Design of DNA strand displacement reactions

DNA strand displacement (SD) reactions are central to the operation of many synthetic nucleic acid systems, including molecular circuits, sensors, and machines. Over the years, a broad set of design frameworks has emerged to accommodate various functional goals, initial configurations, and environmental conditions. Nevertheless, key challenges persist, particularly in reliably predicting reaction kinetics. In contrast to reviews centred on network-level architectures, this article focuses on the design and analysis of individual SD reactions, highlighting kinetic mechanisms, structural determinants, and the current limits of predictive modelling. We identify promising innovations while analysing the factors that continue to hinder predictive accuracy. We conclude by outlining future directions for achieving more robust and programmable behaviour in DNA-based systems.