Dynamics of Double-Knotted DNA Molecules under Nanochannel Confinement

Langevin dynamics simulations of double-knotted DNA molecules in a nanochannel reveal that the interactions between the two knots differ with the degree of channel confinement. In relatively wide channels, the two knots can intertwine with each other, forming a persistently intertwined knot. Moreover, the two knots can pass through each other in large channels. In contrast, for small channel sizes, the knots tend to remain separated, and their crossing is inhibited. The change in knot–knot interactions as the channel size decreases is rationalized through an analysis of the magnitude of the transverse fluctuations, which must be large enough to allow one knot to swell to accommodate the intertwined state.