Knot formation of dsDNA pushed inside a nanochannel

TL;DR

This study uses computer simulations to explore how DNA knots form under compression in nanochannels, revealing factors that influence knot probability and localization, which aids understanding of DNA behavior in nanopores.

Contribution

It provides the first detailed molecular mechanism insights into DNA knot formation under compression in nanochannels through in silico experiments.

Findings

Knot formation probability varies non-monotonically with persistence length.

Increasing piston speed significantly enhances knot formation.

Knots are more abundant and delocalized under compression than at equilibrium.

Abstract

Recent experiments demonstrated that knots in single DNA strands can be formed by hydrodynamic compression in a nanochannel. In this letter, we further elucidate the underlying molecular mechanisms by carrying out a compression experiment in silico, where an equilibrated coarse-grained double-stranded DNA confined in a square channel is pushed by a piston. The probability of forming knots is a non-monotonic function of the persistence length and can be enhanced significantly by increasing the piston speed. Under compression, knots are abundant and delocalized due to a backfolding mechanism from which chain-spanning loops emerge, while knots are less frequent and only weakly localized in equilibrium. Our in silico study thus provides insights into the formation, origin and control of DNA knots in nanopores.