Diffusion of knots in nanochannel-confined DNA molecules

Runfang Mao, Kevin D. Dorfman

Research output: Contribution to journalArticlepeer-review

1 Scopus citations

Abstract

We used Langevin dynamics simulations without hydrodynamic interactions to probe knot diffusion mechanisms and the time scales governing the evolution and the spontaneous untying of trefoil knots in nanochannel-confined DNA molecules in the extended de Gennes regime. The knot untying follows an “opening up process,” wherein the initially tight knot continues growing and fluctuating in size as it moves toward the end of the DNA molecule before its annihilation at the chain end. The mean knot size increases significantly and sub-linearly with increasing chain contour length. The knot diffusion in nanochannel-confined DNA molecules is subdiffusive, with the unknotting time scaling with chain contour length with an exponent of 2.64 ± 0.23 to within a 95% confidence interval. The scaling exponent for the mean unknotting time vs chain contour length, along with visual inspection of the knot conformations, suggests that the knot diffusion mechanism is a combination of self-reptation and knot region breathing for the simulated parameters.

Original languageEnglish (US)
Article number194901
JournalJournal of Chemical Physics
Volume158
Issue number19
DOIs
StatePublished - May 21 2023

Bibliographical note

Funding Information:
This work was supported by the National Science Foundation through Award No. CBET-2016879. Computational resources were provided by the Minnesota Supercomputing Institute.

Funding Information:
This work was supported by the National Science Foundation through Award No. CBET-2016879. Computational resources were provided by the Minnesota Supercomputing Institute.

Publisher Copyright:
© 2023 Author(s).

PubMed: MeSH publication types

  • Journal Article

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