Schurr J M, Babcock H P, Gebe J A
Department of Chemistry, University of Washington, Seattle 98195, USA.
Biopolymers. 1995 Nov;36(5):633-41. doi: 10.1002/bip.360360509.
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.
原则上，在恒定持久长度下，通过增加小环状DNA弯曲势的各向异性，其超螺旋自由能会增强。使用先前提出的算法的扩展，通过蒙特卡罗模拟研究了这种效应的大小。对于含有N =碱基对、扭转常数α = 5.8×10⁻¹²达因厘米、持久长度P = 500埃和10000埃，以及弯曲势各向异性范围从ρ = 1.0到16.0的环状DNA，模拟了298K时的超螺旋自由能。通过假设各向同性弯曲势，根据这些超螺旋自由能计算出的表观扭转常数，当输入各向异性从1.0增加到16.0时，发现增加不到3%。当P = 500埃时，在整个输入各向异性范围内，表观扭转常数从未显著高于输入值。当P = 10000埃时，对于各向异性ρ = 8.0和16.0，表观扭转常数仅比输入值高出约3%。显然，弯曲势的各向异性无法解释小环状DNA报道的扭转常数比长线性DNA报道的扭转常数高出1.6倍或更多这一事实。
