Competition between compaction of single chains and bundling of multiple chains in giant DNA molecules

Journal of Chemical Physics

Volumn 120, Issue 8, 2004, Pages 4004-4011

  Iwataki, Toshio ^a,b   Kidoaki, Satoru ^a,c   Sakaue, Takahiro ^a   Yoshikawa, Kenichi ^a   Abramchuk, Sergey S ^a,d  

^a KYOTO UNIVERSITY   (Japan)

^b UNIVERSITY OF TOKYO   (Japan)

^c KYUSHU UNIVERSITY   (Japan)

^d A N NESMEYANOV INSTITUTE OF ORGANOELEMENT COMPOUNDS   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

CHARGED PARTICLES; COLLOIDS; CONDENSATION; CRYSTALLIZATION; FLUORESCENCE; LIQUID CRYSTALS; MATHEMATICAL MODELS; MICROMETERS; MICROSCOPIC EXAMINATION; MOLECULAR STRUCTURE; SOLUTIONS;

IONIC CRYSTALS; SINGLE CHAINS;

DNA;

DNA;

ARTICLE; BASE PAIRING; CHEMISTRY; COMPARATIVE STUDY; COMPUTER SIMULATION; CONFORMATION; FLUORESCENCE MICROSCOPY; MONTE CARLO METHOD;

BASE PAIRING; COMPUTER SIMULATION; DNA; MICROSCOPY, FLUORESCENCE; MONTE CARLO METHOD; NUCLEIC ACID CONFORMATION;

EID: 1642632778     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.1642610     Document Type: Article

References (50)

