Numerical study of linear and circular model DNA chains confined in a slit: metric and topological properties

Advanced Monte Carlo simulations are used to study the effect of nanoslit confinement on metric and topological properties of model DNA chains. We consider both linear and circularized chains with contour lengths in the 1.2–4.8 μm range and slits widths spanning continuously the 50–1250 nm range. The metric scaling predicted by de Gennes’ blob model is shown to hold for both linear and circularized DNA up to the strongest levels of confinement. More notably, the topological properties of the circularized DNA molecules have two major differences compared to three-dimensional confinement. First, the overall knotting probability is nonmonotonic for increasing confinement and can be largely enhanced or suppressed compared to the bulk case by simply varying the slit width. Second, the knot population consists of knots that are far simpler than for three-dimensional confinement. The results suggest that nanoslits could be used in nanofluidic setups to produce DNA rings having simple topologies (including the unknot) or to separate heterogeneous ensembles of DNA rings by knot type.