Introduction

Abstract

DNA circuit is a highly programmable toolbox based on the dynamic interactions between logic gates driven by a series of hybridization events known as toehold-mediated strand displacements. Since the circuit design is modular and based primarily on the well-studied Watson-Crick base pairing, it is theoretically possible to engineer circuits of varying complexities to operate autonomously with high degree of control. Yet, while much progress has been made in the in silico design and experimental implementation of specific design concepts, the pace at which they are translated into real applications is lagging. One major bottleneck is the issue of circuit leakage which refers to spurious, undesired hybridization events. In this thesis, we aim to overcome this problem by designing localized to favour the strand displacement kinetics of the desired reaction over undesired leak processes. This was achieved by designing a target-responsive, self-contained DNA circuit to execute localized strand displacement reactions (Chaps. 4–6) while minimizing circuit leakage through thermodynamics-driven design concepts (Chaps. 5 and 6). We then demonstrated the applicability of the designed circuit, termed “split proximity circuit”, for probing various biomolecules and their interaction events  (Chaps. 7 and 8).