Discrete model for DNA-promoter dynamics

Abstract

We introduce a discrete model for DNA that takes into account the information about specific base sequences along the double helix. We use this model to study nonlinear wave dynamics of the T7${\mathit{A}}_{1}$ DNA promoter. As results we show the existence in the promoter of a dynamically active region in which static solitons acquire finite velocities, which contrasts with regions where solitons simply remain static. Furthermore, when they pass through this region moving solitons are accelerated, decelerated, or reflected, depending on their initial velocities. The possibility that these dynamical effects play a role in the mechanism of genetic activation is suggested.