DNA TOPOLOGY

Two topological levels are inherent in closed circular (cc) DNA. First , the double helix as a whole can form knots of different types, or fo rm the trivial knot (to be unknotted). Secondly, the two complementary strands are interlinked in ccDNA, which results in a biologically ver y important phenomenon of DNA supercoiling. During the past 20 years w e have elaborated a theoretical model, which makes it possible to trea t the DNA topological properties at equilibrium in a rigorous way by t he Monte Carlo method. Within the framework of the model, the double h elix is considered as a homogeneous, isotropic elastic rod with given values of bending and torsional rigidity parameters and the effective diameter. We have predicted the equilibrium fraction of knotted DNA mo lecules for different DNA lengths and for different values of DNA effe ctive diameter. These theoretical predictions have recently been fully confirmed by experiment. Comparison of theory with experiment also ga ve the value of DNA effective diameter under a variety of ambient cond itions. Calculations of equilibrium distribution of ccDNA over topoiso mers yielded a reliable estimation of the DNA torsional rigidity. As a result, all three parameters of the DNA model have been reliably esti mated. This makes possible unambiguous predictions of various properti es of DNA under topological constraints. In particular, extensive comp uter simulations of supercoiled DNA have been carried out.