Programmable DNA Strand-Displacement Circuits for Emulating Digital Sequential Logic Devices.

DNA strand displacement reactions provide a promising approach for implementing information processing and have been successfully used for encoding combinational logic. However, the construction of circuits with state-dependent behavior and clock-controlled operation remains a significant challenge. In this paper, we present a programmable DNA circuit platform capable of emulating digital sequential logic elements, including a Set-Reset (SR) latch, a clocked Data (D) flip-flop, and a two-bit binary counter. These molecular devices are realized through hierarchically designed DNA strand displacement modules. By encoding temporal information at the domain level and orchestrating reaction cascades on spatially confined DNA modules, we achieve reliable memory storage, clock-gated signal propagation, and input-dependent state transitions. Fluorescence-based kinetic measurements confirm the functional fidelity and timing accuracy of each logic element. Our work establishes a scalable methodology for constructing programmable, state-aware molecular logic systems, advancing the prospects of nanoscale processors and intelligent nanorobots.