Heteroatom-substituted rhodamine dyes: Structure and spectroscopic properties

Fluorogenic Rhodamine-Based Chemigenetic Biosensor for Monitoring Cellular NADPH Dynamics

Ratiometric biosensors employing Förster Resonance Energy Transfer (FRET) enable the real-time tracking of metabolite dynamics. Here, we introduce an approach for generating a FRET-based biosensor in which changes in apparent FRET efficiency rely on the analyte-controlled fluorogenicity of a rhodamine rather than the commonly used distance change between donor-acceptor fluorophores. Our fluorogenic, rhodamine-based, chemigenetic biosensor (FOCS) relies on a synthetic, protein-tethered FRET probe, in which the rhodamine acting as the FRET acceptor switches in an analyte-dependent manner from a dark to a fluorescent state. This allows ratiometric sensing of the analyte concentration. We use this approach to generate a chemigenetic biosensor for nicotinamide adenine dinucleotide phosphate (NADPH). FOCS-NADPH exhibits a rapid and reversible response toward NAPDH with a good dynamic range, selectivity, and pH insensitivity. FOCS-NADPH allows real-time monitoring of cytosolic NADPH fluctuations in live cells during oxidative stress or after drug exposure. We furthermore used FOCS-NADPH to investigate NADPH homeostasis regulation through the pentose phosphate pathway of glucose metabolism. FOCS-NADPH is a powerful tool for studying NADPH metabolism and serves as a blueprint for the development of future fluorescent biosensors.

Fluorescent chemosensors facilitate the visualization of plant health and their living environment in sustainable agriculture

Globally, 91% of plant production encounters diverse environmental stresses that adversely affect their growth, leading to severe yield losses of 50-60%. In this case, monitoring the connection between the environment and plant health can balance population demands with environmental protection and resource distribution. Fluorescent chemosensors have shown great progress in monitoring the health and environment of plants due to their high sensitivity and biocompatibility. However, to date, no comprehensive analysis and systematic summary of fluorescent chemosensors used in monitoring the correlation between plant health and their environment have been reported. Thus, herein, we summarize the current fluorescent chemosensors ranging from their design strategies to applications in monitoring plant-environment interaction processes. First, we highlight the types of fluorescent chemosensors with design strategies to resolve the bottlenecks encountered in monitoring the health and living environment of plants. In addition, the applications of fluorescent small-molecule, nano and supramolecular chemosensors in the visualization of the health and living environment of plants are discussed. Finally, the major challenges and perspectives in this field are presented. This work will provide guidance for the design of efficient fluorescent chemosensors to monitor plant health, and then promote sustainable agricultural development.

Phospha-RosIndolizine Dye with Shortwave Infrared (SWIR) Absorption and Emission

Shortwave infrared (SWIR, 1000-1700 nm) absorbing and emitting dyes are needed for infrared diodes and sensors used in a wide variety of industrial and medical applications. Herein, an electron-withdrawing phosphine oxide (P═O) substituted xanthene is coupled with strong indolizine donors to produce a SWIR absorbing (λabs = 1294 nm in DCM) and emitting (λemis = 1450 nm in DCM) dye called PRos1450. The unique properties of this dye are characterized via photophysical, electrochemical, and computational analyses.

Silicon-RosIndolizine fluorophores with shortwave infrared absorption and emission profiles enable in vivo fluorescence imaging

In vivo fluorescence imaging in the shortwave infrared (SWIR, 1,000-1,700 nm) and extended SWIR (ESWIR, 1,700-2,700 nm) regions has tremendous potential for diagnostic imaging. Although image contrast has been shown to improve as longer wavelengths are accessed, the design and synthesis of organic fluorophores that emit in these regions is challenging. Here we synthesize a series of silicon-RosIndolizine (SiRos) fluorophores that exhibit peak emission wavelengths from 1,300-1,700 nm and emission onsets of 1,800-2,200 nm. We characterize the fluorophores photophysically (both steady-state and time-resolved), electrochemically and computationally using time-dependent density functional theory. Using two of the fluorophores (SiRos1300 and SiRos1550), we formulate nanoemulsions and use them for general systemic circulatory SWIR fluorescence imaging of the cardiovascular system in mice. These studies resulted in high-resolution SWIR images with well-defined vasculature visible throughout the entire circulatory system. This SiRos scaffold establishes design principles for generating long-wavelength emitting SWIR and ESWIR fluorophores.

