A general strategy to develop fluorogenic polymethine dyes for bioimaging

Abstract

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.

Method To Diversify Cyanine Chromophore Functionality Enables Improved Biomolecule Tracking and Intracellular Imaging

“…Additional modifications to both the cyanine and the HaloTag protein may enhance binding properties, fluorogenicity, and photostability of the protein-small molecule pairs. We believe the efficient cyanine-based self labeling tags reported here and in recent studies by Rivera-Fuentes and coworkers will provide a long-wavelength NIR channel for multicolor experiments and, perhaps, improved imaging resolution in complex tissue settings …”

“…We believe the efficient cyanine-based self labeling tags reported here and in recent studies by Rivera-Fuentes and coworkers will provide a long-wavelength NIR channel for multicolor experiments and, perhaps, improved imaging resolution in complex tissue settings. 84 Finally, these studies illustrate the potential for dynamic ringopen/ring-closed chemistry with heptamethine indocyanines, which may enable the discovery for a range of long-wavelength optical probes. The prospect for such efforts is heightened by prior studies on rhodamines, fluoresceins, and rhodols, where a range of fluorogenic sensors and imaging strategies have been developed by taking advantage of nonfluorescent lactone, fluorescent zwitterion equilibria.…”

Spontaneously Blinking Rhodamine Dyes for Single‐Molecule Localization Microscopy

“…Notably, the Rivera-Fuentes group has successfully developed spontaneously blinking polymethine dyes (Figure 9). [37] Secondly, researchers should explore new mechanisms beyond spirocyclization to enable spontaneous blinking. The Urano group demonstrated that spontaneous blinking can be achieved through a reversible nucleophilic reaction between intracellular glutathione and a xanthene-based fluorophore in the ground state (Figure 9).…”

Application of PROTACs in target identification and validation

“…Probes typically consist of three parts: an active drug molecule; a linker; and a reporting label [28]. According to the different reporting labels, the probes are divided into immobilized (solid-phase carriers as report label) [29] and active probes (biotin [30] and fluorescent groups [31] (Figure 3), bio-orthogonal reaction groups [32], and photoaffinity reaction groups [33] as reporting labels). Immobilized probes are a classic tool for target identification.…”