ENGINEERING A ROBUST DNA CIRCUIT FOR THE DIRECT DETECTION OF BIOMOLECULAR INTERACTIONS

Abstract

DNA circuit is a highly programmable bio-system driven by a series of toehold-mediated strand displacement reactions. One key challenge is the occurrence of circuit leakage due to random hybridization. The leakage issue was addressed in this thesis through the design of a localized circuit to promote the rate of desired reactions over the undesired leak reactions. The recognition of biomolecules and their interaction events was used to trigger the dynamic assembly of the localized circuit. The self-contained circuit consisted of three reaction modules – target recognition, signal transduction (based on association toehold) and signal amplification (based on hybridization chain reaction). Design guidelines to generate robust DNA sequences for each module were established. The final “split proximity circuit” could be dynamically assembled by various biomolecules and their interaction events in a “plug-and-play” format. It was successfully applied for detecting biological systems including DNA-RNA hybridization, protein-aptamer binding and cell surface receptor clustering.