Exploiting Flavylium Merocyanine Dyes for Intrinsic, Multiplexed 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 synthesize a new class of far-red (650-700 nm) to near-infrared (NIR, 700-1000 nm) flavylium merocyanine dyes and demonstrate that, unlike conventional scaffolds, they favor the cyanine state with increasing solvent viscosity and hydrogen bond donation, rather than polarity. We leverage these advantageous properties for live cell labeling, where we observed intrinsic targeting to the endoplasmic reticulum (ER) and lipid droplets, and minimal crosstalk with commercial stains. We reveal that intrinsic ER labeling is achieved by the dipolarity in the cyanine state and lipophilicity (ClogP) of the merocyanine architecture, making this class of dyes a simple, red-shifted alternative to the more structurally complex ER stains currently available.