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arXiv · 1002.3485

A three-state model with loop entropy for the over-stretching transition of DNA

Thomas R. Einert·Douglas B. Staple·Hans-Juergen Kreuzer·Roland R. Netz
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Abstract

We introduce a three-state model for a single DNA chain under tension that distinguishes between B-DNA, S-DNA and M (molten or denatured) segments and at the same time correctly accounts for the entropy of molten loops, characterized by the exponent c in the asymptotic expression S ~ - c ln n for the entropy of a loop of length n. Force extension curves are derived exactly employing a generalized Poland-Scheraga approach and compared to experimental data. Simultaneous fitting to force-extension data at room temperature and to the denaturation phase transition at zero force is possible and allows to establish a global phase diagram in the force-temperature plane. Under a stretching force, the effects of the stacking energy, entering as a domain-wall energy between paired and unpaired bases, and the loop entropy are separated. Therefore we can estimate the loop exponent c independently from the precise value of the stacking energy. The fitted value for c is small, suggesting that nicks dominate the experimental force extension traces of natural DNA.

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Thomas R. Einert, Douglas B. Staple, Hans-Juergen Kreuzer, Roland R. Netz. 2010-04-15. A three-state model with loop entropy for the over-stretching transition of DNA. https://doi.org/10.1016/j.bpj.2010.04.046

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