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Physical Properties of Single-Sheet DNA Origami Nanotiles

Stammers, Ashley Connor (2018) Physical Properties of Single-Sheet DNA Origami Nanotiles. Integrated PhD and Master thesis, University of Leeds.

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Stammers_AC_Electronic_and_Electrical_Engineering_Physics_PhD_2018.pdf - Final eThesis - complete (pdf)
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Abstract

Central to DNA origami is the need to have oligomeric DNA bind adjacent DNA helices, whose spacing is dependent on the spatial offset between the helices. In square-based origami, this spacing must be an odd-number of half-turns, requiring a non-integer number as B-form DNA has a helical pitch of 10.50 bp. The inability to have non-integer spacings creates a phasing mismatch, leading to curvature of origami. This work explores how cationic concentration and species affect this curvature. Asymmetric single-sheet DNA origami with varying crossover spacings, said to be overwound, planar and underwound, were imaged under bulk aqueous solution with AFM, where the adsorption orientation served as a metric to infer the magnitude and direction of curvature. The combination of these three designs demonstrated how the effective Mg2+ concentration affects both DNA helicity as well as the electrostatic repulsion between the tightly packed helices. Low Mg2+ concentrations caused helix destabilisation; leading to flatter origami, whilst elevated Mg2+ concentrations appeared to shield electrostatic repulsions, causing a decrease in curvature. These results highlight the importance of Mg2+ concentration and its effect on origami curvature. Exposure to UV radiation induced unwinding of DNA through the formation of photoproducts, causing the overwound origami to experience a decrease in adsorption bias whereas the planar and underwound origami experienced an increase in bias. These results aid the idea that the direction of curvature is independent of crossover spacing. The combination of tiles in varying Mg2+ and those exposed to UV radiation served as a baseline to determine the effects that Ba2+ has on the DNA helix. Ba2+ appeared to induce over-winding of the DNA helix, whilst remaining in an overall destabilised state, compared to that of Mg2+. This caused the underwound origami to exhibit more curvature compared to those of the overwound and planar origami.

Item Type: Thesis (Integrated PhD and Master)
Keywords: Atomic Force Microscopy AFM DNA Origami Curvature Barium Magnesium UVC irradiation
Academic Units: The University of Leeds > Faculty of Engineering (Leeds) > School of Electronic & Electrical Engineering (Leeds)
The University of Leeds > Faculty of Maths and Physical Sciences (Leeds) > School of Physics and Astronomy (Leeds)
Depositing User: Mr Ashley Connor Stammers
Date Deposited: 01 Apr 2019 10:20
Last Modified: 01 Apr 2019 10:20
URI: http://etheses.whiterose.ac.uk/id/eprint/23355

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