Statistical mechanics of RNA folding: a lattice approach

TL;DR

This paper introduces a lattice model for RNA folding that incorporates self-avoidance and tertiary interactions, analyzing phase transitions and denaturation behavior through simulations and theoretical methods.

Contribution

It presents a novel lattice-based approach to RNA folding, explicitly modeling tertiary structure and phase transitions with exact and simulation techniques.

Findings

Denaturation transition is first order.

Transition can be direct or via an intermediate molten phase.

Phase diagram characterized for the simplified hairpin native state.

Abstract

We propose a lattice model for RNA based on a self-interacting two-tolerant trail. Self-avoidance and elements of tertiary structure are taken into account. We investigate a simple version of the model in which the native state of RNA consists of just one hairpin. Using exact arguments and Monte Carlo simulations we determine the phase diagram for this case. We show that the denaturation transition is first order and can either occur directly or through an intermediate molten phase.