Eur. Phys. J. B 39, 357-363 (2004)
https://doi.org/10.1140/epjb/e2004-00201-3

Kinetic barriers in RNA unzipping

Dipartimento di Scienze Fisiche and Unità INFM, Università “Federico II”, Complesso Universitario di Monte S. Angelo, 80126 Napoli, Italy

Corresponding author: ^a imparato@na.infn.it

Received: 19 January 2004
Published online: 12 July 2004

Abstract

We consider a simple model for the unfolding of RNA tertiary structure under dynamic loading. The opening of such a structure is regarded as a two step process, each corresponding to the overcoming of a single energy barrier. The resulting two-barrier energy landscape accounts for the dependence of the unfolding kinetics on the pulling rate. Furthermore at intermediate force, the two barriers cannot be distinguished by the analysis of the opening kinetic, which turns out to be dominated by a single macro-barrier, whose properties depend non-trivially on the two single barriers. Our results suggest that in pulling experiments on RNA molecule containing tertiary structures, the details of the single kinetic barriers can only be obtained using a low pulling rate value, or in the high force regime.