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

TL;DR

This paper develops a unified theoretical framework combining thermodynamics and kinetics to describe RNA unfolding under tension, providing insights into the molecular dynamics and transition mechanisms.

Contribution

It introduces a mesoscopic non-equilibrium thermodynamics approach that unifies thermodynamic and kinetic descriptions of RNA unfolding, connecting to existing models.

Findings

Derives a master equation in the high barrier limit

Reveals non-linear switching kinetics between states

Provides a systematic method for characterizing unfolding dynamics

Abstract

We use mesoscopic non-equilibrium 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. Non-linear 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