A facile strategy for the large-scale preparation of starch-based AIE luminescent nanoaggregates via host-guest interactions and their versatile applications

Luminescent nanomaterials with outstanding optical properties have attracted growing interest due to their widespread applications. However, large-scale fabrication of luminescent nanomaterials with desired properties through a simple and economical process remains challenging. As a renewable natural resource, starch is non-toxic, easily accessible, and inexpensive, making it a popular choice for uses in various biomedical fields. In this work, we present a facile assembly strategy for the fabrication of starch-based luminescent nanoaggregates using starch as the host material and aggregation-induced emission luminogens (AIEgens) as guest molecules. By employing simple procedures under mild conditions, highly luminescent nanoparticles with small sizes, high water dispersibility, and low cytotoxicity are prepared on a large scale. The resulting nano-assemblies demonstrate significantly enhanced fluorescence intensities, reduced susceptibility to photobleaching and low cytotoxicity. These fluorescent supramolecular aggregates can be employed in various application fields, including the fabrication of fluorescent hydrogels, fingerprint detection, cell imaging and in vivo lymphatic system imaging. The methodology developed in this work has immense potential to greatly promote the production of high-quality nanoparticles on the industrial scale, offering a cost-effective solution that can meet the needs of various applications and pave the way for wider implementation of nanotechnology.

Valkyrie Probes: A Novel Class of Enzyme-Activatable Photosensitizers based on Sulfur- and Seleno-Rosamines with Pyridinium Unit

The rational design of activatable photosensitizers (aPSs) uncaged by specific disease biomarkers is currently booming due to their positive attributes to achieve targeted photodynamic therapy (PDT). In this context, we present here the synthesis and detailed photophysical characterization of a novel class of hetero-rosamine dyes bearing sulfur or selenium as bridging heavy atom and 4-pyridyl meso-substituent as optically tunable group. The main feature of such photoactive platforms is the spectacular change of their spectral properties depending on the caging/decaging status of their 4-pyridyl moiety (cationic pyridinium vs. neutral pyridine). The preparation of two alkaline phosphatase (ALP)-responsive probes (named Valkyrie probes) was achieved through formal N-quaternarization with 4-phosphoryloxybenzyl, the traditional recognition moiety for this important diagnostic enzyme. Bio-analytical validations including fluorescence/singlet oxygen phosphorescence enzyme assays and RP-HPLC-fluorescence/-MS analyses have enabled us to demonstrate the viability and effectiveness of this novel photosensitizer activation strategy. Since sulfur-containing Valkyrie probe also retains high fluorogenicity in the orange-red spectral range, this study highlights meso-pyridyl-substituted S-pyronin scaffolds as valuable candidates for the rapid construction of molecular phototheranostic platforms suitable for combined fluorescence diagnosis and PDT.

Xanthene, cyanine, oxazine and BODIPY: the four pillars of the fluorophore empire for super-resolution bioimaging

In the realm of biological research, the invention of super-resolution microscopy (SRM) has enabled the visualization of ultrafine sub-cellular structures and their functions in live cells at the nano-scale level, beyond the diffraction limit, which has opened up a new window for advanced biomedical studies to unravel the complex unknown details of physiological disorders at the sub-cellular level with unprecedented resolution and clarity. However, most of the SRM techniques are highly reliant on the personalized special photophysical features of the fluorophores. In recent times, there has been an unprecedented surge in the development of robust new fluorophore systems with personalized features for various super-resolution imaging techniques. To date, xanthene, cyanine, oxazine and BODIPY cores have been authoritatively utilized as the basic fluorophore units in most of the small-molecule-based organic fluorescent probe designing strategies for SRM owing to their excellent photophysical characteristics and easy synthetic acquiescence. Since the future of next-generation SRM studies will be decided by the availability of advanced fluorescent probes and these four fluorescent building blocks will play an important role in progressive new fluorophore design, there is an urgent need to review the recent advancements in designing fluorophores for different SRM methods based on these fluorescent dye cores. This review article not only includes a comprehensive discussion about the recent developments in designing fluorescent probes for various SRM techniques based on these four important fluorophore building blocks with special emphasis on their effective integration into live cell super-resolution bio-imaging applications but also critically evaluates the background of each of the fluorescent dye cores to highlight their merits and demerits towards developing newer fluorescent probes for SRM.

