The elastic theory of a single DNA molecule |
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Authors: | Haijun Zhou Yang Zhang Zhang-Can Ou-Yang |
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Affiliation: | (1) Institute of Theoretical Physics, The Chinese Academy of Sciences, P.O. Box 2735, China;(2) Max-Planck-Institute of Colloids and Interfaces, 14476 Golm, Germany;(3) Center for Advanced Study, Tsinghua University, 100084 Beijing, China |
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Abstract: | We study the elastic responses of double-(ds) and single-stranded (ss) DNA at external force fields. A double-strand-polymer elastic model is constructed and solved by path integral methods and Monte Carlo simulations to understand the entropic elasticity, cooperative extensibility, and supercoiling property of dsDNA. The good agreement with experiments indicates that short-ranged base-pair stacking interaction is crucial for the stability and the high deformability of dsDNA. Hairpin-coil transition in ssDNA is studied with generating function method. A threshold force is needed to pull the ssDNA hairpin patterns, stabilized by base pairing and base-pair stacking, into random coils. This phase transition is predicted to be of first order for stacking potential higher than some critical level, in accordance with experimental observations. |
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Keywords: | DNA elastic theory stacking interaction supercoiling hairpin-coil transition |
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