Vologodskii A, Cozzarelli N R
Department of Chemistry, New York University, New York 10003, USA.
Biophys J. 1996 Jun;70(6):2548-56. doi: 10.1016/S0006-3495(96)79826-0.
There are many proteins that interact simultaneously with two or more DNA sites that are separated along the DNA contour. These sites must be brought close together to form productive complexes with the proteins. We used Monte Carlo simulation of supercoiled DNA conformations to study the effect of supercoiling and DNA length on the juxtaposition of DNA sites, the angle between them, and the branching of the interwound superhelix. Branching decreases the probability of juxtaposition of two DNA sites but increases the probability of juxtaposition of three sites at branch points. We found that the number of superhelix branches increases linearly with the length of DNA from 3 to 20 kb. The simulations showed that for all contour distances between two sites, the juxtaposition probability in supercoiled DNA is two orders of magnitude higher than in relaxed DNA. Supercoiling also results in a strong asymmetry of the angular distribution of juxtaposed sites. The effect of supercoiling on site-specific recombination and the introduction of supercoils by DNA gyrase is discussed in the context of the simulation results.
有许多蛋白质能同时与沿DNA轮廓分离的两个或更多个DNA位点相互作用。这些位点必须靠近在一起才能与蛋白质形成有效的复合物。我们使用超螺旋DNA构象的蒙特卡罗模拟来研究超螺旋和DNA长度对DNA位点并列、它们之间的角度以及缠绕超螺旋分支的影响。分支降低了两个DNA位点并列的概率，但增加了分支点处三个位点并列的概率。我们发现超螺旋分支的数量随DNA长度从3千碱基对到20千碱基对呈线性增加。模拟表明，对于两个位点之间的所有轮廓距离，超螺旋DNA中的并列概率比松弛DNA中的高两个数量级。超螺旋还导致并列位点角度分布的强烈不对称。在模拟结果的背景下讨论了超螺旋对位点特异性重组的影响以及DNA促旋酶引入超螺旋的情况。
