Enzyme-driven triplex structure-based DNA logic circuits.

DNA logic circuits have emerged as crucial media for biological computing due to their molecular-level parallelism and high biocompatibility. In the two mainstream systems currently prevalent, the strand-displacement system generally suffers from issues such as high strand complexity, signal leakage, and difficulties in cascading. In comparison, the enzyme-driven system has offered a further improvement in high rates and low leakage. However, it continues to encounter challenges pertaining to signal leakage and signal attenuation, which limit the development of intricate computational systems.This study introduces enzyme-powered triplex DNA logic circuits that simplify strand design through input-gate concatenation forming triplex structures, utilizing Bst 3.0 polymerase for efficient operation. System validation includes single-gate analysis, multi-level cascades (secondary/tertiary), complex logic circuits, and large-scale square root operations. Single-gate circuits achieve < 2-min half-completion times with minimal leakage. The two-level cascaded circuits exhibit minimal leakage and the longest half-completion time of less than 8 min, while 10-gate square root circuits maintain < 25-min operation with 24.3% reduced strand complexity and 25% faster reaction rates versus existing systems. The low-leakage architecture enables efficient DNA computing for biosensing, data storage, and synthetic biology applications, while its modular design supports scalable biological computing networks.