Publications
ThesisJan 2018

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

Kishi, JY
Product Used
Oligo Pools
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.
Product Used
Oligo Pools

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