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.
Single‐molecule localization microscopy (SMLM) can reveal nanometric details of biological samples, but its high phototoxicity hampers long‐term imaging in live specimens. A significant part of this phototoxicity stems from repeated irradiations that are necessary for controlled switching of fluorophores to maintain the sparse labeling of the sample. Lower phototoxicity can be obtained using fluorophores that blink spontaneously, but controlling the density of single‐molecule emitters is challenging. We recently developed photoregulated fluxional fluorophores (PFFs) that combine the benefits of spontaneously blinking dyes with photocontrol of emitter density. These dyes, however, were limited to imaging acidic organelles in live cells. Herein, we report a systematic study of PFFs that culminates in probes that are functional at physiological pH and operate at longer wavelengths than their predecessors. Moreover, these probes are compatible with HaloTag labeling, thus enabling timelapse, single‐molecule imaging of specific protein targets for exceptionally long times.
RhoBAST is a novel fluorescence light-up RNA aptamer (FLAP) that transiently binds a fluorogenic rhodamine dye. Fast dye association and dissociation result in intermittent fluorescence emission, facilitating single-molecule localization microscopy (SMLM) with an image resolution not limited by photobleaching. We demonstrate RhoBAST's excellent properties as a RNA marker by resolving subcellular and subnuclear structures of RNA in live and fixed cells by SMLM and structured illumination microscopy (SIM).
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