Authors:	Rothörl, Jan Wettermann, Sarah Virnau, Peter Bhattacharya, Aniket
Title:	Knot formation of dsDNA pushed inside a nanochannel
Online publication date:	7-Nov-2022
Year of first publication:	2022
Language:	english
Abstract:	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.
DDC:	530 Physik 530 Physics
Institution:	Johannes Gutenberg-Universität Mainz
Department:	FB 08 Physik, Mathematik u. Informatik
Place:	Mainz
ROR:	https://ror.org/023b0x485
DOI:	http://doi.org/10.25358/openscience-8175
Version:	Published version
Publication type:	Zeitschriftenaufsatz
Document type specification:	Scientific article
License:	CC BY
Information on rights of use:	https://creativecommons.org/licenses/by/4.0/
Journal:	Scientific reports 12
Pages or article number:	5342
Publisher:	Springer Nature
Publisher place:	London
Issue date:	2022
ISSN:	2045-2322
Publisher DOI:	10.1038/s41598-022-09242-5
Appears in collections:	DFG-491381577-G