Engineering Catalytic Molecular Logic Devices for Biodetection

This dissertation describes the development of DNA computing techniques and molecular logic devices specifically engineered for direct translation to biological sample detection. As disease states originate at the molecular level, it is critical to design diagnostic and therapeutic devices that are capable of molecular-scale sensing and decision-making in the cellular environment. The predictable nature of DNA hybridization and secondary structure formation enables programmable interactions, providing a stable, cost-effective, and biocompatible mechanism for making decisions on the molecular scale. The incorporation of DNAzymes, DNA strands that can perform a variety of chemical reactions, adds innate catalysis and a rich biochemical diversity to DNA logic. By regulating DNAzyme activity via hybridization-based approaches, we have developed a new mechanism for implementing DNA logic, referred to as DNAzyme displacement. This mechanism was used for the construction of DNA logic gates, extended logic cascades, and sensitive biosensors, each capable of operating in non-pristine conditions and under minimal purification and setup restrictions. Logic cascades were constructed through the development of a signal propagation molecule known as a structured chimeric substrate (SCS), which was able to pass a signal between any DNAzyme pair, resulting in the longest synthetic DNA cascade to date. A multi-step DNAzyme displacement reaction was developed for the construction of modular biosensor gates, capable of rapidly multiplexing samples with a limit of detection of 7.4 pM. Other innovative experimental characterization included high-throughput screening efforts of a DNAzyme and alternative methods of compartmentalization including surface-based and lipid-conjugated DNA and protein reactions. This work shows the potential of using DNA to implement molecular logic for the development of intelligent biosensors