Dependence on temperature and GC content of bubble length distributions in DNA

Details Dependence on temperature and GC content of bubble length distributions in DNA Dependence on temperature and GC content of bubble length distributions in DNA

2009-06-25

arxiv.org/abs/0906.4683v1

J. Chem. Phys. 130, 235104 (2009)

Biology

Quantitative Biology

Biomolecules

8 pages, 6 figures. Published on The Journal of Chemical Physics

Scientific paper

10.1063/1.3149859

We present numerical results on the temperature dependence of the distribution of bubble lengths in DNA segments of various guanine-cytosine (GC) concentrations. Base-pair openings are described by the Peyrard-Bishop-Dauxois model and the corresponding thermal equilibrium distributions of bubbles are obtained through Monte Carlo calculations for bubble sizes up to the order of a hundred base pairs. The dependence of the parameters of bubble length distribution on temperature and the GC content is investigated. We provide simple expressions which approximately describe these relations. The variation of the average bubble length is also presented. We find a temperature dependence of the exponent c that appears in the distribution of bubble lengths. If an analogous dependence exists in the loop entropy exponent of real DNA, it may be relevant to understand overstretching in force-extension experiments.

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