The mechanism of DNA mechanical unzipping

Abstract

The process of DNA double helix unzipping is considered to be a nonlinear dynamical process powered by an external force. In the course of unzipping the most probable pathway of the mechanical strands separation is determined. This pathway accounts for the structural organization of the double helix, the manner in which the external force is applied, and the kinetic parameters of the base pair opening in the double-stranded DNA chain. It is assumed in our model that the base pair unzipping includes the stretch of DNA complementary base pairs and the double helix torsion. For the description of the DNA unzipping the two-stage mechanism of the external force action is proposed. The mechanism explains the cooperative nature of the unzipping process under the physiological conditions and the threshold character of external force action. On the first stage the external force transforms the conformational state of the double helix and makes the unzipping possible. On the second stage the unzipping propagates along dsDNA. The boundary between the open and the closed parts of the helix (the so called ‘fork’) is demonstrated to move along the chain as a step-like excitation (kink soliton). It is shown that for stable unzipping propagation along DNA double helix, it is necessary to allow rotation of the DNA chain while keeping the velocity of the unzipping fork propagation small in comparison to the velocity of sound in the DNA. It is demonstrated that fluctuations of the external force at the constant velocity of unzipping and the fluctuations of the DNA unzipping length at the fixed force have the same origin: the heterogeneity of the DNA base pairs.