Statistical Physics of RNA-folding

TL;DR

This paper explores the statistical physics of RNA secondary structures, analyzing phase transitions, disorder effects, and force-extension behavior to deepen understanding of RNA folding and denaturation.

Contribution

It introduces a comprehensive physical model of RNA secondary structure, highlighting phase transitions and the impact of disorder, with insights into force-induced unfolding.

Findings

RNA exhibits a thermal denaturation transition at high pairing energies.

Force induces a second order globular-extended phase transition.

Disorder does not affect the correlation length exponent but modifies other critical exponents.

Abstract

We discuss the physics of RNA as described by its secondary structure. We examine the static properties of a homogeneous RNA-model that includes pairing and base stacking energies as well as entropic costs for internal loops. For large enough costs the model exhibits a thermal denaturation transition which we analyze in terms of the radius of gyration. We point out an inconsistency in the standard approach to RNA secondary structure prediction for large molecules. Under an external force a second order phase transition between a globular and an extended phase takes place. A Harris-type criterion shows that sequence disorder does not affect the correlation length exponent while the other critical exponents are modified in the glass phase. However, at high temperatures, on a coarse-grained level, disordered RNA is well described by a homogeneous model. The characteristics of force-extension curves are discussed as a function of the energy parameters. We show that the force transition is always second order. A re-entrance phenomenon relevant for real disordered RNA is predicted.