Tailoring Homogeneous Hydrogel Nanospheres by Facile Ultra-Sonication Assisted Cross-Linked Copolymerization for Rhodamine B Dye Adsorption

The present paper describes the design of shape-oriented hydrogel nanospheres using a facile ultrasonication-supported crosslinked copolymerization technique. The effect of variable monomer concentration on the homogeneity of hydrogel nanospheres was investigated. The chitosan-cl-poly(MMA) hydrogel nanospheres were well characterized using various techniques such as FTIR, XRD, TGA, SEM, and TEM. The chitosan-cl-poly(MMA) hydrogel nanospheres were studied for their swelling behavior and could potentially be used as a novel adsorbent for rhodamine B dye remediation from aqueous media. The study found that utilizing chitosan-cl-poly(MMA) nanohydrogel spheres at the optimal pH 5 increased RhB dye adsorption capacity from 7.9 to 17.8 mg/g (pH 2 to 5), followed by a slight reduction. Furthermore, when nanohydrogel concentration increased, adsorption capacity dropped from 18.03 to 2.8 mg/g, but adsorption percentage climbed from 90.2% to 97.8%. At an initial dye concentration of 140 mg/L, rhodamine B adsorption achieved 204.3 mg/g in 60 min. The rhodamine B dye adsorption study includes adsorption kinetics, isotherm, and thermodynamics analyses. The interpretation of the adsorption study revealed that Langmuir isotherms fit best with a qmax value of 276.26 mg/g, which is in close approximation with the experimental value, whereas pseudo-second-order kinetics explains the adsorption process rate. The interaction of RhB dye with chitosan-cl-poly(MMA) hydrogel nanospheres involves multiple forces such as electrostatic interactions, hydrogen bonding, van der Waals forces, etc.

A New Boron-Rhodamine-Containing Carboxylic Acid as a Sugar Chemosensor

We propose a boron-rhodamine-containing carboxylic acid (BRhoC) substance as a new sugar chemosensor. BRhoC was obtained by the Friedel-Crafts reaction of 4-formylbenzoic acid and N,N-dimethylphenylboronic acid, followed by chloranil oxidation. In an aqueous buffer solution at pH 7.4, BRhoC exhibited an absorption maximum (Abs_max) at 621 nm. Its molar absorption coefficient at Abs_max was calculated to be 1.4 × 10⁵ M^-1 cm^-1, and it exhibited an emission maximum (Em_max) at 644 nm for the excitation at 621 nm. The quantum yield of BRhoC in CH₃OH was calculated to be 0.16. The borinate group of BRhoC reacted with a diol moiety of sugar to form a cyclic ester, which induced a change in the absorbance and fluorescence spectra. An increase in the D-fructose (Fru) concentration resulted in the red shift of the Abs_max (621 nm without sugar and 637 nm with 100 mM Fru) and Em_max (644 nm without sugar and 658 nm with 100 mM Fru) peaks. From the curve fitting of the plots of the fluorescence intensity ratio at 644 nm and 658 nm, the binding constants (K) were determined to be 2.3 × 10² M^-1 and 3.1 M^-1 for Fru and D-glucose, respectively. The sugar-binding ability and presence of a carboxyl group render BRhoC a suitable building block for the fabrication of highly advanced chemosensors.

The pursuit of xanthenoid fluorophores with near-infrared-II emission for in vivo applications

As fluorescence imaging in the second near-infrared window (NIR-II, 1000-1700 nm) has gained increasing attention, it is inevitable that NIR-II fluorophores, the cornerstone of NIR-II imaging, have come to the middle of the stage. NIR-II xanthenoid fluorophores with good stability, high brightness, and fluorescence adjustability are becoming popular. We here reviewed the recent progress of xanthenoid fluorophores with NIR-II emission for in vivo applications. Especially, we focus on the strategies used for longer wavelength and fluorescence regulation to construct OFF-ON or ratiometric NIR-II fluorescent probes.

