MODELING SELF-CONTACT FORCES IN THE ELASTIC THEORY OF DNA SUPERCOILING

A DNA polymer with thousands of base pairs is modeled as an elastic rod with the capability of treating each base pair independently. Elastic theory is used to develop a model of the double helix which incorporates intrinsic curvature as well as inhomogeneities in the bending, twisting, and stretching along the length of the polymer. Inhomogeneities in the elastic constants can also be dealt with; thus, sequence-dependent structure and deformability can be taken into account. Additionally, external forces have been included in the formalism, and since these forces can contain a repulsive force, DNA self-contact can be explicitly treated. Here the repulsive term takes the form of a modified Debye–Huckel force where screening can be varied to account for the effect of added salt. The supercoiling of a naturally straight, isotropic rod in 0.1M NaCl is investigated and compared with earlier treatments of supercoiled DNA modeled by a line of point charges subject to electrostatic interactions and an elastic po...

[1]  W. Olson,et al.  Computer simulation of DNA supercoiling. , 1991, Methods in enzymology.

[2]  Jill P. Mesirov,et al.  Mathematical approaches to biomolecular structure and dynamics , 1996 .

[3]  Wilma K. Olson,et al.  The dependence of DNA tertiary structure on end conditions: Theory and implications for topological transitions , 1994 .

[4]  W. Olson,et al.  Electrostatic effects in short superhelical DNA. , 1994, Biophysical chemistry.

[5]  C. O’Hern,et al.  Direct determination of DNA twist-stretch coupling , 1996, cond-mat/9611224.

[6]  W. Olson,et al.  Computer simulation of protein-induced structural changes in closed circular DNA. , 1994, Journal of molecular biology.

[7]  N. Cozzarelli,et al.  Modeling of long‐range electrostatic interactions in DNA , 1995, Biopolymers.

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

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

[10]  J. Wang,et al.  Variation of the average rotation angle of the DNA helix and the superhelical turns of covalently closed cyclic lambda DNA. , 1969, Journal of molecular biology.

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

[12]  James R. Wertz,et al.  Spacecraft attitude determination and control , 1978 .

[13]  Marcia O. Fenley,et al.  Fast adaptive multipole method for computation of electrostatic energy in simulations of polyelectrolyte DNA , 1996, J. Comput. Chem..

[14]  M. Hao,et al.  Global equilibrium configurations of supercoiled DNA , 1989 .

[15]  David Swigon,et al.  THEORY OF THE INFLUENCE OF END CONDITIONS ON SELF-CONTACT IN DNA LOOPS , 1995 .

[16]  A. Bensimon,et al.  The Elasticity of a Single Supercoiled DNA Molecule , 1996, Science.

[17]  Wilma K. Olson,et al.  Elasticity Theory and Numerical Analysis of DNA Supercoiling: An Application to DNA Looping , 1995 .

[18]  J. Michael Schurr,et al.  Effect of bending strain on the torsion elastic constant of DNA. , 1996, Journal of molecular biology.

[19]  K. Klenin,et al.  Computer simulation of DNA supercoiling. , 1991, Journal of molecular biology.

[20]  S. Neidle.  Oxford handbook of nucleic acid structure , 1998 .

[21]  W. Olson,et al.  Finite element analysis of DNA supercoiling , 1993 .

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

[23]  H. M. Sobell,et al.  Visualization of drug-nucleic acid interactions at atomic resolution. II. Structure of an ethidium/dinucleoside monophosphate crystalline complex, ethidium:5-iodocytidylyl (3'-5') guanosine. , 1977, Journal of molecular biology.

[24]  G. S. Manning.  The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides , 1978, Quarterly Reviews of Biophysics.

[25]  W. Olson,et al.  Simulating DNA at low resolution. , 1996, Current opinion in structural biology.

[26]  Benham.  Onset of writhing in circular elastic polymers. , 1989, Physical review. A, General physics.

[27]  W. Bauer,et al.  Twist and writhe of a DNA loop containing intrinsic bends. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[28]  Gerald S. Manning,et al.  An attractive force between two rodlike polyions mediated by the sharing of condensed counterions , 1994 .

[29]  J Langowski,et al.  Modulation of intramolecular interactions in superhelical DNA by curved sequences: a Monte Carlo simulation study. , 1995, Biophysical journal.

[30]  M. Waterman.  Mathematical Methods for DNA Sequences , 1989 .

[31]  W. Bauer,et al.  Structure and reactions of closed duplex DNA. , 1978, Annual review of biophysics and bioengineering.

[32]  E. E. Zajac,et al.  Stability of Two Planar Loop Elasticas , 1962 .

[33]  G. S. Manning.  A procedure for extracting persistence lengths from light-scattering data on intermediate molecular weight DNA , 1981 .

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

[35]  E. Dill,et al.  Kirchhoff's theory of rods , 1992 .

[36]  J. Marko.  Supercoiled and braided DNA under tension , 1997 .

[37]  L Greengard,et al.  Fast Algorithms for Classical Physics , 1994, Science.

[38]  T Schlick,et al.  The influence of salt on the structure and energetics of supercoiled DNA. , 1994, Biophysical journal.

[39]  Stephen K. Burley,et al.  Co-crystal structure of TBP recognizing the minor groove of a TATA element , 1993, Nature.

[40]  W. M. Haynes.  CRC Handbook of Chemistry and Physics , 1990 .

[41]  Steven Hahn,et al.  Crystal structure of a yeast TBP/TATA-box complex , 1993, Nature.

[42]  Langer,et al.  Nonlinear dynamics of stiff polymers. , 1995, Physical review letters.

[43]  T. Schlick,et al.  On higher buckling transitions in supercoiled DNA , 1994, Biopolymers.

[44]  V. Katritch,et al.  The effect of intrinsic curvature on conformational properties of circular DNA. , 1997, Biophysical journal.