Thermodynamic and kinetic aspects of RNA pulling experiments

¹ University of Barcelona

^* To whom correspondence should be addressed. E-mail: ritort{at}ffn.ub.es.

Submitted on May 7, 2004
Revised on June 19, 2004
Accepted on 15 February 2005

	Abstract

Recent single-molecule pulling experiments have shown how it is possible to manipulate RNA molecules using laser tweezers. In this paper we investigate a minimal model for the experimental setup which includes a RNA molecule connected to two polymers (handles) and a bead trapped in the optical potential and attached to one of the handles. We start by considering the case of small single-domain RNA molecules which unfold in a cooperative way. The model qualitatively reproduces the experimental results and allow us to investigate the influence of the bead and handles on the unfolding reaction. A main ingredient of our model is to consider the appropriate statistical ensemble and the corresponding thermodynamic potential describing thermal fluctuations in the system. We then investigate several questions relevant to extract thermodynamic information from the experimental data. The kinetics of unfolding is also studied by introducing a dynamical model. Finally, we apply the model to the more general problem of a multidomain RNA molecule with Mg²⁺ tertiary contacts that unfolds in a sequential way.

Key Words: Folding, Optical Tweezers, RNA folding-unfolding, Single Molecules, Statistical Physics, Thermodynamics

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