Fluctuations and supercoiling of DNA.

Frequently, DNA in vivo is organized into loops that are partially underwound and consequently form interwound helical supercoils. Methods from polymer statistical mechanics are used to show how the competition between entropy (thermal fluctuations) and elastic energy determines supercoil radius and pitch, in good agreement with recent experiments and simulations. Supercoil reorganization by means of slithering (reptation) of the DNA along the supercoil is argued to be a slow process. Extension of supercoiled DNA by an applied force shows a number of unexpected features, including coexistence of interwound and helical states.

[1]  N R Cozzarelli,et al.  Probability of DNA knotting and the effective diameter of the DNA double helix. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[2]  C. Benham.  Geometry and mechanics of DNA superhelicity , 1983, Biopolymers.

[3]  James H. White.  Self-Linking and the Gauss Integral in Higher Dimensions , 1969 .

[4]  F. B. Fuller.  The writhing number of a space curve. , 1971, Proceedings of the National Academy of Sciences of the United States of America.

[5]  O. Berg.  Diffusion‐controlled protein–DNA association: Influence of segemental diffusion of the DNA , 1984, Biopolymers.

[6]  Christian N. Parker,et al.  Dynamics of long-range interactions on DNA: The speed of synapsis during site-specific recombination by resolvase , 1991, Cell.

[7]  M Frank-Kamenetskii,et al.  Conformational and thermodynamic properties of supercoiled DNA. , 1992, Journal of molecular biology.

[8]  S. Smith,et al.  Direct mechanical measurements of the elasticity of single DNA molecules by using magnetic beads. , 1992, Science.

[9]  N R Cozzarelli,et al.  Structure of plectonemically supercoiled DNA. , 1990, Journal of molecular biology.

[10]  P. Hagerman.  Flexibility of DNA. , 1988, Annual review of biophysics and biophysical chemistry.

[11]  M. Le Bret,et al.  Twist and writhing in short circular DNAs according to first‐order elasticity , 1984, Biopolymers.

[12]  D. Crothers,et al.  DNA bending, flexibility, and helical repeat by cyclization kinetics. , 1992, Methods in enzymology.

[13]  M. L. Bret.  Catastrophic variation of twist and writhing of circular DNAs with constraint , 1979 .

[14]  P. Hagerman,et al.  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. , 1990, Journal of molecular biology.

[15]  J. Dubochet,et al.  The twist, writhe and overall shape of supercoiled DNA change during counterion-induced transition from a loosely to a tightly interwound superhelix. Possible implications for DNA structure in vivo. , 1994, Journal of molecular biology.

[16]  Fumihiko Tanaka,et al.  Elastic theory of supercoiled DNA , 1985 .

[17]  J. Wang,et al.  Knotting of a DNA chain during ring closure. , 1993, Science.

[18]  T Schlick,et al.  Supercoiled DNA energetics and dynamics by computer simulation. , 1992, Journal of molecular biology.