Programming molecular behavior: development and applications of autonomous DNA synthesis cascades

Abstract

DNA serves many functional roles in living organisms, and dynamic DNA nanotechnology seeks to expand this set of DNA-based behaviors through the rational design of new functions. In the past 20 years, the predictable and programmable structure of DNA based on Watson-Crick base pairing has been utilized to engineer DNA-based chemical reaction pathways capable of performing a number of different tasks, including biosensing, molecular transport of cargo, and logic computation. In this dissertation, I present my work, in collaboration with others, to develop a new mechanism for engineering DNA-based molecular behaviors. The method, primer exchange reactions (PERs), can be used to autonomously synthesize single-stranded DNA using a set of synthetic catalytic hairpin oligos for a range of applications. After first describing the concept and implementation of the method, I go on to demonstrate several behaviors, including molecular sensing, recording, and actuation. I follow up with another application of PER for visualizing nucleic acids in situ, which can be used to reveal information about their spatial organization as well as function. Finally, I conclude with a discussion on the relevance of PER to the emerging field of molecular robotics.