Vologodskii A V, Cozzarelli N R
Institute of Molecular Genetics, Russian Academy of Sciences, Moscow.
J Mol Biol. 1993 Aug 20;232(4):1130-40. doi: 10.1006/jmbi.1993.1465.
We used a Monte Carlo method to study the conformational properties of catenanes between two nicked DNA rings. We calculated the writhe induced by catenation as a function of the linking number between the two rings. The simulations modeled catenated rings of equal size as well as rings differing in length by a factor of 3. For both classes of catenanes, the calculated values of writhe agreed very well with the experimental measurements of catenation-induced supercoiling made by Wasserman et al. Therefore, the equilibrium value of DNA twist is not changed significantly by catenation. We found that the induced writhe increased linearly with catenane linking number, but was independent of DNA length and of effective helical diameter. We conclude that induced writhe is a general feature of catenation, and that it depends primarily on the ratio of lengths of the linked rings and the number of catenane interlocks. In contrast, catenane conformation varied qualitatively with catenation linking number, DNA length, and double helix diameter. At the values of these parameters for catenanes isolated from cells, catenane conformations were strikingly irregular. Nonetheless, the local concentration of two sites on separate but linked rings increased greatly with catenane linking number. This increase is similar to that brought about by (-) supercoiling to DNA sites in cis.
我们使用蒙特卡罗方法研究了两个带切口的DNA环之间连环体的构象性质。我们计算了连环化诱导的扭曲作为两个环之间连接数的函数。模拟对大小相等的连环环以及长度相差3倍的环进行了建模。对于这两类连环体，计算得到的扭曲值与Wasserman等人进行的连环化诱导超螺旋的实验测量结果非常吻合。因此，DNA扭曲的平衡值不会因连环化而发生显著变化。我们发现，诱导扭曲随连环体连接数呈线性增加，但与DNA长度和有效螺旋直径无关。我们得出结论，诱导扭曲是连环化的一个普遍特征，并且它主要取决于相连环的长度比和连环体互锁的数量。相比之下，连环体构象随连环化连接数、DNA长度和双螺旋直径发生定性变化。在从细胞中分离出的连环体的这些参数值下，连环体构象明显不规则。尽管如此，在分开但相连的环上两个位点的局部浓度随连环体连接数大幅增加。这种增加类似于由（-）超螺旋对顺式DNA位点所带来的增加。
