258219 Mobility of a DNA Molecule Confined in a Nanochannel

Wednesday, October 31, 2012: 2:45 PM
409 (Convention Center )
Douglas R. Tree1, Yanwei Wang2 and Kevin D. Dorfman1, (1)Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN, (2)Polymer Science and Engineering, Soochow University, Suzhou, China

Nanochannels are an ideal platform for studying the basic physics of confined polymers, using DNA as the model polymer. In the case of weak confinement, de Gennes predicted that the hydrodynamic mobility of a confined flexible chain will scale inversely with its extension due to the hydrodynamic interactions inside the blobs of the confined chain. In this presentation, we will show that the de Gennes theory breaks down for DNA in a high ionic strength buffer due to the large ratio between the persistence length (53 nm) and the effective width (4.6 nm) of DNA. We have computed the hydrodynamic mobility using Monte Carlo sampling of the Kirkwood mobility and a numerical solution for the Green's function of the confined chain. We show that there is a broad plateau in which the hydrodynamic mobility is independent of the fractional extension of the chain. Moreover, we directly connect the existence of this plateau to a transition regime for the extension of a semiflexible chain where the fractional extension scales inversely with the channel width. The width of the transition regime depends on the ratio of the persistence length to the effective width, and thus vanishes for flexible chains. For DNA, the latter ratio is so large that this Rouse-like regime is predicted to persist for the entire range of experimentally observed extensions of DNA in a nanochannel.  

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See more of this Session: Bio-Fluid Dynamics
See more of this Group/Topical: Engineering Sciences and Fundamentals