1. Knot formation of dsDNA pushed inside a nanochannel
- Author
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Rothörl, Jan, Wettermann, Sarah, Virnau, Peter, and Bhattacharya, Aniket
- Subjects
Quantitative Biology::Biomolecules ,Multidisciplinary ,530 Physics ,food and beverages ,FOS: Physical sciences ,DNA ,Condensed Matter - Soft Condensed Matter ,530 Physik ,Mathematics::Geometric Topology ,Nanopores ,surgical procedures, operative ,stomatognathic system ,Biological Physics (physics.bio-ph) ,Pressure ,Soft Condensed Matter (cond-mat.soft) ,Nanotechnology ,Physics - Biological Physics - 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., Comment: 5 pages, 3 figures
- Published
- 2021