DNA based networks, nanostructures, and meta-stable states

Doctoral Thesis


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University of Cape Town

Nanotechnology is defined as the technology that allows to fabricate nanoscale materials and manipulate them at the molecular or atomic level. Non-biotechnology is one of the sub-disciplines of nanotechnology. Materials used for nano-biotechnology are macromolecular materials found in nature with specific mechanical and biological functions. One of the most important materials is deoxyribonucleic acid (DNA). DNA has several unique properties that make it a good candidate for nanotechnology research. The primary aim of this research is to use DNA three-way junctions as building blocks and to assemble them into a huge DNA networks through self assembly followed by DNA ligation. The second step aims of assembling six DNA three-way junctions with different sticky end sequences to from an opto-mechanical hexagonal DNA nano-switch. The switching mechanism in the righ is based on the conformational change of B- to Z- DNA. This change is influenced by the environmental cation concentrations. The third approach presented here aims to create meta-stable DNA nanostructures based on a DNA hairpin loop that can mimic the enzyme-substrate binding mechanism. This mechanism is demonstrated using a "strand displacement strategy" (SDS). Lastly, we employed a novel way of organizing hairpin loop DNA structures based on the orientation of consecutive hairpin loop DNA structures "on top" of one another.

Includes bibliographical references (leaves 162-170).