This thesis investigates ways in which a nanoscale production line may be built from synthetic DNA components. One property of a production line is motion, the coordinated movement of components, in this case strands of DNA, between specific locations. Another property is the ability to assemble a product, where smaller molecular building blocks are attached to D A and react when brought together by the DNA assembly line. An important fea- ture of either task is the ability of the mechanism to proceed with minimum user interaction: it is preferable that the assembly line be autonomous. The challenges and design principles of molecular machines working in nano- scale environments are first considered. Previous studies demonstrating the use of synthetic DNA not only as a self-assembling material to build nano- structures, but also to coordinate motion, are summarized. All DNA nano- machines that operate through the exchange of DNA strands are coordinated by toeholds. A 'split toehold', one that combines two smaller toeholds on distal sections of DNA held in proximity, is proposed as a way to allow a single cargo strand to interact with many different components. A molecular motor is then developed that transports a cargo between track locations. The fuel strands are hairpins, that carry instructions directing the cargo to the next anchorage. The switching of cargo direction in response to the chemical environment is also investigated. Two mechanisms that may allow the autonomous assembly of components are investigated, one of which is demonstrated using DNA-linked cleavable molecular building blocks. Further extensions to the mechanism are investi- gated, for example, the ability to use the DNA mechanism itself as a barcode containing information on the order of assembled ingredients.
| Identifer | oai:union.ndltd.org:bl.uk/oai:ethos.bl.uk:572658 |
| Date | January 2011 |
| Creators | Muscat, Richard A. |
| Contributors | Turberfield, Andrew |
| Publisher | University of Oxford |
| Source Sets | Ethos UK |
| Detected Language | English |
| Type | Electronic Thesis or Dissertation |
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