Monte Carlo analysis of the conformation of DNA catenanes.
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.