Knot Formation on DNA Pushed Inside Chiral Nanochannels

Abstract

We performed coarse-grained molecular dynamics simulations of DNA polymers pushed inside infinite open chiral and achiral channels. We investigated the behavior of the polymer metrics in terms of span, monomer distributions and changes of topological state of the polymer in the channels. We also compared the regime of pushing a polymer inside the infinite channel to the case of polymer compression in finite channels of knot factories investigated in earlier works. We observed that the compression in the open channels affects the polymer metrics to different extents in chiral and achiral channels. We also observed that the chiral channels give rise to the formation of equichiral knots with the same handedness as the handedness of the chiral channels.

Polymer Physics: From Theory to Experimental Applications

“…Interestingly, the results highlighted that the speed at which the suspension becomes well distributed is almost independent of applying heat both before and during the process. Rusková et al [ 3 ] performed coarse-grained molecular dynamics simulations of DNA polymers pushed inside infinite open chiral and achiral channels. They investigated the behavior of the polymer metrics in terms of span, monomer distributions, and changes in the topological state of the polymer in the channels.…”