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PubMed · 15904042

Distribution functions, loop formation probabilities, and force-extension relations in a model for short double-stranded DNA molecules.

P Ranjith·P B Sunil Kumar·Gautam I Menon
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Abstract

We obtain, using transfer-matrix methods, the distribution function P(R) of the end-to-end distance, the loop formation probability, and force-extension relations in a model for short double-stranded DNA molecules. Accounting for the appearance of "bubbles," localized regions of enhanced flexibility associated with the opening of a few base pairs of double-stranded DNA in thermal equilibrium, leads to dramatic changes in P(R) and unusual force-extension curves. An analytic formula for the loop formation probability in the presence of bubbles is proposed. For short heterogeneous chains, we demonstrate a strong dependence of loop formation probabilities on sequence.

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DNAModels, ChemicalNucleic Acid ConformationThermodynamicsJournal ArticleResearch Support, Non-U.S. Gov't

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P Ranjith, P B Sunil Kumar, Gautam I Menon. 2005-04-07. Distribution functions, loop formation probabilities, and force-extension relations in a model for short double-stranded DNA molecules.. https://doi.org/10.1103/physrevlett.94.138102

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