DOI: 10.1140/epje/e2003-00019-8
Slow nucleic acid unzipping kinetics from sequence-defined barriers
S. Cocco1, J.F. Marko2 and R. Monasson3, 41 CNRS-Laboratoire de Dynamique des Fluides Complexes, 3 rue de l'Université, 67000 Strasbourg, France
2 Department of Physics, The University of Illinois at Chicago, 845 West Taylor Street, Chicago, IL 60607-7059, USA
3 CNRS-Laboratoire de Physique Théorique de l'ENS, 24 rue Lhomond, 75005 Paris, France
4 CNRS-Laboratoire de Physique Théorique, 3 rue de l'Université, 67000 Strasbourg, France
cocco@ldfc.u-strasbg.fr
jmarko@uic.edu
monasson@lpt.ens.fr
(Received 29 July 2002 / Received in final form 5 February 2003 Published online: 16 April 2003)
Abstract
Recent experiments on unzipping of RNA helix-loop structures
by force have shown that
40-base molecules can undergo kinetic
transitions between two well-defined "open" and "closed" states, on a
timescale
1 sec [Liphardt et al.,
Science 297, 733-737 (2001)]. Using a simple
dynamical model, we show that these phenomena result
from the slow kinetics of crossing large free energy barriers
which separate the open and closed conformations.
The dependence of barriers on sequence along
the helix, and on the size of the loop(s) is analyzed. Some DNA and RNA
sequences that could show dynamics on different time scales,
or three(or more)-state unzipping, are proposed. Our dynamical model
is also applied to the unzipping of long (kilo-basepair) DNA molecules
at constant force.
87.15.-v - Biomolecules: structure and physical properties.
© EDP Sciences, Società Italiana di Fisica, Springer-Verlag 2003