Knot Formation on DNA Pushed Inside Chiral Nanochannels
We performed coarse-grained molecular dynamics simulations of DNA polymers pushed inside infinite open chiral and achiral channels. We investigated the behavior of the polymer metrics in terms of span, monomer distributions and changes of topological state of the polymer in the channels. We also com...
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| Format: | Article |
| Language: | English |
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MDPI AG
2023-10-01
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| Series: | Polymers |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2073-4360/15/20/4185 |
| _version_ | 1797572483676635136 |
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| author | Renáta Rusková Dušan Račko |
| author_facet | Renáta Rusková Dušan Račko |
| author_sort | Renáta Rusková |
| collection | DOAJ |
| description | We performed coarse-grained molecular dynamics simulations of DNA polymers pushed inside infinite open chiral and achiral channels. We investigated the behavior of the polymer metrics in terms of span, monomer distributions and changes of topological state of the polymer in the channels. We also compared the regime of pushing a polymer inside the infinite channel to the case of polymer compression in finite channels of knot factories investigated in earlier works. We observed that the compression in the open channels affects the polymer metrics to different extents in chiral and achiral channels. We also observed that the chiral channels give rise to the formation of equichiral knots with the same handedness as the handedness of the chiral channels. |
| first_indexed | 2024-03-10T20:56:55Z |
| format | Article |
| id | doaj.art-b7368d011ace44dd94d801633cc5992d |
| institution | Directory Open Access Journal |
| issn | 2073-4360 |
| language | English |
| last_indexed | 2024-03-10T20:56:55Z |
| publishDate | 2023-10-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Polymers |
| spelling | doaj.art-b7368d011ace44dd94d801633cc5992d2023-11-19T17:52:26ZengMDPI AGPolymers2073-43602023-10-011520418510.3390/polym15204185Knot Formation on DNA Pushed Inside Chiral NanochannelsRenáta Rusková0Dušan Račko1Polymer Institute of the Slovak Academy of Sciences, Dúbravská cesta 9, 845 41 Bratislava, SlovakiaPolymer Institute of the Slovak Academy of Sciences, Dúbravská cesta 9, 845 41 Bratislava, SlovakiaWe performed coarse-grained molecular dynamics simulations of DNA polymers pushed inside infinite open chiral and achiral channels. We investigated the behavior of the polymer metrics in terms of span, monomer distributions and changes of topological state of the polymer in the channels. We also compared the regime of pushing a polymer inside the infinite channel to the case of polymer compression in finite channels of knot factories investigated in earlier works. We observed that the compression in the open channels affects the polymer metrics to different extents in chiral and achiral channels. We also observed that the chiral channels give rise to the formation of equichiral knots with the same handedness as the handedness of the chiral channels.https://www.mdpi.com/2073-4360/15/20/4185polymerDNAmolecular simulationsnanochannelstopologyknot |
| spellingShingle | Renáta Rusková Dušan Račko Knot Formation on DNA Pushed Inside Chiral Nanochannels Polymers polymer DNA molecular simulations nanochannels topology knot |
| title | Knot Formation on DNA Pushed Inside Chiral Nanochannels |
| title_full | Knot Formation on DNA Pushed Inside Chiral Nanochannels |
| title_fullStr | Knot Formation on DNA Pushed Inside Chiral Nanochannels |
| title_full_unstemmed | Knot Formation on DNA Pushed Inside Chiral Nanochannels |
| title_short | Knot Formation on DNA Pushed Inside Chiral Nanochannels |
| title_sort | knot formation on dna pushed inside chiral nanochannels |
| topic | polymer DNA molecular simulations nanochannels topology knot |
| url | https://www.mdpi.com/2073-4360/15/20/4185 |
| work_keys_str_mv | AT renataruskova knotformationondnapushedinsidechiralnanochannels AT dusanracko knotformationondnapushedinsidechiralnanochannels |