Flavylium merocyanine dyes: Exploiting the cyanine state for intrinsic labeling of the endoplasmic reticulum

Merocyanine dyes are a versatile class of donor-acceptor polymethine dyes that exhibit unique properties depending on their structural makeup and surrounding environment. Scaffolds that favor the cyanine state (i.e., narrow, red-shifted absorption and high fluorescence quantum yields) in biologically relevant settings are highly advantageous for multiplexed labeling experiments, but remain limited by their visible absorption. Herein, we report a new class of far-red (650-700 nm) flavylium merocyanine dyes that favor the cyanine state with increasing solvent viscosity and hydrogen bond donation, enhancing their performance in biological settings. We leveraged these properties for live cell labeling, where we observed intrinsic targeting to the endoplasmic reticulum (ER) and lipid droplets, and minimal crosstalk with commercial stains. As such, these dyes are a promising alternative to commercially available ER stains at shorter absorption wavelengths (<600 nm) with complex targeting moieties.