Nanotechnology is a burgeoning field as eager scientists are exploring every facet, driving toward a common goal of understanding the nanoscale world. DNA, aside from being the genetic carrier, is an ideal smart material for nanoscale construction due to the well known structural and molecular recognition properties. This dissertation focuses on using DNA nanostructures to study molecular interactions at the controlled nanometer scale, aiming to explore their applications in creating artificial interactive biomolecular networks.

Presented here, various DNA nanostructures were built as nanoscale scaffolds. Firstly, a multi-helical DNA tile was used as a rigid linker to study bivalent intermolecular interactions with controlled inter-ligand distances. Gel Electrophoresis Shift Assay and Fluorescence Resonance Energy Transfer experiments showed greater than a fifty fold increase in the binding affinity of the bivalent interaction than that of a single ligand interaction. Atomic Force Microscopy (AFM) was used to visualize such interactions at a single-molecule level. Secondly, bacteria and bacteriaphages were used as biochemical factories to replicate DNA nanostructures, a production which can easily be expanded to a large scale. It is intriguing to find that the inserted junction complex secondary structure was tolerated by the cellular machinery, and was replicated efficiently with high fidelity. Thirdly, the helical repeat of Lock Nucleic Acid (LNA), an unnatural analog of DNA, was characterized by AFM. The formation of two-dimensional tile arrays was observed as the number of bases in the DNA/LNA hybrid tile varied systematically. LNA has a superior thermal stability than DNA making it an alternative material for building more robust nanostructures.