Cold denaturation of RNA secondary structures with loop entropy and quenched disorder

TL;DR

This paper investigates how RNA secondary structures undergo cold denaturation as a continuous phase transition influenced by loop entropy and quenched sequence disorder, supported by a thermodynamic phase diagram.

Contribution

It introduces a model combining loop entropy and quenched disorder to explain RNA cold denaturation as a phase transition, extending previous understanding.

Findings

Cold denaturation is a continuous phase transition.

Phase diagram shows dependence on loop exponent and temperature.

Both hot and cold melting temperatures are calculated.

Abstract

We study the folding of RNA secondary structures with quenched sequence randomness by means of the constrained annealing method. A thermodynamic phase transition is induced by including the conformational weight of loop structures. In addition to the expected melting at high temperature, a cold melting transition appears. Our results suggest that the cold denaturation of RNA found experimentally is, in fact, a continuous phase transition triggered by quenched sequence disorder. We calculate both hot and cold melting critical temperatures for the competing energy scenario between favorable and unfavorable base pairs and present a phase diagram as a function of the loop exponent and temperature.