 1766-1773.
10. Wilson, D. M., Takeshita, M., Grollman, A. P. and Demple, B. (1995) J. Biol. Chem. 270, 16002-16007.
11. Sagher, D. and Strauss, B. (1985) Nucleic Acids Res. 13, 4285-4298.
12. Schaaper, R. M. and Loeb, L. A. (1981) Proc. Natl. Acad. Sci. USA 78, 1773-1777.
13. Kunkel, T. A. (1984) Proc. Natl. Acad. Sci. USA 81, 1494-1498.
14. Lawrence, C. W., Borden, A., Banerjee, S. K. and LeClerc, J. E. (1990) Nucleic Acids Res. 18, 2153-2157.
15. Shibutani, S., Takeshita, M. and Grollman A. P. (1997) J. Biol. Chem. 272, 13916-13922.
16. Takeshita, M. and Eisenberg, W. (1994) Nucleic Acids Res. 22, 1897-1902.
17. Cabral Neto, J. B., Cabral, R. E., Margot, A., Le Page, F., Sarasin, A. and Gentil, A. (1994) J. Mol. Biol. 240, 416-420.
18. Klinedinst, D. K. and Drinkwater, N. R. (1992) Mol. Carcinog. 6, 32-42.
19. Gibbs, P. E. and Lawrence, C. W. (1995) J. Mol. Biol. 251, 229-236.
20. Cuniasse, Ph., Sowers, L. C., Eritja, R., Kaplan, B., Goodman, N. F., Cognet, J. A. H., LeBret, M., Guschlbauer, W. and Fazakerly, G. V. (1987) Nucleic Acids Res. 15, 8003-8022.
21. Cuniasse, Ph., Fazakerly, G. V., Guschlbauer, W., Kaplan, B. and Sowers, L. C. (1990) J. Mol. Biol. 213, 303-314.
22. Kalnick, M. W., Chang, C. N., Grollman, A. P. and Patel, D. J. (1988) Biochemistry 27, 924-931.
23. Kalnick, M. W., Chang, C. N., Johnson, F., Grollman, A. P. and Patel, D. J. (1989) Biochemistry 28, 3373-3383.
24. Withka, J. M., Wilde, J. A., Bolton, P. H., Mazumder, A. and Gerlt, J. A. (1991) Biochemistry 30, 9931-9940.
25. Goljer, I., Kumar, S. and Bolton P. H. (1995) J. Biol. Chem. 270, 22980-22987.
26. Singh, M. P., Hill, G. C., Péoc'h, D., Rayner, B., Imbach, J.-L. and Lown, W. (1994) Biochemistry 33, 10271-10285.
27. Coppel, Y., Berthet, N., Coulombeau, C., Coulombeau, C., Garcia, J. and Lhomme, J. (1997) Biochemistry 36, 4817-4830.
28. Cuniasse, Ph., Sowers, L. C., Eritja, R., Kaplan, B., Goodman, N. F., Cognet, J. A. H., LeBret, M., Guschlbauer, W. and Fazakerly, G. V. (1989) Biochemistry 28, 2018-2026.
29. Korobka, A., Cullinan, D., Cosman, M., Grollman, A. P., Patel, D. J., Eisenberg, M. and de los Santos, C. (1996) Biochemistry 35, 13310-13318.
30. States, D. J., Habekorn, R. A. and Ruben, D. J. (1982) J. Magn. Res. 48, 286-292.
31. Plateau, P. and Gueron, M. (1982) J. Am. Chem. Soc. 104, 7310-7311.
32. Sklenar, V., Mishayiro, H., Zon, G., Miles, H. T. and Bax, A. (1986) FEBS Lett. 208, 94-98.
33. Brunger, A. (1993) X-PLOR Version 3.1 A System for X-Ray Crystallography and NMR. Yale University Press, New Haven, CT.
34. Lavery, R. and Sklenar, H. (1988) J. Biomol. Struct. Dyn. 6, 63-91.
35. Lavery, R. and Sklenar, H. (1989) J. Biomol. Struct. Dyn. 6, 655-667.
36. Brooks, B., Bruccoleri, R., Olafson, B., States, D., Swaminathan, S. and Karplus, M. (1983) J. Comp. Chem. 4, 187-217.
37. Borgias, B. A. and James, T. L. (1990) J. Magn. Reson. 87, 475-487.
38. Ryckaert, J. P., Ciccoti, G. and Berendsen, H. J. C. (1977) J. Comput. Phys. 23, 327-341.
39. Lankhorst, P. P., Haasnoot, C. A. G., Erkelens, C. and Altona, C. (1984) J. Biomol. Struct. Dyn. 1, 1387-1405.
40. Hare, D. R., Wemmer, D. E., Chou, S. H., Drobny, G. and Reid, B. R. (1983) J. Mol. Biol. 171, 319-336.
41. Wüthrich, K. (1986) In NMR of Proteins and Nucleic Acids. John Wiley, New York, p.208.
42. Majumdar, A. and Hosur, R. V. (1992) Prog. NMR Spectrosc. 24, 109-158.
43. Kunkel, T. A. (1990) Biochemistry 29, 8003-8011.
44. Schaaper, R. M., Koffel-Schwartz, N. and Fuchs, R. P. P. (1990) Carcinogenesis 11 1087-1095.
45. Shibutani, S. and Grollman, A. P. (1993) J. Biol. Chem. 268, 11703-11710.