Kinetics and Activation Strategies in Toehold-Mediated and Toehold-Free DNA Strand Displacement

Nucleic acid strand displacement reactions (SDRs) are fundamental building blocks of dynamic DNA nanotechnology. A detailed understanding of their kinetics is crucial for designing efficient sequences and regulating reaction networks with applications in biosensing, synthetic biology, biocomputing, and medical diagnostics. Since the development of toehold-mediated strand displacement, researchers have devised many strategies to adjust reaction kinetics. These efforts have expanded the available tools in DNA nanotechnology. This review summarizes the basic principles and recent advances in activation strategies, emphasizing the role of strand proximity as a central driving force. Proximity-based approaches include toehold docking, associative toeholds, remote toeholds, and allosteric designs, as well as strategies that operate without explicit toehold motifs. These methods enable flexible and scalable construction of DNA reaction networks. We further discuss how combining different activation and kinetic control approaches gives rise to dynamic networks with complex and dissipative behaviors, providing new directions for DNA-based nanotechnology.