Sequence-dependent unpeeling dynamics of stretched DNA double helix

Abstract

To verify the theory of overstretching transition of DNA double helix developed by Cocco and coworkers, the overstretching processes of homopolymer, poly(GC) and poly(AT), and heteropolymer, λ DNA, are studied by a three-state Ising-like model. The three possible states are B-DNA, S-DNA, and unpeeled single ssDNA. Equilibrium property is obtained by transfer matrix method, while kinetic unpeeling process is studied by Monte Carlo simulation. For poly(GC) DNA, the unpeeling process begins from S-DNA at forces 200 pN if the extension rate is infinitely slow. At a finite extension rate, unpeeling forces can be much higher than 200 pN, which is dependent on the extension rate. For poly(AT) DNA, the unpeeling process begins from B-DNA, and the process is approximately in equilibrium at experimental accessible extension rate. For segment of λ DNA, unpeeling can begin at the B-S transition force, and it finishes at different forces depending on the extension rate. The results agree well with experiment. Copyright © 2008 American Scientific Publishers. All rights reserved.