Fluorescence labelling of an intracellular biomolecule in native living cells is a powerful strategy to achieve in-depth understanding of the biomolecule's roles and functions. Besides being nontoxic and specific, desirable labelling probes should be highly cell permeable without nonspecific interactions with other cellular components to warrant high signal-to-noise ratio. While it is critical, rational design for such probes is tricky. Here we report the first predictive model for cell permeable background-free probe development through optimized lipophilicity, water solubility and charged van der Waals surface area. The model was developed by utilizing high-throughput screening in combination with cheminformatics. We demonstrate its reliability by developing CO-1 and AzG-1, a cyclooctyne- and azide-containing BODIPY probe, respectively, which specifically label intracellular target organelles and engineered proteins with minimum background. The results provide an efficient strategy for development of background-free probes, referred to as ‘tame' probes, and novel tools for live cell intracellular imaging.

Two complementary one‐pot, three component synthetic strategies based on copper(I)‐catalyzed azide–alkyne cycloadditions (CuAAC) have been developed, which allow the efficient assembly of glycosyl‐derived alkynes or azides with highly fluorescent boron–dipyrromethene (BODIPY) cores containing azido or alkyne moieties, respectively. The resulting carbohydrate–BODIPY derivatives display excellent photophysical and laser properties that relate to the spacer (amino group or aromatic ring) employed in each of the synthetic protocols.

Several new examples of meso-(het)arylBODIPY were prepared via the Liebeskind-Srogl (L-S) cross-coupling reaction of the Biellmann BODIPYs (1a,b) and aryl- and heteroarylboronic acids in good to excellent yield. It was shown that this reaction could be carried out under microwave heating to shorten reaction times and/or increase the yield. It was illustrated that organostannanes also participate in the L-S reaction to give the corresponding BODIPY analogues in short reaction times and also with good to excellent yields. We analyze the role of the substituent at the sensitive meso position in the photophysical signatures of these compounds. In particular, the rotational motion of the aryl ring and the electron donor ability of the anchored moieties rule the nonradiative pathways and, hence, have a deep impact in the fluorescence efficiency.

Eleven formyl-containing BODIPY dyes were prepared by means of either the Liebeskind-Srogl cross-coupling reaction or the Vilsmeier reaction. These dyes were used as components in the Passerini reaction to give highly substituted BODIPY dyes. A joined spectroscopic and theoretical characterization of the synthesized compounds was conducted to unravel the impact of the structural rigidity/flexibility on the photophysical signatures. These dyes were tested as fluorescent trackers for phagocytosis. Additionally, they proved to be useful to stain different blood cells with an intense and stable signal at a very low exposure time.

8-(2-Phenylethenyl)BODIPY has been shown to be an appropriate chromo-fluorogenic probe for cyanide in H2O.

Control of fluorescent dye localization in live cells is crucial for fluorescence imaging. Here, we describe quantitative structure activity relation (QSAR) models for predicting intracellular localization of fluorescent dyes. For generating the QSAR models, electric charge (Z) calculated by pKa, conjugated bond number (CBN), the largest conjugated fragment (LCF), molecular weight (MW) and log P were used as parameters. We identified the intracellular localization of 119 BODIPY dyes in live NIH3T3 cells, and assessed the accuracy of our models by comparing their predictions with the observed dye localizations. As predicted by the models, no BODIPY dyes localized in nuclei or plasma membranes. The accuracy of the model for localization in fat droplets was 92%, with the models for cytosol and lysosomes showing poorer agreement with observed dye localization, albeit well above chance levels. Overall therefore the utility of QSAR models for predicting dye localization in live cells was clearly demonstrated.

Herein, we report the synthetic access to a set of π-extended BODIPYs featuring a penta-arylated (phenyl and/or thiophene) dipyrrin framework. We take advantage of the full chemoselective control of 8-methylthio-2,3,5,6-tetrabromoBODIPY when we conduct the Liebeskind–Srogl cross-coupling (LSCC) to functionalize exclusively the meso-position, followed by the tetra-Suzuki reaction to arylate the halogenated sites. All these laser dyes display absorption and emission bands in the red edge of the visible spectrum reaching the near-infrared with thiophene functionalization. The emission efficiency, both fluorescence and laser, of the polyphenylBODIPYs can be enhanced upon decoration of the peripheral phenyls with electron donor/acceptor groups at para positions. Alternatively, the polythiopheneBODIPYs show an astonishing laser performance despite the charge transfer character of the emitting state. Therefore, these BODIPYs are suitable as a palette of stable and bright laser sources covering the spectral region from 610 nm to 750 nm.

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