"Reduced" Coumarin Dyes with an O-Phosphorylated 2,2-Dimethyl-4-(hydroxymethyl)-1,2,3,4-tetrahydroquinoline Fragment: Synthesis, Spectra, and STED Microscopy

Rh-Catalyzed Environmentally Benign Selective Hydrogenation of a Broad Variety of Functional Groups Using Al-Water as a Hydrogen Source

Supported rhodium catalysts were screened to catalyze the one-step hydrogenation of a broad variety of functional groups. The results show that 5% Rh/Al2O3 and 5% Rh/C performed well in controlling selective hydrogenation under the desired amount of time and temperature. In this regard, partial and full hydrogenation were achieved by controlling reaction time or temperature. In addition to aliphatic C–C, C–N, C–O, and N–O multiple bonds, the applicability of this method was demonstrated by the hydrogenation of C=C double bonds of arenes, which is considered challenging. Importantly, the Al-H2O system producing hydrogen in situ and the high, controllable selectivity make this protocol environmentally benign and highly efficient.

Membrane-Permeant, Bioactivatable Coumarin Derivatives for In-Cell Labelling

The delivery of small molecule fluorophores with minimal compartmentalization is currently one of the most critical technical problems in intracellular labelling. Here we introduce sulfonated and phosphonated coumarin dyes, demonstrate rapid cell entry via a prodrug approach, and show a lack of interaction with membranes, organelles, or other compartments. The dyes show no specific localization and are evenly distributed in the cells. Our fluorogenic, clickable phosphonate derivatives successfully tagged model targets in intact cells and the increase in brightness upon click reaction was around 60‐fold.

Fluorescence sensors for imaging membrane lipid domains and cholesterol

Lipid membrane domains are supramolecular lateral heterogeneities of biological membranes. Of nanoscopic dimensions, they constitute specialized hubs used by the cell as transient signaling platforms for a great variety of biologically important mechanisms. Their property to form and dissolve in the bulk lipid bilayer endow them with the ability to engage in highly dynamic processes, and temporarily recruit subpopulations of membrane proteins in reduced nanometric compartments that can coalesce to form larger mesoscale assemblies. Cholesterol is an essential component of these lipid domains; its unique molecular structure is suitable for interacting intricately with crevices and cavities of transmembrane protein surfaces through its rough β face while "talking" to fatty acid acyl chains of glycerophospholipids and sphingolipids via its smooth α face. Progress in the field of membrane domains has been closely associated with innovative improvements in fluorescence microscopy and new fluorescence sensors. These advances enabled the exploration of the biophysical properties of lipids and their supramolecular platforms. Here I review the rationale behind the use of biosensors over the last few decades and their contributions towards elucidation of the in-plane and transbilayer topography of cholesterol-enriched lipid domains and their molecular constituents. The challenges introduced by super-resolution optical microscopy are discussed, as well as possible scenarios for future developments in the field, including virtual ("no staining") staining.

BODIPY-based fluorescent polymeric probes for selective detection of Fe3+ ions in aqueous solution

It is of scientific and practical significance to sense and to remove heavy metal ions in the environment. In this work, four BODIPY-based fluorescent polymeric probes with the ability to sense and separate Fe3+ ions have been prepared via thiol-ene click reaction. The polymers have good thermal stability. Meanwhile, the results show that they have selective recognition capabilities only for Fe3+, which are mainly manifested as significant quenching of fluorescence and color modulation under visible light. The sensitivity is good, and the limit of detection reaches as low as 0.14 µM. They can also be used as reversible chemical probes to detect Fe3+. Therefore, the click reaction provides us with a facile method for preparing fluorescent polymer probes.

Photophysical properties of 4-(5-methylthiophen-2-yl)pyridinium–cyclic enolate betaine dyes tuned by control of twisted intramolecular transfer

In this paper, thienylpyridinium–cyclic enolate betaine (TPB) dyes were reported as unique skeletons of fluorescent donor–acceptor type molecules.

Quantitative Imaging of Labile Zn2+ in the Golgi Apparatus Using a Localizable Small-Molecule Fluorescent Probe

Fluorescent Zn²⁺ probes used for the quantitative analysis of labile Zn²⁺ concentration ([Zn²⁺]) in target organelles are crucial for understanding the role of Zn²⁺ in biological processes. Although several fluorescent Zn²⁺ probes have been developed to date, there is still a lack of consensus concerning the [Zn²⁺] in intracellular organelles. In this study, we describe the development of ZnDA-1H, a small-molecule fluorescent probe for Zn²⁺, which exhibits less pH sensitivity, high Zn²⁺ selectivity, and large fluorescence enhancement upon binding to Zn²⁺. Through protein labeling technology, ZnDA-1H was precisely targeted in various intracellular organelles, such as the nucleus, mitochondria, endoplasmic reticulum, and Golgi apparatus. ZnDA-1H exhibited a reversible fluorescence response toward labile Zn²⁺ in these organelles in live cells. Using this probe, the [Zn²⁺] in the Golgi apparatus was estimated to be 25 ± 1 nM, suggesting that labile Zn²⁺ plays a physiological role in the secretory pathway.

