Force unfolding kinetics of RNA using optical tweezers. II. Modeling experiments

TL;DR

This paper introduces a mesoscopic model to analyze RNA hopping kinetics in optical tweezers, accounting for experimental setup elements and limitations, to better estimate intrinsic molecular rates and optimize experimental conditions.

Contribution

The study presents a new mesoscopic model that incorporates experimental setup factors and instrument limitations to analyze RNA hopping kinetics.

Findings

Model agrees well with experimental data

Long handles and soft traps improve rate estimation accuracy

Methodology applicable to other molecules and setups

Abstract

By exerting mechanical force it is possible to unfold/refold RNA molecules one at a time. In a small range of forces, an RNA molecule can hop between the folded and the unfolded state with force-dependent kinetic rates. Here, we introduce a mesoscopic model to analyze the hopping kinetics of RNA hairpins in an optical tweezers setup. The model includes different elements of the experimental setup (beads, handles and RNA sequence) and limitations of the instrument (time lag of the force-feedback mechanism and finite bandwidth of data acquisition). We investigated the influence of the instrument on the measured hopping rates. Results from the model are in good agreement with the experiments reported in the companion article (1). The comparison between theory and experiments allowed us to infer the values of the intrinsic molecular rates of the RNA hairpin alone and to search for the optimal experimental conditions to do the measurements. We conclude that long handles and soft laser traps represent the best conditions to extract rate estimates that are closest to the intrinsic molecular rates. The methodology and rationale presented here can be applied to other experimental setups and other molecules.