Xanthone-based solvatochromic fluorophores for quantifying micropolarity of protein aggregates

Proper three-dimensional structures are essential for maintaining the functionality of proteins and for avoiding pathological consequences of improper folding. Misfolding and aggregation of proteins have been both associated with neurodegenerative disease. Therefore, a variety of fluorogenic tools that respond to both polarity and viscosity have been developed to detect protein aggregation. However, the rational design of highly sensitive fluorophores that respond solely to polarity has remained elusive. In this work, we demonstrate that electron-withdrawing heteroatoms with (d-p)-π* conjugation can stabilize lowest unoccupied molecular orbital (LUMO) energy levels and promote bathochromic shifts. Guided by computational analyses, we have devised a novel series of xanthone-based solvatochromic fluorophores that have rarely been systematically studied. The resulting probes exhibit superior sensitivity to polarity but are insensitive to viscosity. As proof of concept, we have synthesized protein targeting probes for live-cell confocal imaging intended to quantify the polarity of misfolded and aggregated proteins. Interestingly, our results reveal several layers of protein aggregates in a way that we had not anticipated. First, microenvironments with reduced polarity were validated in the misfolding and aggregation of folded globular proteins. Second, granular aggregates of AgHalo displayed a less polar environment than aggregates formed by folded globular protein represented by Htt-polyQ. Third, our studies reveal that granular protein aggregates formed in response to different types of stressors exhibit significant polarity differences. These results show that the solvatochromic fluorophores solely responsive to polarity represent a new class of indicators that can be widely used for detecting protein aggregation in live cells, thus paving the way for elucidating cellular mechanisms of protein aggregation as well as therapeutic approaches to managing intracellular aggregates.

Stable, Bright, and Long-Fluorescence-Lifetime Dyes for Deep-Near-Infrared Bioimaging

Near-infrared (NIR) fluorophores absorbing maximally in the region beyond 800 nm, i.e., deep-NIR spectral region, are actively sought for biomedical applications. Ideal dyes are bright, nontoxic, photostable, biocompatible, and easily derivatized to introduce functionalities (e.g., for bioconjugation or aqueous solubility). The rational design of such fluorophores remains a major challenge. Silicon-substituted rhodamines have been successful for bioimaging applications in the red spectral region. The longer-wavelength silicon-substituted congeners for the deep-NIR spectral region are unknown to date. We successfully prepared four silicon-substituted bis-benzannulated rhodamine dyes (ESi5a-ESi5d), with an efficient five-step cascade on a gram-scale. Because of the extensive overlapping of their HOMO-LUMO orbitals, ESi5a-ESi5d are highly absorbing (λ_abs ≈ 865 nm and ε > 10⁵ cm^-1 M^-1). By restraining both the rotational freedom via annulation and the vibrational freedom via silicon-imparted strain, the fluorochromic scaffold of ESi5 is highly rigid, resulting in an unusually long fluorescence lifetime (τ > 700 ps in CH₂Cl₂) and a high fluorescence quantum yield (ϕ = 0.14 in CH₂Cl₂). Their half-lives toward photobleaching are 2 orders of magnitude longer than the current standard (ICG in serum). They are stable in the presence of biorelevant concentration of nucleophiles or reactive oxygen species. They are minimally toxic and readily metabolized. Upon tail vein injection of ESi5a (as an example), the vasculature of a nude mouse was imaged with a high signal-to-background ratio. ESi5 dyes have broad potentials for bioimaging in the deep-NIR spectral region.

A general approach to S-rhodamines from diaryl thioethers and their application in constructing pH probes

A general strategy for the efficient preparation of S-rhodamines from the condensation of diaryl thioether and 2-carboxybenzaldehydes was reported. We further took a morpholine containing spirolactam structure as an example to illustrate that these S-rhodamine dyes could be utilized to construct fluorescent probes based on the ring-opening process. This work provided a general approach for the synthesis of novel S-rhodamine dyes, thus possibly facilitating the development of fluorescence imaging.

Molecular structure perspective on Temperature-Sensitive properties of rhodamine aqueous solutions

As one of the most commonly used organic fluorescent dyes, recently rhodamines have been successfully employed in temperature sensing. However, few works have been reported on their temperature-sensitive properties, which inevitably limiting their further applications. In order to solve such problem, we investigated temperature-sensitive properties of rhodamine 110, 123, 19, 6G, B and 3B focusing on their fluorescence emission spectra; and analyzed them in the molecular structure perspective. It is demonstrated that the fluorescence emission intensities of all studied rhodamines decreased with higher temperature, which inevitably enhances the probability of collisions among molecules, thus definitely leads to energy loss in fluorescence emission. While these rhodamines still have various temperature sensitivities mainly due to the substitutes: the substitute on the benzene carboxylate has little effect; the amino substituents of the three-ring xanthene enhance the temperature sensitivity due to their rotation weakening the rigidity of the three-ring xanthene; and the methyl substituents on the three-ring xanthene reduce the temperature sensitivity by enhancing the rigidity and stability of the three-ring xanthene as well as hindering the rotation of ethylamino. These findings can also be extended to other organic fluorescent dyes proved by coumarins comparable to rhodamines. The results provided by this work can be useful reference and guidance to further develop organic fluorescent dyes especially for temperature sensing.