Visualizing and Manipulating Biological Processes by Using HaloTag and SNAP-Tag Technologies

Visualizing and manipulating the behavior of proteins is crucial to understanding the physiology of the cell. Methods of biorthogonal protein labeling are important tools to attain this goal. In this review, we discuss advances in probe technology specific for self-labeling protein tags, focusing mainly on the application of HaloTag and SNAP-tag systems. We describe the latest developments in small-molecule probes that enable fluorogenic (no wash) imaging and super-resolution fluorescence microscopy. In addition, we cover several methodologies that enable the perturbation or manipulation of protein behavior and function towards the control of biological pathways. Thus, current technical advances in the HaloTag and SNAP-tag systems means that they are becoming powerful tools to enable the visualization and manipulation of biological processes, providing invaluable scientific insights that are difficult to obtain by traditional methodologies. As the multiplex of self-labeling protein tag systems continues to be developed and expanded, the utility of these protein tags will allow researchers to address previously inaccessible questions at the forefront of biology.

Core remodeling leads to long wavelength fluoro-coumarins

Low molecular weight, uncharged far-red and NIR dyes would be enabling for a range of imaging applications. Rational redesign of the coumarin scaffold leads to Fluoro-Coumarins (FCs), the lowest molecular weight dyes with emission maxima beyond 700, 800, and 900 nm. FCs display large Stokes shifts and high environmental sensitivity, with a 40-fold increase in emission intensity in hydrophobic solvents. Untargeted variants exhibit selective lipid droplet and nuclear staining in live cells. Furthermore, sulfo-lipid derivatization enables active targeting to the plasma membrane. Overall, these studies report a promising platform for the development of biocompatible, context-responsive imaging agents.

Fluoro-Coumarins are a novel class of far-red and near-infrared solvent sensitive dyes of exceptionally low molecular weight.

High Photostability in Nonconventional Coumarins with Far-Red/NIR Emission through Azetidinyl Substitution

Replacement of electron-donating N,N-dialkyl groups with three- or four-membered cyclic amines (e.g., aziridine and azetidine, respectively) has been described as a promising approach to improve some of the drawbacks of conventional fluorophores, including low fluorescent quantum yields (Φ_F) in polar solvents. In this work, we have explored the influence of azetidinyl substitution on nonconventional coumarin-based COUPY dyes. Two azetidine-containing scaffolds were first synthesized in four linear synthetic steps and easily transformed into far-red/NIR-emitting fluorophores through N-alkylation of the pyridine moiety. Azetidine introduction in COUPY dyes resulted in enlarged Stokes' shifts with respect to the N,N-dialkylamino-containing parent dyes, but the Φ_F were not significantly modified in aqueous media, which is in contrast with previously reported observations in other fluorophores. However, azetidinyl substitution led to an unprecedented improvement in the photostability of COUPY dyes, and high cell permeability was retained since the fluorophores accumulated selectively in mitochondria and nucleoli of HeLa cells. Overall, our results provide valuable insights for the design and optimization of novel fluorophores operating in the far-red/NIR region, since we have demonstrated that three important parameters (Stokes' shifts, Φ_F, and photostability) cannot be always simultaneously addressed by simply replacing a N,N-dialkylamino group with azetidine, at least in nonconventional coumarin-based fluorophores.

Redesigning the Coumarin Scaffold into Small Bright Fluorophores with Far-Red to Near-Infrared Emission and Large Stokes Shifts Useful for Cell Imaging

Among the palette of previously described fluorescent organic molecules, coumarins are ideal candidates for developing cellular and molecular imaging tools due to their high cell permeability and minimal perturbation of living systems. However, blue-to-cyan fluorescence emission is usually difficult in in vivo applications due to the inherent toxicity and poor tissue penetration of short visible light wavelengths. Here, we introduce a new family of coumarin-based fluorophores, nicknamed COUPY, with promising photophysical properties, including emission in the far-red/near-infrared (NIR) region, large Stokes shifts, high photostability, and excellent brightness. COUPY fluorophores were efficiently synthesized in only three linear synthetic steps from commercially available precursors, with the N-alkylation of a pyridine moiety being the key step at the end of the synthetic route, as it allows for the tuning of the photophysical properties of the resulting dye. Owing to their low molecular weights, COUPY dyes show excellent cell permeability and accumulate selectively in nucleoli and/or mitochondria of HeLa cells, as their far-red/NIR fluorescence emission is easily detected at a concentration as low as 0.5 μM after an incubation of only 20 min. We anticipate that these coumarin scaffolds will open a way to the development of novel coumarin-based far-red to NIR emitting fluorophores with potential applications for organelle imaging and biomolecule labeling.

A highly fluorescent water soluble spirobifluorene dye with a large Stokes shift: synthesis, characterization and bio-applications

The first water-soluble highly emitting spirobifluorene-based dye and its applications for live cell imaging and BSA detection are reported.

Hydroxylated Fluorescent Dyes for Live-Cell Labeling: Synthesis, Spectra and Super-Resolution STED

Hydroxylated rhodamines, carbopyronines, silico‐ and germanorhodamines with absorption maxima in the range of 530–640 nm were prepared and applied in specific labeling of living cells. The direct and high‐yielding entry to germa‐ and silaxanthones tolerates the presence of protected heteroatoms and may be considered for the syntheses of various sila‐ and germafluoresceins, as well as ‐rhodols. Application in stimulated emission depletion (STED) fluorescence microscopy revealed a resolution of 50–75 nm in one‐ and two‐color imaging of vimentin‐HaloTag fused protein and native tubulin. The established structure–property relationships allow for prediction of the spectral properties and the positions of spirolactone/zwitterion equilibria for the new analogues of rhodamines, carbo‐, silico‐, and germanorhodamines using simple additive schemes.