Engineered fluorogenic HaloTag ligands for turn-on labelling in live cells

Recent years have seen dramatic improvements in the design of organic fluorophores based on limiting non-radiative decay pathways. We sought to extend this understanding to benzothiadiazoles that have been used as turn-on fluorescent substrates for the self-labeling protein HaloTag. When conjugated to HaloTag, the benzothiadiazoles reside in a narrow tunnel that precludes twisted internal charge transfer, which allowed us to explore steric and electronic effects on other non-radiative decay pathways. By minimizing both non-radiative decay and nonspecific interactions with cellular components, we produced improved turn-on dyes with 136-fold increase in fluorescence over background in cells.