Advanced Search

Browse by Discipline

Scientific Societies

E-print Alerts

Add E-prints

E-print Network

  Advanced Search  

Distribution of Bubble Lengths in DNA Max Planck Institute for the Physics of Complex Systems, Nothnitzer Strasse 38,

Summary: Distribution of Bubble Lengths in DNA
S. Ares*
Max Planck Institute for the Physics of Complex Systems, No¨thnitzer Strasse 38,
D-01187 Dresden, Germany, and Grupo Interdisciplinar de Sistemas Complejos
G. Kalosakas
Department of Materials Science, UniVersity of Patras, 26504 Patras, Greece
Received September 29, 2006; Revised Manuscript Received December 19, 2006
The distribution of bubble lengths in double-stranded DNA is presented for segments of varying guanine-cytosine (GC) content, obtained
with Monte Carlo simulations using the Peyrard-Bishop-Dauxois model at 310 K. An analytical description of the obtained distribution in the
whole regime investigated, i.e., up to bubble widths of the order of tens of nanometers, is available. We find that the decay lengths and
characteristic exponents of this distribution show two distinct regimes as a function of GC content. The observed distribution is attributed to
the anharmonic interactions within base pairs. The results are discussed in the framework of the Poland-Scheraga and the Peyrard-Bishop
(with linear instead of nonlinear stacking interaction) models.
Fluctuating thermal openings of the double helix of DNA
(bubbles) are known to exist in a regime extending well
below the denaturation transition, which includes physi-
ological temperatures. These openings could be exploited
by regulatory proteins or functional enzymes to perform their


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


Collections: Physics; Biology and Medicine