Multifunctional Exo III-assisted scalability strategy for constructing DNA molecular logic circuits

Abstract

The construction of logic circuits is critical to DNA computing. Simple and effective scalability methods have been the focus of attention in various fields related to constructing logic circuits. We propose a double-stranded separation (DSS) strategy to facilitate the construction of complex circuits. The strategy combines toehold-mediated strand displacement with exonuclease III (Exo III), which is a multifunctional nuclease. Exo III can quickly recognize an apurinic/apyrimidinic (AP) site. DNA oligos with an AP site can generate an output signal by the strand displacement reaction. However, in contrast to traditional strand displacement reactions, the double-stranded waste from the strand displacement can be further hydrolysed by the endonuclease function of Exo III, thus generating an additional output signal. The DSS strategy allows for the effective scalability of molecular logic circuits, enabling multiple logic computing capabilities simultaneously. In addition, we succeeded in constructing a logic circuit with dual logic functions that provides foundations for more complex circuits in the future and has a broad scope for development in logic computing, biosensing, and nanomachines.