Dynamic properties of double-stranded DNA by normal mode analysis

Journal of Chemical Physics

Volumn 110, Issue 22, 1999, Pages 11070-11075

  Matsumoto, Atsushi ^a   Go, Nobuhiro ^a  

^a KYOTO UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0000319912     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.479043     Document Type: Article

References (30)

1. J. C. Wang and A. S. Lynch, Curr. Opin. Gen. Dev. 3, 764 (1993).
2. M. R. Gartenberg and J. C. Wang, Proc. Natl. Acad. Sci. USA 89, 11461 (1992).
3. M. C. Schultz, S. J. Brill, Q. Ju, R. Sternglanz, and R. H. Reeder, Genes Dev. 6, 1332 (1992).
4. J. D. Parvin and P. A. Sharp, Cell 73, 533 (1993).
5. R. Kanaar and N. R. Cozzarelli, Curr. Opin. Struct. Biol. 2, 369 (1992).
6. C. J. Benham, Biopolymers 22, 2477 (1983).
7. M. Le Bret, Biopolymers 23, 1835 (1984).
8. K. V. Klenin, A. V. Vologodskii, V. V. Anshelevich, A. M. Dykhne, and M. D. Frank-Kamenetskii, J. Mol. Biol. 217, 413 (1991).
9. A. V. Vologodskii, S. D. Levene, K. V. Klenin, M. D. Frank-Kamenetskii, and N. R. Cozzarelli, J. Mol. Biol. 227, 1224 (1992).
10. M. H. Hao and W. K. Olson, Macromolecules 22, 3292 (1989).
11. T. Schlick and W. K. Olson, J. Mol. Biol. 223, 1089 (1992).
12. M. Tomimoto and N. Go, J. Phys. Chem. 99, 563 (1995).
13. S. J. Weiner, P. A. Kollman, D. T. Nguyen, and D. A. Case, J. Comput. Chem. 7, 230 (1986).
14. J. Ramstein and R. Lavery, Proc. Natl. Acad. Sci. USA 85, 7231 (1988).
15. V. Daggett, P. A. Kollman, and I. D. Kuntz, Biopolymers 31, 285 (1991).
16. T. Nishikawa and N. Go, Proteins: Struct., Funct., Genet. 2, 308 (1987).
17. M. Tomimoto, H. Wako, and N. Go, J. Comput. Chem. 17, 910 (1996).
18. J. W. Strutt and B. Rayleigh, The Theory of Sound, 2nd ed. (Macmillan, London, 1894).
19. R. E. Dickerson, M. Bansal, C. R. Calladine, S. Diekmann, W. N. Hunter, O. Kennard, E. von Kitzing, R. Lavery, H. C. M. Nelson, W. K. Olson, W. Saenger, Z. Shakked, H. Sklenar, D. M. Soumpasis, C. S. Tung, A. H. J. Wang, and V. B. Zhurkin, Nucleic Acids Res. 17, 1797 (1989).
20. M. S. Babcock, E. P. D. Pednault, and W. K. Olson, J. Biomol. Struct. Dyn. 11, 597 (1993).
21. A. Matsumoto, M. Tomimoto, and N. Go, Eur. Biophys. J. (in press).
22. M. D. Barkley and B. H. Zimm, J. Chem. Phys. 70, 2991 (1979).
23. J. C. Thomas, S. A. Allison, C. J. Appelhof, and J. M. Schurr, Biophys. Chem. 12, 177 (1980).
24. I. Hurley, P. Osei-Gyimah, S. Archer, C. P. Scholes, and L. S. Lerman, Biochemistry 21, 4999 (1982).
25. D. P. Millar, R. J. Robbins, and A. H. Zewail, J. Chem. Phys. 76, 2080 (1982).
26. D. S. Horowitz and J. C. Wang, J. Mol. Biol. 173, 75 (1984).
27. I. Hurley, B. H. Robinson, C. P. Scholes, and L. S. Lerman, in Nucleic Acid Geometry and Dynamics, edited by R. H. Sarma (Pergamon, New York, 1980), pp. 253-271.
28. M. Levitt, Proc. Natl. Acad. Sci. USA 75, 640 (1978).
29. K. J. Miller, Biopolymers 18, 959 (1979).
30. T. Ha Duong and K. Zakrzewska, J. Comput. Chem. 18, 796 (1997).