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.
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15 May 2023
Research Article|
May 15 2023
Diffusion of knots in nanochannel-confined DNA molecules
Runfang Mao
;
Runfang Mao
(Data curation, Formal analysis, Investigation, Methodology, Software, Validation, Visualization, Writing – original draft)
Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities
, 421 Washington Ave. SE, Minneapolis, Minnesota 55455, USA
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Kevin D. Dorfman
Kevin D. Dorfman
a)
(Conceptualization, Formal analysis, Funding acquisition, Project administration, Resources, Supervision, Validation, Writing – review & editing)
Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities
, 421 Washington Ave. SE, Minneapolis, Minnesota 55455, USA
a)Author to whom correspondence should be addressed: dorfman@umn.edu
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a)Author to whom correspondence should be addressed: dorfman@umn.edu
J. Chem. Phys. 158, 194901 (2023)
Article history
Received:
March 17 2023
Accepted:
May 03 2023
Citation
Runfang Mao, Kevin D. Dorfman; Diffusion of knots in nanochannel-confined DNA molecules. J. Chem. Phys. 15 May 2023; 158 (19): 194901. https://doi.org/10.1063/5.0151025
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