A mitochondria targetable near-infrared fluorescence probe for glutathione visual biological detection

Glutathione (GSH), an abundant non-protein thiol, plays a crucial role in numerous biotic processes. Herein, a mitochondria-targeted near-infrared GSH probe (JGP) was synthesized, which displayed desired properties with high specificity and sensitivity, appreciable water solubility, and rapid response time. In the presence of GSH, nearly a 13-fold fluorescence emission growth appeared at 730 nm and the solvent color changed from blue to cyan. The sensing mechanism of JGP and GSH was confirmed by a high-resolution mass spectroscopy analysis. Moreover, good cell penetration enabled JGP to be successfully used for imaging biological samples such as HeLa cells, C. elegans, and especially rat brain slices. Imaging experiments showed that JGP could monitor the GSH concentration changes with a dose-dependent direct ratio in all the tested samples. The successful application of JGP in brain imaging indicates that JGP is a suitable GSH optical probe, which may have wide application value in fields of brain imaging. It also lays a theoretical and practical foundation for the further application of fluorescent probes in brain sciences.

Recent progress in fluorescent probes for bacteria

Food fermentation, antibiotics, and pollutant degradation are closely related to bacteria. Bacteria play an irreplaceable role in life. However, some bacteria seriously threaten human health and cause large-scale infectious diseases. Therefore, there is a pressing need to develop strategies to accurately monitor bacteria. Technology based on molecular probes and fluorescence imaging is noninvasive, results in little damage, and has high specificity and sensitivity, so it has been widely applied in the detection of bacteria. In this review, we summarize the recent progress in bacterial detection using fluorescence. In particular, we generalize the mechanisms commonly used to design organic fluorescent probes for detecting and imaging bacteria. Moreover, a perspective regarding fluorescent probes for bacterial detection is discussed.

Recent Progress in Fluorescent Sensors for Drug-Induced Liver Injury Assessment

Drug-induced liver injury (DILI) is a persistent concern in drug discovery and clinical medicine. The current clinical methods to assay DILI by analyzing the enzymes in serum are still not optimal. Recent studies showed that fluorescent sensors would be efficient tools for detecting the concentration and distribution of DILI indicators with high sensitivity and specificity, in real-time, in situ, and with low damage to biosamples, as well as diagnosing DILI. This review focuses on the assessment of DILI, introduces the current mechanisms of DILI, and summarizes the design strategies of fluorescent sensors for DILI indicators, including ions, small molecules, and related enzymes. Some challenges for developing DILI diagnostic fluorescent sensors are put forward. We believe that these design strategies and challenges to evaluate DILI will inspire chemists and give them opportunities to further develop other fluorescent sensors for accurate diagnoses and therapies for other diseases.

Mitochondria-Anchored Molecular Thermometer Quantitatively Monitoring Cellular Inflammations

Temperature in mitochondria can be a critical indicator of cell metabolism. Given the highly dynamic and inhomogeneous nature of mitochondria, it remains a big challenge to quantitatively monitor the local temperature changes during different cellular processes. To implement this task, we extend our strategy on mitochondria-anchored thermometers from "on-off" probe Mito-TEM to a ratiometric probe Mito-TEM 2.0 based on the Förster resonance energy transfer mechanism. Mito-TEM 2.0 exhibits not only a sensitive response to temperature through the ratiometric changes of dual emissions but also the specific immobilization in mitochondria via covalent bonds. Both characters support accurate and reliable detection of local temperature for a long time, even in malfunctioning mitochondria. By applying Mito-TEM 2.0 in fluorescence ratiometric imaging of cells and zebrafishes, we make a breakthrough in the quantitative visualization of mitochondrial temperature rises in different inflammation states.

