Mechanically probing the folding pathway of single RNA molecules

TL;DR

This paper models the mechanical unfolding of single RNA molecules, showing how fluctuations reveal detailed unfolding pathways and how measurement device stiffness affects resolution, aligning with recent experimental findings.

Contribution

It introduces a theoretical model that links RNA secondary structure unfolding signatures to experimental force fluctuations, highlighting the importance of device stiffness.

Findings

Fluctuations reveal signatures of individual structural element unfolding.

Optimal device spring constant improves resolution of unfolding signatures.

Model aligns with and explains recent experimental observations.

Abstract

We study theoretically the denaturation of single RNA molecules by mechanical stretching, focusing on signatures of the (un)folding pathway in molecular fluctuations. Our model describes the interactions between nucleotides by incorporating the experimentally determined free energy rules for RNA secondary structure, while exterior single stranded regions are modeled as freely jointed chains. For exemplary RNA sequences (hairpins and the Tetrahymena thermophila group I intron), we compute the quasi-equilibrium fluctuations in the end-to-end distance as the molecule is unfolded by pulling on opposite ends. Unlike the average quasi-equilibrium force-extension curves, these fluctuations reveal clear signatures from the unfolding of individual structural elements. We find that the resolution of these signatures depends on the spring constant of the force-measuring device, with an optimal value intermediate between very rigid and very soft. We compare and relate our results to recent experiments by Liphardt et al. [Science 292, 733-737 (2001)].