Metastable Tight Knots in Semiflexible Chains
Knotted structures can spontaneously occur in polymers such as DNA and proteins, and the formation of knots affects biological functions, mechanical strength and rheological properties. In this work, we calculate the equilibrium size distribution of trefoil knots in linear DNA using off-lattice simu...
| Main Authors: | , , |
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| Other Authors: | |
| Format: | Article |
| Language: | en_US |
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American Chemical Society (ACS)
2017
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| Online Access: | http://hdl.handle.net/1721.1/107211 https://orcid.org/0000-0003-1687-4522 |
| _version_ | 1826214941192880128 |
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| author | Dai, Liang Renner, Christopher Benjamin Doyle, Patrick S |
| author2 | Massachusetts Institute of Technology. Department of Chemical Engineering |
| author_facet | Massachusetts Institute of Technology. Department of Chemical Engineering Dai, Liang Renner, Christopher Benjamin Doyle, Patrick S |
| author_sort | Dai, Liang |
| collection | MIT |
| description | Knotted structures can spontaneously occur in polymers such as DNA and proteins, and the formation of knots affects biological functions, mechanical strength and rheological properties. In this work, we calculate the equilibrium size distribution of trefoil knots in linear DNA using off-lattice simulations. We observe metastable knots on DNA, as predicted by Grosberg and Rabin. Furthermore, we extend their theory to incorporate the finite width of chains and show an agreement between our simulations and the modified theory for real chains. Our results suggest localized knots spontaneously occur in long DNA and the contour length in the knot ranges from 600 to 1800 nm. |
| first_indexed | 2024-09-23T16:13:59Z |
| format | Article |
| id | mit-1721.1/107211 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T16:13:59Z |
| publishDate | 2017 |
| publisher | American Chemical Society (ACS) |
| record_format | dspace |
| spelling | mit-1721.1/1072112022-10-02T07:10:15Z Metastable Tight Knots in Semiflexible Chains Dai, Liang Renner, Christopher Benjamin Doyle, Patrick S Massachusetts Institute of Technology. Department of Chemical Engineering Renner, Christopher Benjamin Doyle, Patrick S Knotted structures can spontaneously occur in polymers such as DNA and proteins, and the formation of knots affects biological functions, mechanical strength and rheological properties. In this work, we calculate the equilibrium size distribution of trefoil knots in linear DNA using off-lattice simulations. We observe metastable knots on DNA, as predicted by Grosberg and Rabin. Furthermore, we extend their theory to incorporate the finite width of chains and show an agreement between our simulations and the modified theory for real chains. Our results suggest localized knots spontaneously occur in long DNA and the contour length in the knot ranges from 600 to 1800 nm. National Science Foundation (U.S.) (NSF Grant No. 1335938) Singapore. National Research Foundation Singapore-MIT Alliance for Research and Technology (SMART) 2017-03-07T16:27:13Z 2017-03-07T16:27:13Z 2014-08 2014-08 Article http://purl.org/eprint/type/JournalArticle 0024-9297 1520-5835 http://hdl.handle.net/1721.1/107211 Dai, Liang, C. Benjamin Renner, and Patrick S. Doyle. “Metastable Tight Knots in Semiflexible Chains.” Macromolecules 47, no. 17 (September 9, 2014): 6135–6140. https://orcid.org/0000-0003-1687-4522 en_US http://dx.doi.org/10.1021/ma501585x Macromolecules Article is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use. application/pdf American Chemical Society (ACS) MIT Web Domain |
| spellingShingle | Dai, Liang Renner, Christopher Benjamin Doyle, Patrick S Metastable Tight Knots in Semiflexible Chains |
| title | Metastable Tight Knots in Semiflexible Chains |
| title_full | Metastable Tight Knots in Semiflexible Chains |
| title_fullStr | Metastable Tight Knots in Semiflexible Chains |
| title_full_unstemmed | Metastable Tight Knots in Semiflexible Chains |
| title_short | Metastable Tight Knots in Semiflexible Chains |
| title_sort | metastable tight knots in semiflexible chains |
| url | http://hdl.handle.net/1721.1/107211 https://orcid.org/0000-0003-1687-4522 |
| work_keys_str_mv | AT dailiang metastabletightknotsinsemiflexiblechains AT rennerchristopherbenjamin metastabletightknotsinsemiflexiblechains AT doylepatricks metastabletightknotsinsemiflexiblechains |