title: Effect of anisotropy of the bending rigidity on the supercoiling free energy of small circular DNAs.
abstract: In principle, the supercoiling free energy of a small circular DNA will be enhanced by increasing the anisotropy of its bending potential at constant persistence length. The magnitude of this effect is investigated by Monte Carlo simulation using an extension of a previously proposed algorithm. The supercoiling free energy at 298 K is simulated for circular DNAs containing N = bp with torsion constant alpha = 5.8 X 10(-12) dyne cm, persistence lengths P = 500 A and 10,000 A, and a range of anisotropies of the bending potential from rho = 1.0 to 16.0. The apparent torsion constants, reckoned from these supercoiling free energies by assuming an isotropic bending potential, are found to increase by less than 3% as the input anisotropy increases from 1.0 to 16.0 When P = 500 A, the apparent torsion constant never rises significantly above the input value over the entire range of input anisotropies. When P = 10,000 A, the apparent torsion constant rises only about 3% above the input value for anisotropies rho = 8.0 and 16.0. Evidently, anisotropy of the bending potential cannot account for the fact that the torsion constants reported for small circular DNAs exceed those reported for long linear DNAs by a factor of 1.6 or more.
authors.affiliation: Department of Chemistry, University of Washington, Seattle 98195, USA.
authors.forename: J M
authors.initials: JM
authors.lastname: Schurr
authors.forename: H P
authors.initials: HP
authors.lastname: Babcock
authors.forename: J A
authors.initials: JA
authors.lastname: Gebe
mesh_terms: D000465:Algorithms; D016880:Anisotropy; D003198:Computer Simulation; D004270:DNA, Circular / Q000737:chemistry*; D004278:DNA, Superhelical / Q000737:chemistry*; D009010:Monte Carlo Method; D009690:Nucleic Acid Conformation; D013816:Thermodynamics
chemical_list: D004270:DNA, Circular; D004278:DNA, Superhelical