1. M. Yanagida, Y. Hiraoka, and I. Katsuya, Cold Spring Harbor Symp. Quant. Biol. 47, 177 (1983).
2. C. Bustamante, Annu. Rev. Biophys. Biophys. Chem. 20, 415 (1991).
3. K. Yoshikawa, Y. Matsuzawa, K. Minagawa, M. Doi, and M. Matsumoto, Biochem. Biophys. Res. Commun. 188, 1274 (1992).
4. K. Yoshikawa and Y. Matsuzawa, Physica D 84, 220 (1995).
5. K. Yoshikawa, S. Kidoaki, M. Tiakahashi, V. V. Vasilevskaya, and A. R. Khokhlov, Ber. Bunsenges. Phys. Chem. 100, 876 (1996).
6. M. Takahashi, K. Yoshikawa, V. V. Vasilevskaya, and A. R. Khokhlov, J. Phys. Chem. B 101, 9396 (1997).
7. Y. Yamasaki, Y. Tcramoto, and K. Yoshikawa, Biophys. J. 80, 2823 (2001).
8. V. A. Bloomfield, Curr. Opin. Struct. Biol. 6, 334 (1996).
9. J. A. Schellman and N. J. Parthasaratary, Mol. Biol. 175, 313 (1984).
10. J.-L. Sikorav, J. Pelta, and F. Livolant, Biophys. J. 67, 1387 (1994).
11. J. Pelta, D. Durand, J. Doucet, and F. Livolant, Biophys. J. 71, 48 (1994).
12. J. Pelta, F. Livolant, and J.-L. Sikorav, J. Biol. Chem. 271, 5656 (1996).
13. P. G. de Gennes and J. Prost, The Physics of Liquid Crystals, 2nd ed. (Oxford University Press, New York, 1993).
14. L. C. Gosule and J. A. Schellman, Nature (London) 259, 333 (1976).
15. D. K. Chattoraj, L. C. Gosule, and J. A. Schellman, J. Mol. Biol. 121, 327 (1978).
16. K. A. Marx and G. C. Ruben, Nucleic Acids Res. 11, 1839 (1983).
17. C. B. Post and B. H. Zimm, Biopolymers 21, 2139 (1982).
18. B. G. Feuerstein, N. Pattabiraman, and L. J. Marton, Proc. Natl. Acad. Sci. U.S.A. 83, 5948 (1986).
19. I. S. Haworth, A. Rodger, and W. G. Richards, J. Biomol. Struct. Dyn. 10, 195 (1992).
20. A. P. Lyubartsev and L. Nordenskiöld, J. Phys. Chem. B 101, 4335 (1997).
21. N. Korolev, A. P. Lyubartsev, L. Nordenskiöld, and A. Laaksonen, J. Mol. Biol. 308, 907 (2001).
22. N. Yoshinaga, T. Akitaya, and K. Yoshikawa, Biochem. Biophys. Res. Commun. 286, 264 (2001).
23. M. J. Stevens, Phys. Rev. Lett. 82, 101 (1999).
24. H. Noguchi and K. Yoshikawa, J. Chem. Phys. 109, 5070 (1998).
25. T. Sakaue and K. Yoshikawa, J. Chem. Phys. 117, 6323 (2002).
26. J. Widom and R. L. Baldwin, J. Mol. Biol. 144, 431 (1980).
27. J. Widom and R. L. Baldwin, Biopolymers 22, 1595 (1983).
28. H. Deng and V. A. Bloomfield, Biophys. J. 77, 1556 (1999).
29. L. S. Lerman, Proc. Natl. Acad. Sci. U.S.A. 68, 1886 (1971).
30. Yu, M. Evdokimov, A. L. Platonov, A. S. Tikhonenko, and Ya. M. Varshavskii, FEBS Lett. 23, 180 (1972).
31. U. K. Laemmli, Proc. Natl. Acad. Sci. U.S.A. 72, 4288 (1975).
32. K. Yoshikawa, Y. Yoshikawa, Y. Koyama, and T. Kanbe, J. Am. Chem. Soc. 119, 6473 (1997).
33. A. L. Martin, B. J. Davies, B. J. Raokstraw, C. J. Roberts, S. Stolnik, S. J. B. Tendler, and P. M. Williams, FEBS Lett. 480, 106 (2000).
34. K. Hayakawa, J. P. Santerre, and J. C. T. Kwak, Biophys. Chem. 17, 175 (1983).
35. K. Shirahama, K. Takashima, and N. Takisawa, Bull. Chem. Soc. Jpn. 60, 43 (1987).
36. K. Shirakawa, T. Masaki, and K. Takashima, in Microdomains in Polymer Solutions, edited by P. Dubin (Plenum, New York, 1985), p. 299.
37. E. P. Geiduschek and I. Gray, J. Am. Chem. Soc. 78, 879 (1956).
38. D. Lang, J. Mol. Biol. 46, 209 (1969).
39. T. H. Eickbush and E. N. Moudrianakis, Cell 13, 295 (1976).
40. V. A. Bloomfield, Biopolymers 44, 269 (1997).
41. G. E. Plum, P. G. Arscott, and V. A. Bloomfield, Biopolymers 30, 631 (1990).
42. P. G. Arscott, C. Ma, J. R. Wenner, and V. A. Bloomfield, Biopolymers 36, 345 (1995).
43. H. M. Harreis, A. A. Kornyshev, C. N. Licos, H. Löwen, and G. Sutmann, Phys. Rev. Lett. 89, 018303 (2000).
44. J. X. Tang, S. Wong, P. T. Tran, and P. A. Janmey, Ber. Bunsenges. Phys. Chem. 100, 796 (1996).
45. J. X. Tang, P. A. Janmey, A. Lyubartsev, and L. Nordenskiöld, Biophys. J. 83, 566 (2002).
46. K. Yoshikawa, J. Biol. Phys. 28, 701 (2002).
47. K. Yoshikawa and Y. Yoshikawa, in Pharmaceutical Perspectives of Nucleic Acid-Based Therapeutics, edited by R. I. Mahato and S. W. Kim (Taylor & Francis, London, 2002), p. 136.
48. A. Yu. Grosberg and A. V. Zhestkov, J. Biomol. Struct. Dyn. 3, 859 (1986).
49. B.-Y. Ha and A. J. Liu, Phys. Rev. Lett. 81, 1011 (1998).
50. L. D. Landau and E. M. Lifshits, Statistical Physics (Elsevier, New York, 1994).