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Title: Folding pathways of DNA nanostructures
Author: Young, Katherine Gwyneth
Awarding Body: University of Oxford
Current Institution: University of Oxford
Date of Award: 2018
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DNA origami is a robust technique for the production of DNA whereby a long scaffold strand is folded through interactions with many short staple strands. This thesis describes my work on two DNA origami-based systems. One is an origami tile whose folding can be kinetically-controlled through the use of `helper strands', which are designed to bind to the scaffold. This allows the tile to be folded rapidly at temperatures below the tile melting temperature, which is not otherwise possible due to the formation and persistence of off-target staple-template interactions at such temperatures. Omission of selected helpers changes the folding pathway of the tile; this may allow the use of helper strands to `prime' a template to preferentially fold with a specific staple set in a mixture of different staple sets. The second system is a novel `origami-like' structure in which the equivalent of the scaffold and staples are both double-stranded structures which interact through DNA T-motifs. This differs from conventional origami in that: a) binding domain sequences are reused, and b) the interactions which govern folding (T-motifs) are less stable than the staple-template hybridisations used in conventional origami. The structure I designed uses only four unique binding domains (seven copies of each) and two types of `linker' (equivalent to staples), which means there are a large number of potential structures which could form. Despite this, folding of the target structure was seen at room temperature, suggesting that off-target interactions can be reversed at these temperatures to allow the structure to reach its minimum free energy. Changing the identity of only one of the linkers results in folding of a different target structure. These `T-motif origami' structures can be used to investigate the minimum number of unique binding domains required to specify a structure, and for applications which require reconfigurability. Both systems were characterised using gel electrophoresis and AFM imaging.
Supervisor: Turberfield, Andrew ; Bath, Jonathan Sponsor: Engineering and Physical Sciences Research Council
Qualification Name: Thesis (Ph.D.) Qualification Level: Doctoral
EThOS ID:  DOI: Not available