RNA secondary structure formation: a solvable model of heteropolymer folding

TL;DR

This paper presents an exactly solvable model for RNA secondary structure formation, analyzing the transition between native and molten phases driven by energy-entropic competition, supported by numerical enumeration.

Contribution

It introduces a simplified Go-like model for heteropolymer folding, providing exact solutions and insights into RNA structural transitions.

Findings

Identifies a temperature-driven transition between native and molten phases.

Verifies critical behavior through numerical enumeration of sequences.

Demonstrates the balance of energy and entropy in RNA folding.

Abstract

The statistical mechanics of heteropolymer structure formation is studied in the context of RNA secondary structures. A designed RNA sequence biased energetically towards a particular native structure (a hairpin) is used to study the transition between the native and molten phase of the RNA as a function of temperature. The transition is driven by a competition between the energy gained from the polymer's overlap with the native structure and the entropic gain of forming random contacts. A simplified Go-like model is proposed and solved exactly. The predicted critical behavior is verified via exact numerical enumeration of a large ensemble of similarly designed sequences.