Thesis
The structural properties of DNA origami
- Abstract:
-
In this thesis, we have investigated the suitability of using oxDNA to model DNA origami nanostructures. We used oxDNA to simulate a variety of DNA origami systems, then analysed the results to determine their key structural properties. Specifically, after introducing the area and outlining the procedure to simulate these systems, we report on three case studies that were based on experimental work; a theoretical project in which we designed an auxetic system based on knowledge gathered from the previous chapters, and a collaborative project with an experimental group looking into novel ‘barrel’ structures.
More specifically, the case studies we looked at were previously experimentally assembled DNA structures including a Möbius strip, six and twelve helix bundle kite structures that were connected with linkers of varying lengths, and ball structures containing six-way Holliday junctions. For these case studies, we found that oxDNA was able to replicate well existing experimental data, and therefore provide reliable insight into the subtleties of these systems that would be hard to elucidate using experimental techniques. As such, we were then able to design an auxetic-style system (in this case meaning a system which expands in two directions simultaneously) and predict its behaviour with confidence. Lastly, we assisted an experimental group by simulating and analysing a series of barrel structures to provide detailed information about these systems.
Looking to the future, we hope that the work outlined here will further encourage other groups, particularly experimental ones, to utilise oxDNA in their own work on DNA origami by both providing evidence of oxDNA’s utility, as well as sufficient guidance and assistance to get started.
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Authors
Contributors
- Institution:
- University of Oxford
- Division:
- MPLS
- Department:
- Chemistry
- Role:
- Supervisor
- ORCID:
- 0000-0002-2226-9524
- Funder identifier:
- http://dx.doi.org/10.13039/501100000266
- Funding agency for:
- Fowler, H
- Grant:
- EP/L015722/1
- DOI:
- Type of award:
- DPhil
- Level of award:
- Doctoral
- Awarding institution:
- University of Oxford
- Language:
-
English
- Keywords:
- Subjects:
- Deposit date:
-
2023-06-25
Terms of use
- Copyright holder:
- Fowler, H
- Copyright date:
- 2022
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