Multiple folding and packing in DNA modeling

Computers and Mathematics with Applications

Volumn 55, Issue 5, 2008, Pages 1044-1053

  Ricca, Renzo L ^a,b   Maggioni, Francesca ^a  

^a UNIVERSITY OF MILANO BICOCCA   (Italy)

^b UNIVERSITY COLLEGE LONDON   (United Kingdom)

Author keywords

Coiling; Deformation energy; DNA writhing; Packing

Indexed keywords

DEFORMATION; DISTRIBUTION FUNCTIONS; HIERARCHICAL SYSTEMS; KINEMATICS; SET THEORY;

DNA MODELING; ELASTIC ENERGY RELAXATION; HIERARCHICAL HELICAL COILING;

DNA;

EID: 38349091434     PISSN: 08981221     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.camwa.2006.12.084     Document Type: Article

References (20)

1. Baker D. A surprising simplicity to protein folding. Nature 405 (2000) 39-42
2. Socolich M., Lockless S.W., Russ W.P., Lee H., Gardner K.H., and Ranganathan R. Evolutionary information for specifying a protein fold. Nature 437 (2005) 512-518
3. Coulombe B., and Burton Z.F. DNA bending and wrapping around RNA polymerase: A "revolutionary" model describing transcriptional mechanisms. Microb. Mol. Biol. Rev. 63 (1999) 457-478
4. Zhang P., Tobias I., and Olson W.K. Computer simulation of protein-induced structural changes in closed circular DNA. J. Mol. Biol. 242 (1994) 271-290
5. Behnam C., and Miller D. Writhing and linking densities for closed, circular DNA. J. Knot Theory Ramifications 9 (2000) 577-585
6. Dean F.B., Stasiak A., Koller T., and Cozzarelli N.R. Duplex DNA knots produced by Escherichia coli Topoisomerase. I. J. Biol. Chem. 260 (1985) 4975-4983
7. Wasserman S.A., and Cozzarelli N.R. Supercoiled DNA-directed knotting by T4 topoisomerase. J. Biol. Chem. 266 (1991) 20567-20573
8. Stasiak A. Circular DNA. In: Semlyen J.A. (Ed). Large Ring Molecules (1996), John Wiley & Sons Ltd. 43-97
9. In: Cozzarelli N.R., and Wang J.C. (Eds). DNA Topology and its Biological Effects (1990), Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
10. Ricca R.L. Structural complexity. In: Scott A. (Ed). Encyclopedia of Nonlinear Science (2005), Routledge, New York, London 885-887
11. Vologodskii A.V., Crisona N.J., Laurie B., Pieranski P., Katritch V., Dubochet J., and Stasiak A. Sedimentation and electrophoretic migration of DNA knots and catenanes. J. Mol. Biol. 278 (1998) 1-3
12. Maggioni F., and Ricca R.L. Writhing and coiling of closed filaments. Proc. R. Soc. A 462 (2006) 3151-3166
13. Fuller F.B. The writhing number of a space curve. Proc. Natl. Acad. Sci. USA 68 (1971) 815-819
14. Moffatt H.K., and Ricca R.L. Helicity and the Cǎlugǎreanu invariant. Proc. R. Soc. A 439 (1992) 411-429
15. Cǎlugǎreanu G. Sur les classes d'isotopie des nœuds tridimensionnels et leurs invariants. Czechoslovak Math. J. 11 (1961) 588-625
16. White J.H. Self-linking and the Gauss integral in higher dimensions. Amer. J. Math. 91 (1969) 693-728
17. Ricca R.L. The energy spectrum of a twisted flexible string under elastic relaxation. J. Phys. A 28 (1995) 2335-2352
18. Calladine C.R., and Drew H.R. Understanding DNA (1992), Academic Press
19. Zajac E.E. Stability of two planar loop elasticas. J. Appl. Mech. 29 (1962) 136-142
20. Klapper I. Biological applications of the dynamics of twisted elastic rods. J. Comput. Phys. 125 (1996) 325-337