Equilibrium properties and force-driven unfolding pathways of RNA molecules

TL;DR

This paper models the mechanical unfolding of RNA molecules, revealing simple two-state behavior for hairpins and intermediate states for ribozymes, with simulations matching experimental unfolding pathways.

Contribution

It introduces an exact Ising-like model to analyze RNA unfolding, providing detailed phase diagrams, free energy landscapes, and unfolding pathways.

Findings

Hairpin exhibits two-state unfolding behavior.

Ribozyme shows intermediate states during unfolding.

Simulated pathways align with experimental observations.

Abstract

The mechanical unfolding of a simple RNA hairpin and of a 236--bases portion of the Tetrahymena thermophila ribozyme is studied by means of an Ising--like model. Phase diagrams and free energy landscapes are computed exactly and suggest a simple two--state behaviour for the hairpin and the presence of intermediate states for the ribozyme. Nonequilibrium simulations give the possible unfolding pathways for the ribozyme, and the dominant pathway corresponds to the experimentally observed one.