Hierarchical Logic Control via DNA Polymerase-Driven Molecular Circuits

DNA is considered an ideal medium for constructing molecular circuits due to its high programmability and exceptional information density. Current DNA-based circuits are primarily constructed by using toehold-mediated strand displacement (TMSD) or enzyme-assisted reactions. While TMSD-based systems can perform logical operations, their functionality relies heavily on precise base pairing, resulting in complicated design processes and limited scalability. In contrast, enzyme-driven circuits offer a simplified design and support functional diversification. In this study, we developed a DNA polymerase-driven circuit that establishes a system-level programming framework for managing complex molecular states. By regulating strand binding, we defined three stable operational modes: OFF, ON, and the Blocked state (BLC). Based on this mechanism, programmable logic gates were constructed to achieve controllable computing operations. The system incorporates a modular input domain design, enabling dynamic switching among operational modes in response to different input signals: matched inputs specifically activate the target circuit, whereas mismatched inputs drive nontarget circuits into a blocked state. This programmability supports multilevel logical access control and path backtracking, mimicking computer directory mechanisms. Furthermore, this architecture enables conditional signal isolation and regulation, providing an innovative strategy for the hierarchical organization and state-aware management of complex molecular information systems.