Implementing complex nucleic acid circuits in living cells.

Synthetic nucleic acid-based computing has demonstrated complex computational capabilities in vitro. However, translating these circuits into living cells remains challenging because of instability and cellular interference. We introduce an allosteric strand exchange (ASE) strategy for complex intracellular computing. Leveraging conformational cooperativity to regulate strand exchange, ASE offers a modular platform for designing intracellular circuits with flexible programmability. We engineer a scalable circuit architecture based on ASE that can execute AND and OR logic and scale to an eight-input expression. We demonstrate ASE-based circuits can detect messenger RNAs with high specificity in mammalian cells via AND logic computation. The capacity of ASE-based circuits to accept messenger RNAs as inputs enables integration of endogenous cellular information for efficient multi-input information processing, demonstrated by a multi-input molecular classifier monitoring key cell reprogramming events. Reprogramming ASE-based circuit to interface with CRISPR-Cas9 enables programmable control of Cas9-targeting activity for gene editing, highlighting their potential for advancing intracellular biocomputation.