DNA Confined in Nanochannels: Hairpin Tightening by Entropic Depletion

TL;DR

This paper develops a theory describing how DNA hairpins are constrained and tightened within nanochannels due to entropic forces, impacting DNA elongation and persistence length, with comparisons to experimental data.

Contribution

It introduces a theoretical model for DNA hairpins in nanochannels, accounting for entropic depletion effects and providing predictions for hairpin shape, size, and DNA elongation.

Findings

Hairpins are significantly constrained near channel walls.

The global persistence length can reach tens of micrometers or millimeters.

Theoretical predictions align with experimental observations.

Abstract

A theory is presented of DNA hairpins enclosed in a nanochannel. A hairpin becomes constrained as it approaches the wall of a channel which leads to an entropic force causing the hairpin to tighten. The free energy of the hairpin computed in the classical limit is significantly larger than what one would expect. As a result, the distance between hairpins or the global persistence length is often tens of micrometers long and may even reach mm sizes for 10 nm thin channels. The hairpin shape and size, and the DNA elongation are computed for nanoslits, and circular and square nanoschannels. A comparison with experiment is given.