Coarse-grained simulations of dsDNA polycatenanes and network formation in annular nanochannels with topoisomerase II

Abstract

We numerically investigate the behavior of a system of initially unlinked nicked dsDNA rings confined into an annular square nanochannel in the presence of TopoII. Channel confinement can enhance the catenation likelihood by bringing highly bent regions from different rings in close proximity, while at the same time reducing the emergence of knots. The annular channel topology simplifies the characterization of the system by removing periodic boundary conditions and can lead to the formation of circular catenanes.We characterize the equilibrium and dynamical properties of the steady-state system, including the amount of catenation and the topologies explored by the system, under different parameters of the model and for different levels of confinement. We argue that a similar setup could allow for a direct comparison between experiments and simulations under well characterized and controlled conditions, thus providing a way to select and tune computational models of TopoII, as well as provide a way to obtain dsDNA interlocked materials in a controlled fashion.