Light-Controlled Assembly and Disassembly of Covalent RNA–Protein Conjugates to Control RNA Base Editing

Self-labeling enzymes, like SNAP-, CLIP- and Halo-tag have found wide application in biology, biochemistry, materials science and bioengineering. For example, they have been applied with high versatility to rewrite genetic information inside the living cell by providing rationally programmable RNA-targeting strategies of protein-based effectors. Such approaches benefit from the engineering capability of the small molecule-based self-labeling moieties. Here, we further engineered that approach to control RNA-targeting by light. Specifically, we combined two orthogonal self-labeling enzymes for the recruitment of two distinct fusion proteins to a target RNA inside the living cell and achieved concurrent assembly and disassembly of distinct guide RNA–protein conjugates. We applied this to control RNA base editing and achieved a photo-induced swap of two distinct editing events. Overall, this work describes new ways for tool development, RNA imaging, and transcript engineering.