Peptide Nucleic Acids (PNA)-Based Structures for Nanotechnology and Biodetection Applications

This thesis incorporates projects within the field of nucleic acid nanotechnology and targets DNA G-Quadruplexes (GQ) within a biological context. Due to the synthesis and use of peptide nucleic acids (PNA). Specifically, PNA is coupled to metal binding ligands and used to form Watson and Crick (WC) base pairs with an oxidized guanine base.

Chapter 1 introduces DNA, PNA, metal-mediated PNA, and their incorporation into the large nucleic acid nanostructure. This chapter also explores the unique characteristics of each type of nucleic acid and of the structures they form. It concludes by setting up the introductory metalmediated nanostructure to be synthesized. Chapter 2 shows the construction and confirmation of tiles bridged by [CuQ₂] complexes. The metal-bridged DNA/PNA tiles are more stable than the “traditional” tiles based exclusively on DNA strands. Thermal melting studies show that incorporating PNA rails in the DNA tiles increases the tile stability even in the absence of metal ions. The metal complex formation did not substantially impact the tile stability. Metal titrations show the Cu²⁺coordination to 8-hydroxyquinoline (Q) ligands. UV-vis titrations give a lower M/L ratio than the 0.5 expected if [CuQ₂] complexes formed in the tile. Spin quantification by EPR shows that all PNA-Q strands participated in the formation of complexes with Cu²⁺. Future studies will be focused on the design and imaging of larger metal-containing DNA/PNA tiles. Chapter 3 builds from this by using DNA sticky-ends to link tiles together into wires, which were shown to have similar stabilities as the tiles. AFM studies of DNA(SE) show that DNA hybridization can connect tiles into wires. Wires were also synthesized with [CuQ₂] at the terminal ends of a duplex, and wire formation occurred through complexation instead of nucleic acid crossovers. Metal titrations confirm the formation of the complex. Chapter 4 departs from nanostructures to using PNA to target oxidized guanine (OxoG) base. The OxoG destabilizes the GQ and therefore exposes it to duplex attack. Preliminary results for this project show duplex formation even to the non-Oxo GQ. Lastly, Chapter 5 explores the next steps in these projects, delving into the future work and what the potential future of these projects could entail.