Thesis
Design and modular self-assembly of nanostructures
- Abstract:
-
As nucleic acid nanostructures grow larger and more complex, new tools and methods are needed to facilitate their design. DNA origami structures, for example, are limited by the lengths of their scaffolds but larger assemblies can be bound together by interactions between multiple components. This thesis presents two projects, each approaching the design of such modular structures at a different level of abstraction.
Project 1 presents the polycube self-assembly model, where building blocks assemble stochastically using bindings between complementary patches. The assembly of both 2D polyominoes, as well as 3D polycubes, is considered. First, the mapping between input rules (defining the set of available species) and output shapes is investigated, revealing a clear bias toward low--complexity structures. Frequent shapes also tend to be highly modular and symmetric. Secondly, the reversed mapping is explored, presenting a method to find the minimal rule that assembles a specified output shape. Differences in assembly kinetics between possible solutions are investigated using patchy particle simulations, showing that minimal rules can assemble as well as fully addressable rules.
Project 2 presents a more detailed approach to the design of modular structures and individual modules: the oxView toolkit for the design, analysis, and visualisation of DNA, RNA and protein nanostructures. While many other design tools exist, oxView makes it easy to import and connect their designs into complete assemblies. Furthermore, oxView allows for free-form editing and rigid-body manipulation. Designs can then be interactively simulated using the oxDNA model, providing a more intuitive understanding of the resulting dynamics.
In conclusion, the design of self-assembling nucleic acid nanostructures has been investigated on both an abstract and a more detailed level. The presented projects have resulted in tools and methods for creating, simulating and analysing modular structures with minimal complexity, potentially containing building blocks created in multiple design software.
Actions
Authors
Contributors
- Institution:
- University of Oxford
- Division:
- MPLS
- Department:
- Physics
- Role:
- Supervisor
- ORCID:
- 0000-0002-3876-0190
- Institution:
- University of Oxford
- Division:
- MPLS
- Department:
- Physics
- Role:
- Supervisor
- ORCID:
- 0000-0002-8438-910X
- Institution:
- University of Oxford
- Division:
- MPLS
- Department:
- Computer Science
- Role:
- Examiner
- ORCID:
- 0000-0002-8705-8488
- Institution:
- University of Bergen
- Role:
- Examiner
- Funder identifier:
- http://dx.doi.org/10.13039/501100000780
- Grant:
- 765703
- Programme:
- DNA-robotics. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 765703
- DOI:
- Type of award:
- DPhil
- Level of award:
- Doctoral
- Awarding institution:
- University of Oxford
- Language:
-
English
- Keywords:
- Subjects:
- Deposit date:
-
2023-02-16
Terms of use
- Copyright holder:
- Bohlin, J
- Copyright date:
- 2022
If you are the owner of this record, you can report an update to it here: Report update to this record