Rybenkov V V, Vologodskii A V, Cozzarelli N R
Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.
Nucleic Acids Res. 1997 Apr 1;25(7):1412-8. doi: 10.1093/nar/25.7.1412.
We determined the free energy of DNA supercoiling as a function of the concentration of magnesium and sodium chloride in solution by measuring the variance of the equilibrium distribution of DNA linking number,<(DeltaLk)2>. We found that the free energy of supercoiling changed >1.5-fold over the range of ionic conditions studied. Comparison of the experimental results with those of computer simulations showed that the ionic condition dependence of<(DeltaLk)2>is due mostly to the change in DNA effective diameter, d, a parameter characterizing the electrostatic interaction of DNA segments. To make this comparison we determined values of d under all ionic conditions studied by measuring the probability of knot formation during random cyclization of linear DNA molecules. From the topoisomer distributions we could also determine the changes in DNA helical repeat, gamma, in mixed NaCl/MgCl2 solutions. Both gamma and d exhibited a complex pattern of changes with changing ionic conditions, which can be described in terms of competition between magnesium and sodium ions for binding to DNA.
我们通过测量DNA连接数平衡分布的方差<(ΔLk)²>，确定了DNA超螺旋的自由能作为溶液中镁离子和氯化钠浓度的函数。我们发现，在所研究的离子条件范围内，超螺旋的自由能变化超过1.5倍。将实验结果与计算机模拟结果进行比较表明，<(ΔLk)²>对离子条件的依赖性主要是由于DNA有效直径d的变化，d是一个表征DNA片段静电相互作用的参数。为了进行这种比较，我们通过测量线性DNA分子随机环化过程中形成结的概率，确定了所有研究离子条件下的d值。从拓扑异构体分布中，我们还可以确定混合NaCl/MgCl₂溶液中DNA螺旋重复率γ的变化。γ和d都表现出随离子条件变化的复杂变化模式，这可以用镁离子和钠离子与DNA结合的竞争来描述。
