Self-assembling DNA based molecular pegboards as nanoscale scaffolds and prescriptive molecular landscapes

• Main Author: Lund, Kyle Ryan
• Format: Dissertation
• Language: English
• Published: ProQuest Dissertations & Theses 01-01-2008
• Subjects: Biochemistry
• ISBN: 0549934634; 9780549934639

Deoxyribonucleic acid (DNA), nature's genetic material, has been used as programmable building blocks for nanoscale constructions. DNA has been utilized to make self-assembling one-dimensional (1D) and two-dimensional (2D) arrays, to organize other molecular species and materials, and to make nanomechanical devices. An important challenge for realizing practical application of DNA based nanotechnology is to be able to obtain spatially addressable 2D arrays with finite dimension. Cross-shaped DNA nanostructures were used to assemble fully addressable DNA molecular pegboards. The assembly method yielded 70 percent array formation. Topographically indexed addressable arrays were used as a platform to detect DNA strand hybridization. Strand hybridization events can be visualized at the single molecule level using atomic force microscope (AFM) imaging. A new approach was then developed to assemble finite dimensions DNA nanoarrays by assembling modular DNA tile building blocks in a combinatorial fashion. Two-dimensional DNA tiling arrays were used to organize a peptide-DNA fusion molecule and its antibody to form protein nanoarrays. DNA origami (a novel addressable array) was used as prescriptive landscape to direct the movement an autonomous DNA walker. The DNA walker moved along connected pathways from point A to point B. The movement of the walker was studied at the single molecule level through AFM and Total Internal Reflectance Fluorescence (TIRF) spectroscopy. A novel group of spiral DNA nanotubes with controlled chirality were designed and self-assembled. Through the use of DNA nanotechnology addressable arrays were developed, proteins were displayed on 2D DNA nanoarrays, a molecular walker moved autonomously across a prescriptive landscape, and DNA spiraling tubes were developed.