Tuning the topology of a two-dimensional catenated DNA network
Molecular topology of polymers plays a key role in determining their physical properties. We studied herein the topological effects on the static and dynamic properties of a 2D catenated network of DNA rings called a kinetoplast. Restriction enzymes that cleave DNA at sequence-specific sites are use...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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American Physical Society
2025
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| Online Access: | https://hdl.handle.net/1721.1/158281 |
| _version_ | 1826216643496247296 |
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| author | Yadav, Indresh Al Sulaiman, Dana Doyle, Patrick S |
| author2 | Massachusetts Institute of Technology. Department of Chemical Engineering |
| author_facet | Massachusetts Institute of Technology. Department of Chemical Engineering Yadav, Indresh Al Sulaiman, Dana Doyle, Patrick S |
| author_sort | Yadav, Indresh |
| collection | MIT |
| description | Molecular topology of polymers plays a key role in determining their physical properties. We studied herein the topological effects on the static and dynamic properties of a 2D catenated network of DNA rings called a kinetoplast. Restriction enzymes that cleave DNA at sequence-specific sites are used to selectively cut and remove rings from the network and hence tune the molecular topology while maintaining overall structural integrity. We find that topology has minimal effects over the spatial extension of the 2D network; however, it significantly affects the relaxation behavior. The shape fluctuations of the network are governed by two distinct characteristic time scales attributed to the thermal fluctuations and confinement of the network. The relationship between the time constant of thermal relaxation and the amplitude of anisotropy fluctuations yields a universal scaling. Interestingly, this scaling is independent of the detailed arrangements of rings and/or perforation within the catenated networks. This study provides a route to tune the elastic properties of 2D catenated DNA networks and other polymeric materials by modifying the underlying topology in a rational and highly controllable manner. |
| first_indexed | 2025-03-10T14:11:49Z |
| format | Article |
| id | mit-1721.1/158281 |
| institution | Massachusetts Institute of Technology |
| language | English |
| last_indexed | 2025-03-10T14:11:49Z |
| publishDate | 2025 |
| publisher | American Physical Society |
| record_format | dspace |
| spelling | mit-1721.1/1582812025-02-28T21:41:45Z Tuning the topology of a two-dimensional catenated DNA network Yadav, Indresh Al Sulaiman, Dana Doyle, Patrick S Massachusetts Institute of Technology. Department of Chemical Engineering Molecular topology of polymers plays a key role in determining their physical properties. We studied herein the topological effects on the static and dynamic properties of a 2D catenated network of DNA rings called a kinetoplast. Restriction enzymes that cleave DNA at sequence-specific sites are used to selectively cut and remove rings from the network and hence tune the molecular topology while maintaining overall structural integrity. We find that topology has minimal effects over the spatial extension of the 2D network; however, it significantly affects the relaxation behavior. The shape fluctuations of the network are governed by two distinct characteristic time scales attributed to the thermal fluctuations and confinement of the network. The relationship between the time constant of thermal relaxation and the amplitude of anisotropy fluctuations yields a universal scaling. Interestingly, this scaling is independent of the detailed arrangements of rings and/or perforation within the catenated networks. This study provides a route to tune the elastic properties of 2D catenated DNA networks and other polymeric materials by modifying the underlying topology in a rational and highly controllable manner. 2025-02-28T21:41:43Z 2025-02-28T21:41:43Z 2023 2025-02-28T21:34:27Z Article http://purl.org/eprint/type/JournalArticle https://hdl.handle.net/1721.1/158281 Yadav, Indresh, Al Sulaiman, Dana and Doyle, Patrick S. 2023. "Tuning the topology of a two-dimensional catenated DNA network." Physical Review Research, 5 (1). en 10.1103/physrevresearch.5.013141 Physical Review Research Creative Commons Attribution https://creativecommons.org/licenses/by/4.0/ application/pdf American Physical Society American Physical Society |
| spellingShingle | Yadav, Indresh Al Sulaiman, Dana Doyle, Patrick S Tuning the topology of a two-dimensional catenated DNA network |
| title | Tuning the topology of a two-dimensional catenated DNA network |
| title_full | Tuning the topology of a two-dimensional catenated DNA network |
| title_fullStr | Tuning the topology of a two-dimensional catenated DNA network |
| title_full_unstemmed | Tuning the topology of a two-dimensional catenated DNA network |
| title_short | Tuning the topology of a two-dimensional catenated DNA network |
| title_sort | tuning the topology of a two dimensional catenated dna network |
| url | https://hdl.handle.net/1721.1/158281 |
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