Force-induced misfolding in RNA

TL;DR

This paper presents a mechanical force-based model to understand RNA folding and misfolding, successfully interpreting experimental force-extension data and revealing force-induced misfolding mechanisms in RNA molecules.

Contribution

The study introduces a minimal, two-parameter model for RNA folding kinetics under force, capturing misfolding phenomena and aligning with experimental results.

Findings

Force induces misfolding in RNA, stabilizing non-native structures.

The model accurately reproduces experimental force-extension curves.

Force influences the folding pathway, promoting non-native hairpins.

Abstract

RNA folding is a kinetic process governed by the competition of a large number of structures stabilized by the transient formation of base pairs that may induce complex folding pathways and the formation of misfolded structures. Despite of its importance in modern biophysics, the current understanding of RNA folding kinetics is limited by the complex interplay between the weak base-pair interactions that stabilize the native structure and the disordering effect of thermal forces. The possibility of mechanically pulling individual molecules offers a new perspective to understand the folding of nucleic acids. Here we investigate the folding and misfolding mechanism in RNA secondary structures pulled by mechanical forces. We introduce a model based on the identification of the minimal set of structures that reproduce the patterns of force-extension curves obtained in single molecule experiments. The model requires only two fitting parameters: the attempt frequency at the level of individual base pairs and a parameter associated to a free energy correction that accounts for the configurational entropy of an exponentially large number of neglected secondary structures. We apply the model to interpret results recently obtained in pulling experiments in the three-helix junction S15 RNA molecule (RNAS15). We show that RNAS15 undergoes force-induced misfolding where force favors the formation of a stable non-native hairpin. The model reproduces the pattern of unfolding and refolding force-extension curves, the distribution of breakage forces and the misfolding probability obtained in the experiments.