Fluorescent sensing film decorated with ratiometric probe for visual and recyclable monitoring of Cu2

Specifically, visually, and quantitatively monitor copper ion (Cu²⁺) is critical in the area of biological and environmental detection. Herein, a ratiometric fluorescent probe with benzoxazole appended xanthenes skeleton was constructed and further employed to monitor Cu²⁺ in Hela cells, real water samples, and test strips. An easily distinguishable colorimetric (colorless to red) and fluorescence (green to red) change could be observed by naked eye under the portable UV lamp (365 nm) and the changes could be recovered by adding S^2-. Furthermore, electrospinning technique was employed to fabricate a probe composited fluorescent sensing film (PMMA) for realizing the visual and recyclable monitoring of Cu²⁺, indicating that the probe-composited fluorescent sensing film has great potential for on-site and naked-eye detection of Cu²⁺ in practical.

An ICT-based fluorescent probe guided by theoretical calculation for selectively mapping endogenous GSH in living cells

Glutathione (GSH) is one of the most essential bio-thiols to maintain the redox balance of organisms which is strongly associated with many physiological processes. Detecting the concentration and mapping the distribution of GSH in the living system is significant to study many related diseases. In this work, we have successfully constructed an ICT-based model to guide the design and synthesis of GSH specific fluorescent probe CF1. A serials spectroscopy test demonstrated that the response of CF1 towards GSH owned large stokes shift (~167 nm) and an excellent linear relationship (0-120 μM, R² = 0.9961). Furthermore, CF1 was successfully applied to image endogenous GSH in different cell lines with high sensitivity. This work is instructive for the oriented synthesis of ICT-based functional fluorescent probe and the further visualization of intracellular targets in the living system.

Structurally-thrifty and visible-absorbing fluorophores

Fluorophores with a minimal push-pull backbone are actively pursued due to their potentials in biological labelling. Herein a series of structurally-thrifty and visible-absorbing fluorophores (SDXs) were successfully constructed following the D'D-π-A design strategy, in which a secondary donor (D') was introduced in conjugation with the donor (D) to enhance its electron donating capability. For a very small scaffold, SDXs exhibit a surprisingly long-wavelength absorption band in the visible spectral range (λ_abs = 420 nm) and a strong green fluorescence emission (λ_em = 530 nm) with a fluorescence quantum yield up to 0.84. Notably, fluorescence of SDXs was quenched in hydrogen-bonding solvents, e.g. MeOH and H₂O. This phenomenon renders SDXs feasibility for imaging of cellular non-hydrogen-bonding microenvironment, as demonstrated with BEAS-2B cells. These results proved that the D'D-π-A is a powerful design strategy to construct novel structurally-thrifty fluorophores.

Facile Microwave-Assisted Synthesis of Functionalized Carbon Nitride Quantum Dots as Fluorescence Probe for Fast and Highly Selective Detection of 2,4,6-Trinitrophenol

Functionalized carbon nitride quantum dots (CNQDs) are fabricated by moderate carbonization of L-tartaric acid and urea in oil acid media by a facile microwave-assisted solvothermal method. The obtained CNQDs are monodispersed with a narrow size distribution (average size of 3.5 nm), and exhibit excellent selectivity and sensitivity of fluorescence quenching for 2,4,6-trinitrophenol (TNP) with a quenching efficiency coefficient Ksv of 4.75 × 104 M-1. This sensing system exhibits a fast response time within 1 min and a wide linear response range from 0.1 to 15 μM. The limit of detection is as low as 87 nM, which is comparable or lower than the other probes. The application of the developed probe to the detection of TNP in spiked water samples yields satisfactory results. The mechanism of fluorescence quenching is also discussed. Graphical Abstract An optical sensor based on functionalized carbon nitride quantum dots (CNQDs) were fabricated from L-tartaric acid and urea by a facile one-pot microwave-assisted solvothermal method, and were effectively utilized to the detection of 2,4,6-trinitrophenol (TNP) based on fluorescence (FL) quenching.

Recent Progress in Small Spirocyclic, Xanthene-Based Fluorescent Probes

The use of fluorescent probes in a multitude of applications is still an expanding field. This review covers the recent progress made in small molecular, spirocyclic xanthene-based probes containing different heteroatoms (e.g., oxygen, silicon, carbon) in position 10'. After a short introduction, we will focus on applications like the interaction of probes with enzymes and targeted labeling of organelles and proteins, detection of small molecules, as well as their use in therapeutics or diagnostics and super-resolution microscopy. Furthermore, the last part will summarize recent advances in the synthesis and understanding of their structure-behavior relationship including novel computational approaches.

