Diffusion of Knots along DNA Confined in Nanochannels

Abstract

We study the diffusion of knots along relaxed deoxyribonucleic acid (DNA) in nanochannels using a nanofluidic “knot factory” device for knot generation. The apparent scaling exponent for the growth in the ensemble-averaged mean-squared displacement is 0.82 ± 0.01 when accounting for random errors and [0.79, 0.88] when accounting for systematic errors. Both estimates indicate subdiffusion and support a model of self-reptation. These results contradict the prevailing theory for knot diffusion along nanochannel-confined DNA, where knot region breathing is presumed to control knot diffusion in long polymers, but are consistent with previous observations of self-reptation of knots for unconfined DNA under tension.

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