MD simulation of the transitions between B-DNA and A-DNA in the framework of a coarse-grained model

Abstract

Transitions between the B and A forms of a short DNA double helix (12 base pairs) at different salt concentrations in an aqueous solution have been studied by the molecular dynamics method in the framework of a coarse-grained model with explicit ions but without friction. It has been shown that the A-DNA, stable at high salt concentrations, is a dynamic conglomerate of the molecule and the ions coming from the solution into the deep major groove and then leaving it. In such a short helix, in the model without friction, even at low salt concentrations, transitions from B-DNA to A-DNA and back are frequent and fast. Stable ADNA (without transitions to B-DNA) forms at salt concentrations greater than 0.45 mol/L.