Use this URL to cite or link to this record in EThOS: https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.729995
Title: Dynamic DNA motors and structures
Author: Lucas, Alexandra
ISNI:       0000 0004 6499 7006
Awarding Body: University of Oxford
Current Institution: University of Oxford
Date of Award: 2016
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Abstract:
DNA nanotechnology uses the Watson-Crick base-pairing of DNA to self-assemble structures at the nanoscale. DNA nanomachines are active structures that take energy from the system to drive a programmed motion. In this thesis, a new design for a reversible DNA motor and an automatically regenerating track is presented. Ensemble fluorescence measurements observe motors walking along the same 42nm track three times. A second new motor was designed to allow motors on intersecting tracks to block each other, which can be used to perform logical computation. Multiple design approaches are discussed. The chosen approach showed limited success during ensemble fluorescence measurements. The 'burnt bridges' motor originally introduced by Bath et al. 2005 was also sent down tracks placed along the inside of stacked origami tubes that are able to polymerise to micrometre lengths. Preliminary optical microscopy experiments show promise in using such a system for observing micrometre motor movement. Scaffold-based DNA origami is the technique of folding a long single-stranded DNA strand into a specific shape by adding small staple strands that hold it in place. Extended staple strands can be modified to functionalise the origami surface. In this thesis, the threading of staple extensions through a freely-floating origami tile was observed using single-molecule Förster resonance energy transfer (smFRET). Threading was reduced by bracing the bottom of the extension or by using a multilayered origami. smFRET was also used to investigate the process of staple repair, whereby a missing staple is added to a pre-formed origami missing the staple. This was found to be successful when the staple is single-stranded, and imperfect when partially double-stranded. Finally the idea for a new "DNA cage", a dynamic octahedron called the "Holliday Octahedron", is presented. The octahedron is made of eight strands, one running around each face. Mobile Holliday junctions at each face allow the stands to rotate causing a conformational change.
Supervisor: Turberfield, Andrew Sponsor: Engineering and Physical Sciences Research Council
Qualification Name: Thesis (Ph.D.) Qualification Level: Doctoral
EThOS ID: uk.bl.ethos.729995  DOI: Not available
Keywords: DNA Nanotechnology ; Holliday junction ; DNA structures ; DNA computation ; DNA motor ; DNA origami ; smFRET
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