(503b) DNA Extension In Nanochannels

A polymer extends when it is confined inside a channel whose dimensions are smaller than the size of the polymer in bulk. In the context of DNA, two-dimensional channel confinement is emerging as an important tool for single-molecule genomics. Operating these devices entails imaging stretched DNA, so they provide a straightforward test of theories for confined chains. Remarkably, even the simplest problem of the equilibrium extension of a semiflexible chain in a nanochannel remains controversial; disagreement exists among experiments, theory and computer simulations over how the extension depends on channel width in the transition regimes between the de Gennes and Odijk limits. 

In this work, we used a realistic model for DNA and Monte Carlo simulations to compute the mean span (extension) of DNA confined in nanochannels ranging from the de Gennes regime to the Odjik regime in a high ionic strength buffer.  Different from a previous Monte Carlo study, our results are wholly consistent with a scaling theory proposed recently by Odijk and thus represent, to the best of our knowledge, the first numerical confirmation of the existence of an intermediate regime where the chain forms anisometric blobs of ideal chains. Using a Flory-type approach, we also provide an improved scaling result for the relaxation time in this transition regime. As most genomic devices operate in the transition regime, its analysis is important for both fundamental physics and practical applications in genomics.