A general strategy to develop fluorogenic polymethine dyes for bioimaging

Fluorescence imaging is an invaluable tool to study biological processes and further progress depends on the development of advanced probes. Fluorogenic dyes are crucial to reach intracellular targets and label them with high specificity. Excellent fluorogenic rhodamine dyes have been reported, but they often require a long and low-yielding synthesis and are spectrally limited to the visible range. Here, we present a general strategy to transform polymethine compounds into fluorogenic dyes using an intramolecular ring closure approach. We illustrate the generality of this method by creating both spontaneously blinking and no-wash, turn-on polymethine dyes with emissions across the visible and near-infrared spectrum. These probes are compatible with self-labeling proteins and small-molecule targeting ligands and can be combined with rhodamine-based dyes for multicolor and fluorescence lifetime multiplexing imaging. This strategy provides access to bright, fluorogenic dyes that emit at wavelengths that are significantly more red-shifted than those of existing rhodamine-based dyes.