DNA-Based Dynamic Reaction Networks

Deriving from logical and mechanical interactions between DNA strands and complexes, DNA-based artificial reaction networks (RNs) are attractive for their high programmability, as well as cascading and fan-out ability, which are similar to the basic principles of electronic logic gates. Arising from the dream of creating novel computing mechanisms, researchers have placed high hopes on the development of DNA-based dynamic RNs and have strived to establish the basic theories and operative strategies of these networks. This review starts by looking back on the evolution of DNA dynamic RNs; in particular’ the most significant applications in biochemistry occurring in recent years. Finally, we discuss the perspectives of DNA dynamic RNs and give a possible direction for the development of DNA circuits. If only the disassociation constant is considered, a strand migration reaction should be extremely slow (with a half-life of even thousands of year). However, it is a super-fast process with a half-life of seconds, and the reason is base breathing. Toehold exchange reactions are more flexible compared with traditional strand displacement reactions. Thus, toehold exchange can be used, at least in theory, to construct higher scaled circuits. DNA circuits are like logically programmed mechanical controllers that allow temporally and spatially programmable regulation of biological systems. Considering the electrolyte-rich cellular microenvironment and abundant membrane molecules which play significant roles in metabolism, the cell surface has been found to be an effective and essential platform to build a DNA RN.