The secondary structure of RNA under tension

TL;DR

This paper investigates how random disordered RNA and single-stranded DNA unfold under tension, revealing a phase transition and providing insights into their ground state properties and force-extension behavior.

Contribution

It demonstrates the universality of critical exponents in force-induced unfolding and introduces a method to study ground state properties through zero-force extrapolation.

Findings

Identifies a second order phase transition from globular to extended phase.

Provides numerical evidence for universal critical exponents.

Analyzes rearrangement statistics relevant to force-extension experiments.

Abstract

We study the force-induced unfolding of random disordered RNA or single-stranded DNA polymers. The system undergoes a second order phase transition from a collapsed globular phase at low forces to an extensive necklace phase with a macroscopic end-to-end distance at high forces. At low temperatures, the sequence inhomogeneities modify the critical behaviour. We provide numerical evidence for the universality of the critical exponents which, by extrapolation of the scaling laws to zero force, contain useful information on the ground state (f=0) properties. This provides a good method for quantitative studies of scaling exponents characterizing the collapsed globule. In order to get rid of the blurring effect of thermal fluctuations we restrict ourselves to the groundstate at fixed external force. We analyze the statistics of rearrangements, in particular below the critical force, and point out its implications for force-extension experiments on single molecules.