Thermodynamic and kinetic aspects of RNA pulling experiments

TL;DR

This paper models RNA pulling experiments to understand thermodynamics and kinetics, focusing on small and multi-domain RNAs, and proposes methods to extract reliable kinetic parameters from experimental data.

Contribution

It introduces a minimal model incorporating statistical ensembles and thermodynamic potentials, providing insights into unfolding mechanisms and data analysis techniques for complex RNA structures.

Findings

Model reproduces experimental unfolding results

Analyzes influence of handles and bead on unfolding

Proposes methods to extract kinetic parameters

Abstract

Recent single-molecule pulling experiments have shown how it is possible to manipulate RNA molecules using optical tweezers force microscopy. We investigate a minimal model for the experimental setup which includes a RNA molecule connected to two polymers (handles) and a bead, trapped in the optical potential, attached to one of the handles. Initially, we focus on small single-domain RNA molecules which unfold in a cooperative way. The model qualitatively reproduces the experimental results and allow us to investigate the influence of the bead and handles on the unfolding reaction. A main ingredient of our model is to consider the appropriate statistical ensemble and the corresponding thermodynamic potential describing thermal fluctuations in the system. We then investigate several questions relevant to extract thermodynamic information from the experimental data. Next, we study the kinetics using a dynamical model. Finally, we address the more general problem of a multidomain RNA molecule with Mg2+-tertiary contacts that unfolds in a sequential way and propose techniques to analyze the breakage force data in order to obtain the reliable kinetics parameters that characterize each domain.