Molecular Origins of Heteroatom Engineering on the Emission Wavelength Tuning, Quantum Yield Variations and Fluorogenicity of NBD-like SCOTfluors

Molecular engineering of fluorophore scaffolds, especially heteroatom replacement, is a promising method to yield novel fluorophores with tailored properties for various applications. Yet, molecular origins of the distinct fluorescent properties in newly developed SCOTfluors, i. e., varied emission wavelengths, distinct quantum yields, and fluorogenicity, remain elusive. Such understanding, however, is critical for the rational molecular engineering of high-performance fluorophores. Herein, we employed quantum chemical calculations to understand the structure-property relationships of nitrobenzoxadiazole (NBD)-like SCOTfluors. Our findings are important not only for the rational deployment of SCOTfluors, but also for the effective modifications of other fluorophore scaffolds, for satisfying the increasingly diversified requirements of bioimaging and biosensing applications.

Imaging GPCR internalization using near-infrared Nebraska red-based reagents

Internalization of G protein-coupled receptor (GPCRs) represents a nearly universal pathway for receptor downregulation. Imaging this process provides a means for the identification of pharmaceutical agents as well as potential ligands for orphan receptors. However, there is a need for the further development of near-infrared (NIR) probes capable of monitoring internalization in order to enable multiplexing with existing green fluorescent GPCR activity assays. Our laboratory has recently described a series of near-infrared (NIR) fluorophores in which a phosphinate functionality is inserted at the bridging position of the xanthene scaffold. These fluorophores, termed Nebraska Red (NR) dyes, provide attractive reagents for imaging protein localization. Herein, we disclose the development of NR-based HaloTag ligands for imaging membrane proteins on living cells. These new probes are utilized to image membrane pools of the human orexin type 2 receptor, an established target for the treatment of insomnia. We demonstrate the ability of fetal bovine serum (FBS) to noncovalently associate with a spirolactonized NR probe, enabling no-wash imaging with a 45-fold enhancement of fluorescence. Furthermore, we characterize the utility of NR-based HaloTag ligands for real-time monitoring of receptor internalization upon agonist stimulation. These new reagents enable potential multiplexing with existing GPCR activity assays in order to identify new modulators of GPCR activity as well as ligands for orphan receptors.

Systematic study of synthesizing various heteroatom-substituted rhodamines from diaryl ether analogues

The dye rhodamine, as the most popular scaffold to construct fluorescent labels and probes, has been explored extensively on its structure-fluorescence relationships. Particularly, the replacement of the oxygen atom in the 10th position with heteroatoms obtained various new rhodamines with improved photophysical properties, such as brightness, photostability, red-shifted emission and fluorogenicity. However, the applications of heteroatom-substituted rhodamines have been hindered by difficult synthetic routes. Herein, we explored the condensation strategy of diaryl ether analogues and o-tolualdehyde to synthesize various heteroatom-substituted rhodamines. We found that the electron property and steric effect in the rhodamine 10th position determined the synthetic yield. It's concluded that this condensation method was more suitable for the synthesis of heteroatom-substituted rhodamines with small or electron-donating groups like rhodamine, S-rhodamine and Si-rhodamine. We hope these results will benefit the design and synthesis of heteroatom-substituted rhodamines.

Multiple Factors Regulate the Spirocyclization Equilibrium of Si-Rhodamines

Si-rhodamine has been extensively used in super-resolution fluorescence imaging in recent years. Its equilibrium between ring-closed nonfluorescent spirolactones and ring-opened fluorescent zwitterions endows Si-rhodamine with excellent fluorogenicity, membrane permeability, and photostability. In this paper, the equilibrium of Si-rhodamine between lactones and zwitterions was revealed to be greatly affected by various environmental factors, including molecular aggregation, solvent polarity, pH, metal ions, irradiation, and temperature. These environmental sensitivities make Si-rhodamine useful as a hydrochromic material, a fluorescent sensor array for metal ions or solvents, and a photoactivatable switch. Importantly, these results indicate that using Si-rhodamine as a fluorogenic probe or a blinking fluorophore in single-molecule localization super-resolution microscopy requires caution on possible false signals caused by its environmental sensitivity.