‘Guide and Prejudice’— How Argonautes recognize targets across domains of life

Argonaute proteins mediate RNA interference in eukaryotes and nucleic-acid defence in prokaryotes. Although these systems operate in distinct biological contexts and produce diverse downstream outcomes, they share a conserved structural architecture and mechanism of guide-dependent target recognition. Here, we argue that Argonautes function as programmable surveillance platforms that kinetically sample nucleic acids, engage targets through sequential pairing and conformational checkpoints, and couple recognition to functional outputs through regulated structural transitions. Rather than representing distinct recognition mechanisms, the diverse targeting behaviours observed across Argonaute families reflect different implementations of this shared framework, in which guide biogenesis, target accessibility, pairing requirements and effector coupling are weighted differently according to biological context. Viewing Argonautes through this common operational logic reconciles apparent differences in specificity, mismatch tolerance and target selection across systems, while providing a unified conceptual framework for understanding their evolution and guiding the engineering of programmable nucleic-acid recognition technologies.