Optimizing DNA nanotechnology through coarse-grained modeling: a two-footed DNA walker.
DNA has enormous potential as a programmable material for creating artificial nanoscale structures and devices. For more complex systems, however, rational design and optimization can become difficult. We have recently proposed a coarse-grained model of DNA that captures the basic thermodynamic, str...
| Main Authors: | , , , , , |
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| Format: | Journal article |
| Sprog: | English |
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2013
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| _version_ | 1826291578456506368 |
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| author | Ouldridge, T Hoare, R Louis, A Doye, J Bath, J Turberfield, A |
| author_facet | Ouldridge, T Hoare, R Louis, A Doye, J Bath, J Turberfield, A |
| author_sort | Ouldridge, T |
| collection | OXFORD |
| description | DNA has enormous potential as a programmable material for creating artificial nanoscale structures and devices. For more complex systems, however, rational design and optimization can become difficult. We have recently proposed a coarse-grained model of DNA that captures the basic thermodynamic, structural, and mechanical changes associated with the fundamental process in much of DNA nanotechnology, the formation of duplexes from single strands. In this article, we demonstrate that the model can provide powerful insight into the operation of complex nanotechnological systems through a detailed investigation of a two-footed DNA walker that is designed to step along a reusable track, thereby offering the possibility of optimizing the design of such systems. We find that applying moderate tension to the track can have a large influence on the operation of the walker, providing a bias for stepping forward and helping the walker to recover from undesirable overstepped states. Further, we show that the process by which spent fuel detaches from the walker can have a significant impact on the rebinding of the walker to the track, strongly influencing walker efficiency and speed. Finally, using the results of the simulations, we propose a number of modifications to the walker to improve its operation. |
| first_indexed | 2024-03-07T03:01:30Z |
| format | Journal article |
| id | oxford-uuid:b11d1c8d-3ea1-4052-9605-7e49f20b0a8a |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-07T03:01:30Z |
| publishDate | 2013 |
| record_format | dspace |
| spelling | oxford-uuid:b11d1c8d-3ea1-4052-9605-7e49f20b0a8a2022-03-27T04:01:33ZOptimizing DNA nanotechnology through coarse-grained modeling: a two-footed DNA walker.Journal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:b11d1c8d-3ea1-4052-9605-7e49f20b0a8aEnglishSymplectic Elements at Oxford2013Ouldridge, THoare, RLouis, ADoye, JBath, JTurberfield, ADNA has enormous potential as a programmable material for creating artificial nanoscale structures and devices. For more complex systems, however, rational design and optimization can become difficult. We have recently proposed a coarse-grained model of DNA that captures the basic thermodynamic, structural, and mechanical changes associated with the fundamental process in much of DNA nanotechnology, the formation of duplexes from single strands. In this article, we demonstrate that the model can provide powerful insight into the operation of complex nanotechnological systems through a detailed investigation of a two-footed DNA walker that is designed to step along a reusable track, thereby offering the possibility of optimizing the design of such systems. We find that applying moderate tension to the track can have a large influence on the operation of the walker, providing a bias for stepping forward and helping the walker to recover from undesirable overstepped states. Further, we show that the process by which spent fuel detaches from the walker can have a significant impact on the rebinding of the walker to the track, strongly influencing walker efficiency and speed. Finally, using the results of the simulations, we propose a number of modifications to the walker to improve its operation. |
| spellingShingle | Ouldridge, T Hoare, R Louis, A Doye, J Bath, J Turberfield, A Optimizing DNA nanotechnology through coarse-grained modeling: a two-footed DNA walker. |
| title | Optimizing DNA nanotechnology through coarse-grained modeling: a two-footed DNA walker. |
| title_full | Optimizing DNA nanotechnology through coarse-grained modeling: a two-footed DNA walker. |
| title_fullStr | Optimizing DNA nanotechnology through coarse-grained modeling: a two-footed DNA walker. |
| title_full_unstemmed | Optimizing DNA nanotechnology through coarse-grained modeling: a two-footed DNA walker. |
| title_short | Optimizing DNA nanotechnology through coarse-grained modeling: a two-footed DNA walker. |
| title_sort | optimizing dna nanotechnology through coarse grained modeling a two footed dna walker |
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