Nanoconfined circular and linear DNA - equilibrium conformations and unfolding kinetics

TL;DR

This study investigates the equilibrium conformations and unfolding kinetics of nanoconfined circular and linear DNA, revealing how confinement affects their extension ratios, unfolding rates, and how to distinguish them experimentally.

Contribution

It provides experimental validation of theoretical models for confined DNA and introduces a method to distinguish DNA topologies via emission intensity measurements.

Findings

Extension ratio increases as buffer concentration decreases.

Experimental results align with extended de Gennes and Odijk regimes.

Unfolding rate is higher for more confined DNA.

Abstract

Studies of circular DNA confined to nanofluidic channels are relevant both from a fundamental polymer-physics perspective and due to the importance of circular DNA molecules in vivo. We here observe the unfolding of DNA from the circular to linear configuration as a light-induced double strand break occurs, characterize the dynamics, and compare the equilibrium conformational statistics of linear and circular configurations. This is important because it allows us to determine to which extent existing statistical theories describe the extension of confined circular DNA. We find that the ratio of the extensions of confined linear and circular DNA configurations increases as the buffer concentration decreases. The experimental results fall between theoretical predictions for the extended de Gennes regime at weaker confinement and the Odijk regime at stronger confinement. We show that it is possible to directly distinguish between circular and linear DNA molecules by measuring the emission intensity from the DNA. Finally, we determine the rate of unfolding and show that this rate is larger for more confined DNA, possibly reflecting the corresponding larger difference in entropy between the circular and linear configurations.