Simulation of DNA catenanes

Abstract

DNA catenanes are important objects in biology, foremost as they appear during replication of circular DNA molecules. In this review we analyze how conformational properties of DNA catenanes can be studied by computer simulation. We consider classification of catenanes, their topological invariants and the methods of calculation of these invariants. We briefly analyze the DNA model and the simulation procedure used to sample the equilibrium conformational ensemble of catenanes with a particular topology. We consider how to avoid direct simulation of many DNA molecules when we need to account for the linking–unlinking process. The simulation methods and their comparisons with experiments are illustrated by some examples. We also describe an approach that allows simulating the steady state fraction of DNA catenanes created by type II topoisomerases.