Fuel-Driven Transient DNA Strand Displacement Circuitry with Self-Resetting Function

Toehold-mediated DNA strand displacement (DSD) is a powerful strategy to engineer dynamics in DNA-based devices and for molecular computing. However, facile strategies for autonomously self-resettable DSD cascades with programmable lifetimes are still missing. Here, we concatenate an ATP-powered ligation/restriction network with toehold-mediated DSD reactions realizing ATP-driven transient DSD with self-resetting behavior. The ATP-fueled ligation biases strand displacement reactions by increasing the toehold length and increasing the local concentration by covalent fixation, while the concurrent endonuclease restriction eliminates this bias, allowing to reset the system. The lifetimes and adaptive dynamic steady states for the DSD are engineered by the ATP-fueled uphill-driven nonequilibrium ligation/restriction system. By programming the toeholds for downstream DSD reaction networks, we realize ATP-fueled transient DSD cascades. A higher level of fuel-driven automaton is achieved by combining two subsystems for the transient DSD, where the expelled strands are each other's input strands and the restriction-induced double-stranded DNA melting resets the systems.