Stretching and twisting of the DNA duplexes in coarse-grained dynamical models

Abstract

Three coarse-grained molecular dynamics models of the double-stranded DNA are proposedand compared in the context of single molecule mechanical manipulation such as twistingand various schemes of stretching—unzipping, shearing, two-strand stretching andstretching of only one strand. The models differ in the number of effective beads (betweentwo and five) representing each nucleotide. They all show similar behaviour, but the biggerthe resolution, the more details in the force patterns. The models incorporate the effectiveLennard-Jones potentials in the couplings between two strands and harmonicpotentials to describe the structure of a single strand. The force patterns are shown todepend on the sequence studied. In particular, both shearing and unzipping for anall-AT sequence lead to lower forces than for an all-CG sequence. The unzippingpatterns and the corresponding scenario diagrams for the contact rupture eventsare found to reflect the sequential information if the temperature is moderateand initial transients are discarded. The derived torque–force phase diagram isfound to be qualitatively consistent with experiments and all-atom simulations.