RNA denaturation: excluded volume, pseudoknots and transition scenarios

TL;DR

This paper introduces a lattice model for RNA denaturation that considers excluded volume effects and demonstrates that pseudoknot interactions are essential for a sharp transition, revealing different denaturation scenarios.

Contribution

It presents a comprehensive lattice model including pseudoknots and excluded volume effects, highlighting their impact on RNA denaturation transition scenarios.

Findings

Pseudoknot interactions are crucial for a sharp transition.

Without pseudoknots, a smooth crossover occurs.

Scaling laws describe loop and branch length distributions.

Abstract

A lattice model of RNA denaturation which fully accounts for the excluded volume effects among nucleotides is proposed. A numerical study shows that interactions forming pseudoknots must be included in order to get a sharp continuous transition. Otherwise a smooth crossover occurs from the swollen linear polymer behavior to highly ramified, almost compact conformations with secondary structures. In the latter scenario, which is appropriate when these structures are much more stable than pseudoknot links, probability distributions for the lengths of both loops and main branches obey scaling with nonclassical exponents.