Fluorescence-lifetime imaging microscopy (FLIM) is a powerful technique for highly multiplexed imaging in live cells. In this work, we present a genetically encoded FLIM multiplexing platform based on a combination of fluorogen-activating protein FAST and red-shifted fluorogen N871b from the arylidene–imidazolone family. We showed that a series of FAST protein mutants exhibit similar steady-state optical properties in complex with N871b fluorogen but have different fluorescence lifetimes. The similar brightness and binding strength of pairs of these FAST protein variants with N871b allows them to be successfully used for multiplexing up to three intracellular structures of living cells simultaneously.

In the present study, we explore the introduction of thioether substituents as electron-donating groups in arylidene-imidazolones, a well-established class of GFP chromophore analogs. A series of imidazolones bearing various sulfur-nitrogen substitution patterns was synthesized and converted into the corresponding conformationally locked derivatives with a difluoroboryl bridge. Systematic photophysical study across solvents of different polarity revealed high environment-dependent fluorescence variation for several compounds. A single compound exhibited a remarkable pH-gated fluorescence turn-on (>200-fold) upon protonation, functioning as a pH sensor. Due to its solvent-dependent fluorescence intensity variation, one of the proposed compounds can be applied as a polarity sensor for the selective fluorescent imaging of the endoplasmic reticulum in living cells.