Extension of torsionally stressed DNA by external force

Biophysical Journal

Volumn 73, Issue 1, 1997, Pages 123-132

  Vologodskii, Alexander V ^a   Marko, John F ^b  

^a NEW YORK UNIVERSITY   (United States)

^b UNIVERSITY OF ILLINOIS AT CHICAGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ARTICLE; COMPUTER SIMULATION; DNA CONFORMATION; DNA HELIX; DNA SUPERCOILING; ELASTICITY; ENTROPY; SHEAR STRESS; TORSION;

EID: 0030973367     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(97)78053-6     Document Type: Article

References (50)

1. Barkley, M. D., and B. H. Zimm. 1979. Theory of twisting and bending of chain macromolecules; analysis of the fluorescence depolarization of DNA. J. Chem. Phys. 70:2991-3007.
2. Brian, A. A., H. L. Frisch, and L. S. Lerman. 1981. Thermodynamics and equilibrium sedimentation analysis of the close approach of DNA molecules and a molecular ordering transition. Biopolymers. 20:1305-1328.
3. Bustamante, C., J. F. Marko, E. D. Siggia, and S. Smith. 1994. Entropic elasticity of lambda-phage DNA. Science. 265:1599-1600.
4. Cluzel, P., A. Lebrun, C. Heller, R. Lavery, J. L. Viovy, D. Chatenay, and F. Caron. 1996. DNA: an extensible molecule. Science. 271:792-794.
5. Crothers, D. M., J. Drak, J. D. Kahn, and S. D. Levene. 1992. DNA bending, flexibility, and helical repeat by cyclization kinetics. Methods Enzymol. 212:3-29.
6. de Gennes, P. G. 1979. Scaling Concepts in Polymer Physics. Cornell University Press, Ithaca, NY.
7. Frank-Kamenetskii, M. D., A. V. Lukashin, V. V. Anshelevich, and A. V. Vologodskii. 1985. Torsional and bending rigidity of the double helix from data on small DNA rings. J. Biomol. Struct. Dyn. 2:1005-1012.
8. Frank-Kamenetskii, M. D., A. V. Lukashin, and M. D. Vologodskii. 1975. Statistical mechanics and topology of polymer chains. Nature. 258: 398-402.
9. Fuller, F. B. 1971. The writhing number of a space curve. Proc. Natl. Acad. Sci. USA. 68:815-819.
10. Gebe, J. A., S. A. Allison, J. B. Clendenning, and J. M. Schurr. 1995. Monte Carlo simulations of supercoiling free energies for unknotted and trefoil knotted DNAs. Biophys. J. 68:619-633.
11. 2+ on the structures of supercoiled DNAs: comparison of simulations with experiments. J. Mol. Biol. 262:105-128.
12. Hagerman, P. J. 1988. Flexibility of DNA. Annu. Rev. Biophys. Biophys. Chem. 17:265-286.
13. Hao, M.-H., and W. K. Olson. 1989. Global equilibrium configurations of supercoiled DNA. Macromolecules. 22:3292-3303.
14. Horowitz, D. S., and J. C. Wang. 1984. Torsional rigidity of DNA and length dependence of the free energy of DNA supercoiling. J. Mol. Biol. 173:75-91.
15. Katritch, V., and A. Vologodskii. 1997. The effect of intrinsic curvature on conformational properties of circular DNA. Biophys. J. 72:1070-1079.
16. Klenin, K. V., A. V. Vologodskii, V. V. Anshelevich, A. M. Dykhne, and M. D. Frank-Kamenetskii. 1991. Computer simulation of DNA supercoiling. J. Mol. Biol. 217:413-419.
17. Klenin, K. V., A. V. Vologodskii, V. V. Anshelevich, V. Y. Klisko, A. M. Dykhne, and M. D. Frank-Kamenetskii. 1989. Variance of writhe for wormlike DNA rings with excluded volume. J. Biomol. Struct. Dyn. 6:707-714.
18. Levene, S. D., and D. M. Crothers. 1986. Ring closure probabilities for DNA fragments by Monte Carlo simulation. J. Mol. Biol. 189:61-72.
19. Marko, J. F. 1997. Supercoiled and braided DNA under tension. Phys. Rev. E. 55:1758-1772.
20. Marko, J. F., and E. D. Siggia. 1994. Fluctuations and supercoiling of DNA. Science. 265:506-508.
21. Marko, J. F., and E. D. Siggia. 1995a. Statistical mechanics of supercoiled DNA. Phys. Rev. E. 52:2912-2938.
22. Marko, J. F., and E. D. Siggia. 1995b. Stretching DNA. Macromolecules. 28:8759-8770.
23. Metropolis, N., A. W. Rosenbluth, M. N. Rosenbluth, A. H. Teller, and E. Teller. 1953. Equation of state calculations by fast computing machines. J. Chem. Phys. 21:1087-1092.
24. Perkins, T. T., S. R. Quake, D. E. Smith, and S. Chu. 1994. Relaxation of a single DNA molecule observed by optical microscopy. Science. 264: 822-826.
25. Perkins, T. T., D. E. Smith, R. G. Larson, and S. Chu. 1995. Stretching of a single tethered polymer in a uniform flow. Science. 268:83-86.
