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Effect of anisotropy of the bending rigidity on the supercoiling free energy of small circular DNAs
Author(s) -
Schurr J. Michael,
Babcock Hazen P,
Gebe John A
Publication year - 1995
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.360360509
Subject(s) - chemistry , dna supercoil , rigidity (electromagnetism) , anisotropy , flexural rigidity , bending , crystallography , chemical physics , dna , thermodynamics , physics , optics , biochemistry , quantum mechanics , dna replication
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 = 100 bp with torsion constant α = 5.8 × 10 −12 dyne cm. persistence lengths P = 500 Å and 10,000 Å and a range of anisotropies of the bending potential from p = 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 Å, the apparent torsion constant never rises significantly above the input value over the entire range of input anisotropies. When P = 10,000 Å, the apparent torsion constant rises only about 3% above the input value for anisotropies ρ = 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 longlinear DNAs by a factor of 1.6 or more. © 1995 John Wiley & Sons, Inc.