Elucidating the Mechanical Energy for Cyclization of a DNA Origami Tile
DNA origami has emerged as a versatile method to synthesize nanostructures with high precision. This bottom-up self-assembly approach can produce not only complex static architectures, but also dynamic reconfigurable structures with tunable properties. While DNA origami has been explored increasingl...
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| Format: | Article |
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Multidisciplinary Digital Publishing Institute
2021
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| Online Access: | https://hdl.handle.net/1721.1/131343 |
| _version_ | 1826214727766769664 |
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| author | Li, Ruixin Chen, Haorong Lee, Hyeongwoon Choi, Jong Hyun |
| author2 | Massachusetts Institute of Technology. Department of Biological Engineering |
| author_facet | Massachusetts Institute of Technology. Department of Biological Engineering Li, Ruixin Chen, Haorong Lee, Hyeongwoon Choi, Jong Hyun |
| author_sort | Li, Ruixin |
| collection | MIT |
| description | DNA origami has emerged as a versatile method to synthesize nanostructures with high precision. This bottom-up self-assembly approach can produce not only complex static architectures, but also dynamic reconfigurable structures with tunable properties. While DNA origami has been explored increasingly for diverse applications, such as biomedical and biophysical tools, related mechanics are also under active investigation. Here we studied the structural properties of DNA origami and investigated the energy needed to deform the DNA structures. We used a single-layer rectangular DNA origami tile as a model system and studied its cyclization process. This origami tile was designed with an inherent twist by placing crossovers every 16 base-pairs (bp), corresponding to a helical pitch of 10.67 bp/turn, which is slightly different from that of native B-form DNA (~10.5 bp/turn). We used molecular dynamics (MD) simulations based on a coarse-grained model on an open-source computational platform, oxDNA. We calculated the energies needed to overcome the initial curvature and induce mechanical deformation by applying linear spring forces. We found that the initial curvature may be overcome gradually during cyclization and a total of ~33.1 kcal/mol is required to complete the deformation. These results provide insights into the DNA origami mechanics and should be useful for diverse applications such as adaptive reconfiguration and energy absorption. |
| first_indexed | 2024-09-23T16:10:13Z |
| format | Article |
| id | mit-1721.1/131343 |
| institution | Massachusetts Institute of Technology |
| last_indexed | 2024-09-23T16:10:13Z |
| publishDate | 2021 |
| publisher | Multidisciplinary Digital Publishing Institute |
| record_format | dspace |
| spelling | mit-1721.1/1313432023-01-11T17:32:03Z Elucidating the Mechanical Energy for Cyclization of a DNA Origami Tile Li, Ruixin Chen, Haorong Lee, Hyeongwoon Choi, Jong Hyun Massachusetts Institute of Technology. Department of Biological Engineering DNA origami has emerged as a versatile method to synthesize nanostructures with high precision. This bottom-up self-assembly approach can produce not only complex static architectures, but also dynamic reconfigurable structures with tunable properties. While DNA origami has been explored increasingly for diverse applications, such as biomedical and biophysical tools, related mechanics are also under active investigation. Here we studied the structural properties of DNA origami and investigated the energy needed to deform the DNA structures. We used a single-layer rectangular DNA origami tile as a model system and studied its cyclization process. This origami tile was designed with an inherent twist by placing crossovers every 16 base-pairs (bp), corresponding to a helical pitch of 10.67 bp/turn, which is slightly different from that of native B-form DNA (~10.5 bp/turn). We used molecular dynamics (MD) simulations based on a coarse-grained model on an open-source computational platform, oxDNA. We calculated the energies needed to overcome the initial curvature and induce mechanical deformation by applying linear spring forces. We found that the initial curvature may be overcome gradually during cyclization and a total of ~33.1 kcal/mol is required to complete the deformation. These results provide insights into the DNA origami mechanics and should be useful for diverse applications such as adaptive reconfiguration and energy absorption. 2021-09-20T14:16:18Z 2021-09-20T14:16:18Z 2021-03-06 2021-03-12T14:42:27Z Article http://purl.org/eprint/type/JournalArticle https://hdl.handle.net/1721.1/131343 Applied Sciences 11 (5): 2357 (2021) PUBLISHER_CC http://dx.doi.org/10.3390/app11052357 Creative Commons Attribution https://creativecommons.org/licenses/by/4.0/ application/pdf Multidisciplinary Digital Publishing Institute Multidisciplinary Digital Publishing Institute |
| spellingShingle | Li, Ruixin Chen, Haorong Lee, Hyeongwoon Choi, Jong Hyun Elucidating the Mechanical Energy for Cyclization of a DNA Origami Tile |
| title | Elucidating the Mechanical Energy for Cyclization of a DNA Origami Tile |
| title_full | Elucidating the Mechanical Energy for Cyclization of a DNA Origami Tile |
| title_fullStr | Elucidating the Mechanical Energy for Cyclization of a DNA Origami Tile |
| title_full_unstemmed | Elucidating the Mechanical Energy for Cyclization of a DNA Origami Tile |
| title_short | Elucidating the Mechanical Energy for Cyclization of a DNA Origami Tile |
| title_sort | elucidating the mechanical energy for cyclization of a dna origami tile |
| url | https://hdl.handle.net/1721.1/131343 |
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