Dynamics of force-induced DNA slippage

Abstract

We study the basepairing dynamics of DNA with repetitive sequences where local strand slippage can create, annihilate, and move bulge loops. Using an explicit theoretical model, we find a rich dynamical behavior as a function of an applied shear force f: reptation-like dynamics at f=f_c with a rupture time scaling as N^3 with its length N, drift-diffusion dynamics for f_c < f < f^*, and a dynamical transition to an unraveling mode of strand separation at f = f^*. We predict a viscoelastic behavior for periodic DNA with time and force scales that can be programmed into its sequence.

revised version with minor changes as will be published in Phys. Rev. Lett