XOR Gate Design Toward a Practical Complete Set for DNA Computing

Practical design of the XOR gate is an important milestone in the field of DNA computing. In this study, we aim to develop an enzyme-free XOR gate driven by a toehold-mediated strand displacement mechanism possessing the true detection property. The advantages of our design are as follows: dual-rail logic is not required, the explicit use of the NOT gate is avoided, the circuit structure is simple, and the design is achievable with fewer DNA strands than that designed by the combination of four NAND gates. A rational circuit design is performed and the dynamic behaviors of the biochemical reaction and the secondary structures of DNA strands are confirmed by computer simulation. In particular, both the domain-level design technique with G-T mismatched base pairs and base sequence-level fine-tuning are successfully achieved to alleviate the performance degradation arising from unintended and leaky reactions present in the circuit. The validity of the XOR gate design is confirmed by experimental studies.