Knot formation of dsDNA pushed inside a nanochannel
| dc.contributor.author | Rothörl, Jan | |
| dc.contributor.author | Wettermann, Sarah | |
| dc.contributor.author | Virnau, Peter | |
| dc.contributor.author | Bhattacharya, Aniket | |
| dc.date.accessioned | 2022-11-07T11:02:05Z | |
| dc.date.available | 2022-11-07T11:02:05Z | |
| dc.date.issued | 2022 | |
| dc.description.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. | en_GB |
| dc.description.sponsorship | Gefördert durch die Deutsche Forschungsgemeinschaft (DFG) - Projektnummer 491381577 | de |
| dc.identifier.doi | http://doi.org/10.25358/openscience-8175 | |
| dc.identifier.uri | https://openscience.ub.uni-mainz.de/handle/20.500.12030/8190 | |
| dc.language.iso | eng | de |
| dc.rights | CC-BY-4.0 | * |
| dc.rights.uri | https://creativecommons.org/licenses/by/4.0/ | * |
| dc.subject.ddc | 530 Physik | de_DE |
| dc.subject.ddc | 530 Physics | en_GB |
| dc.title | Knot formation of dsDNA pushed inside a nanochannel | en_GB |
| dc.type | Zeitschriftenaufsatz | de |
| jgu.journal.title | Scientific reports | de |
| jgu.journal.volume | 12 | de |
| jgu.organisation.department | FB 08 Physik, Mathematik u. Informatik | de |
| jgu.organisation.name | Johannes Gutenberg-Universität Mainz | |
| jgu.organisation.number | 7940 | |
| jgu.organisation.place | Mainz | |
| jgu.organisation.ror | https://ror.org/023b0x485 | |
| jgu.pages.alternative | 5342 | de |
| jgu.publisher.doi | 10.1038/s41598-022-09242-5 | de |
| jgu.publisher.issn | 2045-2322 | de |
| jgu.publisher.name | Springer Nature | de |
| jgu.publisher.place | London | de |
| jgu.publisher.year | 2022 | |
| jgu.rights.accessrights | openAccess | |
| jgu.subject.ddccode | 530 | de |
| jgu.subject.dfg | Naturwissenschaften | de |
| jgu.type.contenttype | Scientific article | de |
| jgu.type.dinitype | Article | en_GB |
| jgu.type.resource | Text | de |
| jgu.type.version | Published version | de |