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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.
Keywords
B-DNA, DNA overstretching, S-DNA, ssDNA, Unpeeling
Source Title
Journal of Computational and Theoretical Nanoscience
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Series/Report No.
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Date
2008-07
DOI
10.1166/jctn.2008.024
Type
Article