Construction And Characterization Of DNA Origami Structures Used As Templates For Assembly Of Gold Nanoparticles

This dissertation is about using DNA origami to organize matter at the nanoscale. There are several approaches that are used to organize matter at this scale. These organizational methods are mainly classified into two groups:Top down and bottom up approaches. In the top down approach the bulk material is reduced chip by chip to the nanoscale material. The bottom up approach which is the reverse of the top down approach builds the bulk material from nanoscale materials. There are several methods used to build the nanoscale materials from the bulk which include e-beam lithography, AFM manipulation, focused ion beam milling, and direct laser writing. There are problems associated with these methods in reducing the bulk materials to the nano level. Bottom up approaches can make use of appropriate methods to have control over size and geometry of designed objects. Biomaterials are effective in organizing matter at the nanoscale. These biomaterials include biotin-streptavidin, antigen-antibodies, peptides, proteins, and DNA.For about3decades now, DNA-based nanotechnology has been undergoing development generally as an assembly method for nano-structured materials. The DNA origami method pioneered by Rothemund paved the way for the formation of3D structures using DNA self assembly. The origami approach makes use of a long scaffold strand as the input to self assembles with a few hundred staple strands into desired shapes. In this work, we investigate the formation of two novel3D DNA origami structures designed using the caDNAno software. Our first structure which we shall call "roller" is a double nanotube with one nanotube wound around the other in the middle and the structure is shaped like a roller. Our second novel3D DNA origami structure is shaped like a cross. These two structures are thoroughly characterized by agarose gel electrophoresis, atomic force microscopy and transmission electron microscopy. We also investigate the potential of these two3D DNA origami structures to assemble gold nanoparticles at the nanoscale by making use of thiol chemistry. Controlling matter at the nanoscale holds a lot of promise in nanotechnology. The DNA origami is promising if used as a template to design and arrange matter at the nanoscale. We have used the DNA origami approach to engineer staple strands at selected sites for attachment of gold nanoparticles. The covalent attachment of thiol-modified DNA oligomers was used to functionalize gold nanoparticles. These oligomers then hybridize with complementary strands extended on selected staple strands on the DNA origami surface with nanometer precision. Gold nanoparticles of5nm diameter were arranged across a DNA origami tube to form a C-shape which has potential use in electronics and plasmonics. We also used this approach to organize10and15nm gold nanoparticles that have the potential of having chiral properties. Finally, we make use of the specific affinity interaction between biotin and streptavidin to connect DNA origami templated AuNP helices to our cross-like structures. Agarose gel electrophoresis, AFM, UV-vis spectroscopy and TEM were used to characterize these structures.