A theory of thermal fluctuations in DNA miniplasmids

Biophysical Journal

Volumn 74, Issue 5, 1998, Pages 2545-2553

  Tobias, Irwin ^a  

^a RUTGERS UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ARTICLE; MATHEMATICAL ANALYSIS; MECHANICS; MOLECULAR DYNAMICS; MOTION; THEORY; THERMODYNAMICS; VIBRATION;

EID: 0031957256     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(98)77962-7     Document Type: Article

References (19)

1. Coleman, B. D., E. H. Dill, M. Lembo, Z. Lu, and I. Tobias. 1993. On the dynamics of rods in the theory of Kirchhoff and Clebsch. Arch. Rational Mech. Anal. 121:339-359.
2. Coleman, B. D., M. Lembo, and I. Tobias. 1996. A new class of flexure-free vibrations of annular rods. Meccanica. 31:565-575.
3. Depew, R. E., and J. C. Wang. 1975. Conformational fluctuations of DNA helix. Proc. Natl. Acad. Sci. USA. 72:4275-4279.
4. Dill, E. H. 1992. Kirchhoff's theory of rods. Arch. Hist. Exact Sci. 44:1-23.
5. 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.
6. Fuller, F. B. 1971. The writhing number of a space curve. Proc. Natl. Acad. Sci. USA. 68:815-819.
7. 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.
8. Goldstein, H. 1981. Classical Mechanics. Addison-Wesley Publishing Company, Reading, MA.
9. Goriely, A., and M. Tabor. 1997. Nonlinear dynamics of filaments. I. Dynamical instabilities. Physica D. 105:20-44.
10. Hagerman, P. J. 1988. Flexibility of DNA. Annu. Rev. Biophys. Biophys. Chem. 17:265-286.
11. 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.
12. Jolley, L. 1925. Summation of Series. Chapman and Hall, London.
13. Pulleyblank, D. E., M. Shure, D. Tang, J. Vinigrad, and H. P. Vosberg. 1975. Action of nicking-closing enzyme on supercoiled and nonsupercoiled closed circular DNA: formation of a Boltzmann distribution of topological isomers. Proc. Natl. Acad. Sci. USA. 72:4280-4284.
14. Shimada, J., and H. Yamakawa. 1984. DNA topoisomer analysis on the basis of the helical worm-like chain. Biopolymers. 23:853-857.
15. Shimada, J., and H. Yamakawa. 1985. Statistical mechanics of DNA topoisomers. The helical worm-like chain. J. Mol. Biol. 184:319-329.
16. Shore, D., and R. L. Baldwin. 1983. Energetics of DNA twisting. II. Topoisomer analysis. J. Mol. Biol. 170:983-1007.
17. Tobias, I., B. D. Coleman, and M. Lembo. 1996. A class of exact dynamical solutions in the elastic rod model of DNA with implications for the theory of fluctuations in the torsional motion of plasmids. J. Chem. Phys. 105:2517-2526.
18. White, J. 1969. Self-linking and the Gauss-integral in higher dimensions. Am. J. Math. 91:693-728.
19. Zajac, E. E. 1962. Stability of two planar loop elasticas. J. Appl. Mech. Trans. ASME Ser. E. 29:136-142.