26. Rybenkov, V. V., N. R. Cozzarelli, and A. V. Vologodskii. 1993. Probability of DNA knotting and the effective diameter of the DNA double helix. Proc. Natl. Acad. Sci. USA. 90:5307-5311.
27. Shaw, S. Y., and J. C. Wang. 1993. Knotting of a DNA chain during ring closure. Science. 260:533-536.
28. Shibata, J. M., B. S. Fujimoto, and J. M. Schurr. 1985. Rotational dynamics of DNA from 10e-10 to 10e-5 seconds: comparison theory with optical experiments. Biopolymers. 24:1909-1930.
29. Shore, D., and R. L. Baldwin. 1983a. Energetics of DNA twisting. I. Relation between twist and cyclization probability. J. Mol. Biol. 170: 957-981.
30. Shore, D., and R. L. Baldwin. 1983b. Energetics of DNA twisting. II. Topoisomer analysis. J. Mol. Biol. 170:983-1007.
31. Smith, S. B., Y. Cui, and C. Bustamante. 1996. Overstretching B-DNA: the elastic response of individual double-stranded and single-stranded DNA molecules. Science. 271:795-799.
32. Smith, S. B., L. Finzi, and C. Bustamante. 1992. Direct mechanical measurements of the elasticity of single DNA molecules by using magnetic beads. Science. 258:1122-1126.
33. Stigter, D. 1977. Interactions of highly charged colloidal cylinders with applications to double-stranded DNA. Biopolymers. 16:1435-1448.
34. Strick, T. R., J. F. Allemand, D. Bensimon, A. Bensimon, and V. Croquette. 1996. The elasticity of a single supercoiled DNA molecule. Science. 271:1835-1837.
35. Tan, R. K. Z., and S. C. Harvey. 1989. Molecular mechanics model of supercoiled DNA. J. Mol. Biol. 205:573-591.
36. Taylor, W. H., and P. J. Hagerman. 1990. Application of the method of phage T4 DNA ligase-catalyzed ring-closure to the study of DNA structure. II. NaCl-dependence of DNA flexibility and helical repeat. J. Mol. Biol. 212:363-376.
37. Thomas, J. C., S. A. Allison, C. J. Appelof, and J. M. Schurr. 1980. Torsional dynamics and depolarization of fluorescence of linear macromolecules. II. Flourescence polarization anisotropy measurements on a clean viral f29 DNA. Biophys. Chem. 12:177-188.
38. Vologodskii, A. V. 1992. Topology and Physics of Circular DNA. CRC Press, Boca Raton, FL.
39. Vologodskii, A. V. 1994. DNA extension under the action of an external force. Macromolecules. 27:5623-5625.
40. Vologodskii, A. V., V. V. Anshelevich, A. V. Lukashin, and M. D. Frank-Kamenetskii. 1979. Statistical mechanics of supercoils and the torsional stiffness of the DNA. Nature. 280:294-298.
41. Vologodskii, A. V., and N. R. Cozzarelli. 1993. Monte Carlo analysis of the conformation of DNA catenanes. J. Mol. Biol. 232:1130-1140.
42. Vologodskii, A. V., and N. R. Cozzarelli. 1994a. Conformational and thermodynamic properties of supercoiled DNA. Annu. Rev. Biophys. Biomol. Struct. 23:609-643.
43. Vologodskii, A. V., and N. R. Cozzarelli. 1994b. Supercoiling, knotting, looping, and other large-scale conformational properties of DNA. Curr. Opin. Struct. Biol. 4:372-375.
44. Vologodskii, A. V., S. D. Levene, K. V. Klenin, M. D. Frank-Kamenetskii, and N. R. Cozzarelli. 1992. Conformational and thermodynamic properties of supercoiled DNA. J. Mol. Biol. 227:1224-1243.
45. Vologodskii, A. V., A. V. Lukashin, V. V. Anshelevich, and M. D. Frank-Kamenetskii. 1979. Fluctuations in superhelical DNA. Nucleic Acids Res. 6:967-982.
46. Vologodskii, A. V., A. V. Lukashin, M. D. Frank-Kamenetskii, and V. V. Anshelevich. 1974. Problem of knots in statistical mechanics of polymer chains. Sov. Phys. JETP. 39:1059-1063.
47. White, J. H. 1969. Self-linking and the Gauss integral in higher dimensions. Am. J. Math. 91:693-728.
48. White, J. H. 1989. An introduction to the geometry and topology of DNA structure. In Mathematical Methods for DNA Sequences. M. S. Waterman, editor. CRC Press, Boca Raton, FL.
49. Wu, P. G., B. S. Fujimoto, L. Song, and J. M. Schurr. 1991. Effect of ethidium on the torsion constants of linear and supercoiled DNAs. Biophys. Chem. 41:217-236.
50. Zechiedrich, E. L., and N. R. Cozzarelli. 1995. Roles of topoisomerase IV and DNA gyrase in DNA unlinking during replication in Escherichia coli. Genes Dev. 9:2859-2869.