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Unifying thermodynamic and kinetic descriptions of single-molecule processes: RNA unfolding under tension.

Rubi JM, Bedeaux D, Kjelstrup S

Departament de Fisica Fonamental, Universitat de Barcelona, Diagonal 647, 08028 Barcelona, Spain.

We use mesoscopic nonequilibrium thermodynamics theory to describe RNA unfolding under tension. The theory introduces reaction coordinates, characterizing a continuum of states for each bond in the molecule. The unfolding considered is so slow that one can assume local equilibrium in the space of the reaction coordinates. In the quasi-stationary limit of high sequential barriers, our theory yields the master equation of a recently proposed sequential-step model. Nonlinear switching kinetics is found between open and closed states. Our theory unifies the thermodynamic and kinetic descriptions and offers a systematic procedure to characterize the dynamics of the unfolding process.

Published 9 August 2007 in J Phys Chem B, 111(32): 9598-602.
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