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

References in corpus (5)

• Driven Polymer Translocation Through a Narrow Pore
• Pulling Pinned Polymers and Unzipping DNA
• DNA unzipped under a constant force exhibits multiple metastable intermediates
• Single Molecule Statistics and the Polynucleotide Unzipping Transition
• Localization of Denaturation Bubbles in Random DNA Sequences

Cited by in corpus (5)

• Molecular Dynamics of a kB DNA Element: Base Flipping via Cross-strand Intercalative Stacking in a Microsecond-scale Simulation
• An intermediate phase in DNA melting
• Force induced melting of the constrained DNA
• Effect of shear force on the separation of double stranded DNA
• DNA as a programmable viscoelastic nanoelement