DNA Confined in Nanochannels: Hairpin Tightening by Entropic Depletion

Details DNA Confined in Nanochannels: Hairpin Tightening by Entropic Depletion DNA Confined in Nanochannels: Hairpin Tightening by Entropic Depletion

2006-10-02

arxiv.org/abs/cond-mat/0610050v1

Physics

Condensed Matter

Soft Condensed Matter

13 pages, 4 figures

Scientific paper

10.1063/1.2400227

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.

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