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.
Bibliographical noteFunding Information:
The authors thank Dr. Hui-Min Chuang for her assistance in device fabrication protocols. This work was supported by NIH (R01-HG006851) and NSF (CBET-2016879). Device fabrication was conducted in the Minnesota Nano Center, which is supported by the National Science Foundation through the National Nano Coordinated Infrastructure Network (NNCI) under Award Number ECCS-1542202.