Reconfigurable Biochemical Circuit Synthesis from Biomachine Specification

A synthetic biology approach to engineering non-living vesicles, referred to as biomachines, in contrast to living cells, much simplifies system design complexity and has proven effective in commercial healthcare applications. Despite the relative simplicity of biomachine design, its design process requires tremendous efforts, including mining circuits from a real-world reaction database, which may not guarantee feasible solutions exist. For a multi-function design, prior work often requires constructing and implementing each individual function separately to prevent undesirable interference among the reactions of different functions. In this work, we devise a mechanism for reconfigurable circuit design and propose an effective algorithm for mining such circuits. Our method enables integrated multi-function design and allows the flexible switch between different functions. A case study on a diabetes diagnostic application demonstrates the feasibility of our method. The feasibility of our method is demonstrated via a case study on finding reactions to realize reconfigurable functions for diabetes diagnostic tasks.