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Sobey, Thomas L. (2010): Self-assembly of Artificial DNA Nano and Microscale Motifs. Dissertation, LMU München: Faculty of Physics
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Abstract

Nanotechnology attempts to control matter at the nanometer scale so that new types of materials, components and devices for a wide variety of applications can be developed. There are two approaches possible. The first stems from semiconductor technology in which improvements in processing small structures have led to a drastic reduction in the size of electronic components. The inverse approach - which is used in this work - orientates itself around structures based on biological systems, in which highly dynamic nanometer size components assemble themselves. In this thesis it is shown how defined structures with sizes ranging from nanometers to micrometres and made up of DNA molecules can self assemble. Self-assembly has four defining features: structured particles, a suitable environment, a driving force and reversible binding. DNA molecules are relatively stable and can be synthesised with arbitrary sequences of four units, diffuse freely in an aqueous buffer under Brownian motion, and can bind and unbind (using hydrogen bonding) with one another in the practical temperature range between 0 and 100°C. They are thus useful building blocks for self-assembly. A review is provided of some physical properties of DNA, and of self-assembled DNA ‘motifs’ and devices developed to date, along with examples that have been demonstrated here in the laboratory. Such examples include DNA nanotubes, lattices, and ‘origami’ structures. The idea of assembling structures - not by creating and breaking hydrogen bonds using temperature changes - but rather by changing the concentration of small molecules known as denaturants is introduced. The denaturants also form hydrogen bonds and can occupy the binding sites of the DNA molecules. Decreasing the concentration of denaturants frees the binding sites and allows the self-assembly of structures. This is demonstrated with successful motifs, and provides an isothermal assembly technique that allows the use of many temperature-sensitive components in DNA self-assembly. It is shown that self-assembled motifs are useful as templates for nanoscale objects such as fluorescent molecules, which can be set out in defined geometries. Moreover, using newly developed optical super-resolution techniques, such geometries are resolved below the optical diffraction limit, providing the possibility for nanoscale optical calibration standards. And finally the intrinsic stability of three-dimensional structures as compared to two-dimensional structures is investigated, in that the assembly and ‘melting’ of DNA nanotubes is shown to be fundamentally different to that of DNA lattices, with the closed form of the tubes providing a natural and significantly higher stability. This will be useful for designing and building stronger structures in DNA nanotechnology.