Entropic depletion of DNA in triangular nanochannels |
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Authors: | Wesley F Reinhart Douglas R Tree Kevin D Dorfman |
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Institution: | Department of Chemical Engineering and Materials Science, University of Minnesota–Twin Cities, 421 Washington Ave. SE, Minneapolis, Minnesota 55455, USA |
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Abstract: | Using Monte Carlo simulations of a touching-bead model of double-stranded DNA, we show that DNA extension is enhanced in isosceles triangular nanochannels (relative to a circular nanochannel of the same effective size) due to entropic depletion in the channel corners. The extent of the enhanced extension depends non-monotonically on both the accessible area of the nanochannel and the apex angle of the triangle. We also develop a metric to quantify the extent of entropic depletion, thereby collapsing the extension data for circular, square, and various triangular nanochannels onto a single master curve for channel sizes in the transition between the Odijk and de Gennes regimes. |
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