Improving signal-to-noise resolution in single molecule experiments using molecular constructs with short handles

TL;DR

This study demonstrates that using short DNA handles in optical tweezers experiments improves the signal-to-noise ratio and enables better detection of fast folding transitions in DNA hairpins, with implications for single-molecule force spectroscopy.

Contribution

The paper introduces a new approach with short DNA handles that enhances SNR and provides insights into elastic properties affecting measurement limits.

Findings

Short handles increase SNR in optical tweezers experiments.

Short handles slow down folding/unfolding kinetics, aiding detection.

Elastic property analysis shows limits due to reduced persistence length.

Abstract

We investigate unfolding/folding force kinetics in DNA hairpins exhibiting two and three states with newly designed short dsDNA handles (29 bp) using optical tweezers. We show how the higher stiffness of the molecular setup moderately enhances the signal-to-noise ratio (SNR) in hopping experiments as compared to conventional long handles constructs (approximately 700 bp). The shorter construct results in a signal of higher SNR and slower folding/unfolding kinetics, thereby facilitating the detection of otherwise fast structural transitions. A novel analysis of the elastic properties of the molecular setup, based on high-bandwidth measurements of force fluctuations along the folded branch, reveals that the highest SNR that can be achieved with short handles is potentially limited by the marked reduction of the effective persistence length and stretch modulus of the short linker complex.