Knotting and Unknotting Dynamics of DNA Strands in Nanochannels

Confinement of dsDNA in nanochannels can enhance or suppress altogether the strand’s knotting probability, affecting their metric, mechanical properties and interfering with the elongation process in nanofuidics devices. We characterize, through Langevin dynamic simulations, how knottedness arise from the internal dynamics of the chain, recovering the well characterized equilibrium knotting probability. Different channel widths are considered, covering various metric scaling regimes from 50 to 300 nm \footnote{C. Micheletti and E. Orlandini. \textbf{ACS Macro Lett} 3.9 (2014): 876-880.}, and different DNA lengths, from 1.2 to 4.8 nm \footnote{A. Suma, E. Orlandini and C. Micheletti. \textbf{J. Phys. Condens. Matter} 27.35 (2015): 354102.}. We explain the interplay between knot and unknot lifetimes and the channel and DNA parameters, relating these quantities to the equilibrium knotting probability. We show the basic knotting mechanism, which involves deep looping and back-foldings of the chain ends. The results can aid the design of nanochannels capable of harnessing the self-knotting dynamics to quench or relax the DNA topological state as desired.