Folding and unfolding of a triple-branch DNA molecule with four conformational states

TL;DR

This study combines optical tweezers experiments and theoretical modeling to analyze the folding and unfolding kinetics of a triple-branch DNA molecule with four conformational states, revealing distinct force rips and a method to identify frayed molecules.

Contribution

It introduces a combined experimental and theoretical approach to characterize complex DNA conformational transitions and identifies a novel method to detect frayed molecules.

Findings

Three distinct force rips observed in folding/unfolding trajectories.

Theoretical predictions match experimental rupture force distributions.

A method to identify frayed molecules by force jump analysis.

Abstract

Single-molecule experiments provide new insights into biological processes hitherto not accessible by measurements performed on bulk systems. We report on a study of the kinetics of a triple-branch DNA molecule with four conformational states by pulling experiments with optical tweezers and theoretical modelling. Three distinct force rips associated with different transitions between the conformational states are observed in the folding and unfolding trajectories. By applying transition rate theory to a free energy model of the molecule, probability distributions for the first rupture forces of the different transitions are calculated. Good agreement of the theoretical predictions with the experimental findings is achieved. Furthermore, due to our specific design of the molecule, we found a useful method to identify permanently frayed molecules by estimating the number of opened basepairs from the measured force jump values.