Eur. Phys. J. E 10, 153-161 (2003)
DOI: 10.1140/epje/e2003-00019-8

Slow nucleic acid unzipping kinetics from sequence-defined barriers

S. Cocco¹, J.F. Marko² and R. Monasson<sup>3, 4

1</sup>  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.

PACS
87.15.-v - Biomolecules: structure and physical properties.

© EDP Sciences, Società Italiana di Fisica, Springer-Verlag 2003