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Dependence on temperature and guanine-cytosine content of bubble length distributions in DNA

Summary: Dependence on temperature and guanine-cytosine content
of bubble length distributions in DNA
G. Kalosakas1,a
and S. Ares2
Department of Materials Science, University of Patras, GR-26504 Rio, Greece
Max Planck Institute for the Physics of Complex Systems, Nöthnitzer Str. 38, D-01187 Dresden, Germany
and Grupo Interdisciplinar de Sistemas Complejos (GISC)
Received 16 January 2009; accepted 14 May 2009; published online 18 June 2009
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 Peyrard­Bishop­Dauxois 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. © 2009 American Institute of Physics.


Source: Ares, Saúl - Max-Planck-Institut für Physik komplexer Systeme


Collections: Physics; Biology and Medicine