Fluorescent chemogenetic tags: ligand design and biological applications

Chemogenetic tags, as semi-synthetic labeling systems, represent a powerful and versatile class of tools for biological imaging. By integrating genetically encoded protein scaffolds with chemically tunable small-molecule ligands, these systems offer both high targeting specificity and remarkable functional versatility. These characteristics have collectively driven the rapid development and widespread applications of chemogenetic labeling technologies. Beyond conventional fluorescence imaging, chemogenetic tags are increasingly being explored in emerging fields such as super-resolution microscopy, biosensing and therapeutic intervention. In this review, we present a comprehensive overview of the development and biological applications of representative chemogenetic tags, encompassing covalent labeling systems such as FlAsH, SNAP-tag, HaloTag, PYP and CRABPII, as well as non-covalent systems like FAP and FAST. We focus particularly on the molecular engineering of ligands, highlighting diverse design strategies and advancements in small-molecule probes for fluorescence imaging, biosensing, protein function modulation and disease therapy. This review aims to provide meaningful insights into the rational design of next-generation chemogenetic tools tailored for leading-edge biological research.