Effect of neighboring bases on base-pair stacking orientation: A molecular dynamics study

Journal of Biomolecular Structure and Dynamics

Volumn 18, Issue 1, 2000, Pages 29-43

  Bandyopadhyay, Debashree ^a   Bhattacharyya, Dhananjay ^a  

^a SAHA INSTITUTE OF NUCLEAR PHYSICS   (India)

Author keywords

[No Author keywords available]

Indexed keywords

ADENINE; CYTOSINE; DNA; GUANINE; OLIGOMER; POLYMER; THYMINE;

ARTICLE; BASE PAIRING; CRYSTAL STRUCTURE; DNA HELIX; DNA STRUCTURE; GEOMETRY; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; MOLECULAR MODEL; PRIORITY JOURNAL; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; SIMULATION; STRUCTURE ANALYSIS; X RAY CRYSTALLOGRAPHY;

EID: 0033801065     PISSN: 07391102     EISSN: 15380254     Source Type: Journal    
DOI: 10.1080/07391102.2000.10506645     Document Type: Article

References (46)

1. Crothers, D. M., Haran, T. E., and Nadeau, J. G., 1990. J. Biol. Chem., 265:7093–7096.
2. Hagerman, P. J., 1990. Annual Rev. Biochem, 59:755–781.
3. Chou, P. Y., and Fasman, G. D., 1974. Biochemistry, 13:222–245.
4. Garnier, J., 1978. J. Mol. Biol., 120:97–120.
5. Dickerson, R. E., and Drew, H. R., 1981. J. Mol. Biol., 149:761–786.
6. Calladine, C. R. 1982. J. Mol. Biol., 161:343–352.
7. Yanagi, K., Prive, G. G, and Dickerson, R. E. 1991. J. Mol. Biol., 217:201–214.
8. Gorin, A. A, Zhurkin, V. B., and Olson, W. K., 1995. J. Mol. Biol., 247:34–48.
9. Suzuki, M., Amano, N., Kakinuma, J., and Tateno, M., 1997. J. Mol. Biol., 274:421–435.
10. Bhattacharyya, D., Kundu, S., Thakur, A. R., and Majumder, R., 1999. J. Biomol. Struct. Dynam., 17:289–300.
11. Bansal, M., Bhattacharyya, D., and Mohanty, D., 1991. Edited by:Balaram, P., and Ramaseshan, S., 347–362. Molecular conformation and Biological Interactions (Eds
12. Hunter, C. A., and Lu, X. J., 1997. J. Mol. Biol., 265:603–619.
13. Subirana, J. A., and Faria, T., 1997. Biophys J., 73:333–338.
14. Urpi, L., Tereshko, V., Malinina, L., H-Dinh, T., and Subirana, J. A. 1996. Nature Structural Biology, 3:325–328.
15. Berman, H. M., Olson, W. K., Beveridge, D. L., Westbrook, J., Gelbin, A., Demeny, T., Hsieh, S. H., Srinivasan, A. R., and Scneider, B., 1992. Biophys. J, 63:751–759.
16. Young, M. A., Ravishanker, G., and Beveridge, D. L., 1997. Biophys. J, 73:2313–2336.
17. Koo, H. S., Wu, H. M., and Crothers, D. M., 1986. Nature, 320:501–506.
18. Bolshoy, A., McNamara, P., Harrington, R. E., and Trifonov, E. N., 1991. Proc. Natl. Acad. Sci, U.S.A, 88:7046–7050.
19. Burkhoff, A. M., and Tullius, T. D., 1987. Cell, 27:935–43.
20. Losa, R., Omari, S., and Thoma, F., 1990. Nucleic. Acids. Res, 18:3495–3502.
21. Nagaich, A. K., Bhattacharyya, D., Brahmachari, S. K., and Bansal, M., 1994. J. Biol. Chem, 269:7824–783.
22. MacKerell, A. D., Jr., Wiorkirwicz-Kuczera and Karplus, M. 1995. J. Am. Chem. Soc., 117:11946–11975.
23. Brooks, B. R., Bruccoleri, R. E., Olafson, B. D., States, D. J., Swaminathan, S., and Karplus, M., 1983. J. Comp. Chem., 4:187–217.
24. Steinbach, P. J., and Brooks, B. R., 1993. Proc. Natl. Acad. Sci. USA, 91:35–9139.
25. Arnold, G. E., and Ornstein, R. L., 1994. Proteins, 18:19–33.
26. Nilsson, L., and Sen, S., 1999. Biophys. J., 77:1801–1810.
27. Chong, L. T., Duan, Y., Wang, L., Massova, I., and Kollman, P. A., 1999. Proc. Natl. Acad. Sci, 96:14330–14335.
28. Chandrasekaran, R., and Arnott, S., 1996. J. Biomol. Struct. Dynam., 13:1015–1027.
29. Darden, T., Perera, L., Li, L., and Pedersen, L., 1999. Structure, 7:R55–R60.
30. Bansal, M., Bhattacharyya, D., and Ravi, B., 1995. Comput. Appl. Biosi, 11:281–287.
31. Dickerson, R. E., Bansal, M., 1989. EMBO J, 8:1–4.
32. Bhattacharyya, D., and Bansal, M., 1990. J. Biomol. Struct. Dynam., 8:539–572.
33. Grezeskowiak, K., Yanagi, K., Prive, G. G., and Dickerson, R. E., 1991. J. Biol. Chem., 266:8861–8883.
34. Feig, M., and Pettitt, M., 1998. Biophys J., 75:134–149.
35. Snedecor, W. G, and Cochran, W. G., 1989. Statistical Methods., Eighth Edition Ames, Iowa:Iowa State University Press.
36. Fratini, A. V, Kopka, M. L., Drew, H. R., and Dickerson, R. E., 1992. J. Biol. Chem., 257:14686–14707.
37. Prive, G. G., Yanagi, K., and Dickerson, R. E., 1991. J. Mol. Biol., 217:177–199.
38. Heinemann, U., and Hahn, M. J., 1992. J. Biol. Chem., 267:7332–7341.
39. Yuan, H., Quintana, J., and Dickerson, R. E., 1992. Biochemistry, 31:8009–8021.
40. Hartmann, B., Piazzola, D., and Lavery, R., 1993. Nucleic. Acids. Res., 21:561–568.
41. Bertrand, H., Ha-Duong, T., Fermandjian, S., and Hartmann, B., 1998. Nucleic. Acids. Res., 26:1261–1267.
42. Dornberger, U., Flemming, J., and Fritzsche, H., 1998. J. Mol. Biol., 284:1453–1463.
43. Tisne, C., Hantz, E., Hartmann, B., and Delecipierre, M., 1998. J. Mol. Biol., 279:127–142.
44. Wu, H. M., and Crothers, D. M., 1984. Nature, 308:509–513.
45. Tereshko, V., and Subirana, J. A., 1999. Acta Crystallogr D. Biol. Crystallogr, 55:810–819.
46. Haran, T. E., Kahn, J. D., and Crothers, D. M., 1994. J. Mol. Biol., 244:135–143.