Computational Analysis of the Chiral Action of Type II DNA Topoisomerases

It was found recently that bacterial type II DNA topoisomerase, topo IV, is much more efficient in relaxing (+) DNA supercoiling than (−) supercoiling. This means that the DNA–enzyme complex is chiral. This chirality can appear upon binding the first segment that participates in the strand passing reaction (G segment) or only after the second segment (T segment) joins the complex. The former possibility is analyzed here. We assume that upon binding the enzyme, the G segment forms a part of left-handed helical turn. This model is an extension of the hairpin model introduced earlier to explain simplification of DNA topology by these enzymes. Using statistical–mechanical simulation of DNA properties, we estimated different consequences of the model: (1) relative rates of relaxation of (+) and (−) supercoiling by the enzyme; (2) the distribution of positions of the G segment in supercoiled molecules; (3) steady-state distribution of knots in circular molecules created by the topoisomerase; (4) the variance of topoisomer distribution created by the enzyme; (5) the effect of (+) and (−) supercoiling on the binding topo II with G segment. The simulation results are capable of explaining nearly all available experimental data, at least semiquantitatively. A few predictions obtained in the model analysis can be tested experimentally.