Knot formation of dsDNA pushed inside a nanochannel

Recent experiments demonstrated that knots in single molecule dsDNA can be formed by compression in a nanochannel. In this manuscript, 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.

Automated summary

Recent experiments have shown that knots can be formed in single molecule dsDNA by compression in a nanochannel. In this study, we conducted a compression experiment in silico to elucidate the underlying molecular mechanisms. The probability of knot formation was found to be a non-monotonic function of the persistence length and could be significantly enhanced by increasing the piston speed. Under compression, knots were abundant and delocalized, resulting from a backfolding mechanism that led to the emergence of chain-spanning loops. In contrast, knots were less frequent and weakly localized in equilibrium. Our in silico study provides insights into the formation, origin, and control of DNA knots in nanopores.