Photophysical behavior of lipophilic xanthene dyes without the involvement of photoinduced electron transfer mechanism

The correlation of dibutyl-ether-ester of xanthene dye structures with their photophysical properties is discussed with respect to their capability as fluorescent probes based on ultraviolet–visible absorption, fluorescence spectra and fluorescence lifetimes measured in different solvents. It was found that the dibutyl-ether-ester of fluorescein is very weakly emissive in aprotic solvents, but fairly strong fluorescent in alcohols. The dependence of fluorescence quantum yield (Φ_f) and lifetime (τ_f) on solvent polarity suggests non-involvement of the intra-molecular photoinduced electron transfer (PeT) mechanism, suggested previously to account for the emission efficiency of fluorescein derivatives. The xanthene dyes intend to self-assemble in aprotic solvents, less polar solvents facilitate the aggregation while hydrogen bonding disfavor it. The formation of non-emissive H-aggregates is proposed to be responsible for their fluorescent behavior. The esterification showed stronger influences on the photophysics than the etherification, i.e. the former caused larger reduction of Φ_f owing to the internal conversion. The halogenation decreases the fluorescence quantum yield and lifetime of the xanthene dyes, owing to the enhancement of inter-system crossing process.     

Synthesis of a Far‐Red Photoactivatable Silicon‐Containing Rhodamine for Super‐Resolution Microscopy

The rhodamine system is a flexible framework for building small‐molecule fluorescent probes. Changing N‐substitution patterns and replacing the xanthene oxygen with a dimethylsilicon moiety can shift the absorption and fluorescence emission maxima of rhodamine dyes to longer wavelengths. Acylation of the rhodamine nitrogen atoms forces the molecule to adopt a nonfluorescent lactone form, providing a convenient method to make fluorogenic compounds. Herein, we take advantage of all of these structural manipulations and describe a novel photoactivatable fluorophore based on a Si‐containing analogue of Q‐rhodamine. This probe is the first example of a “caged” Si‐rhodamine, exhibits higher photon counts compared to established localization microscopy dyes, and is sufficiently red‐shifted to allow multicolor imaging. The dye is a useful label for super‐resolution imaging and constitutes a new scaffold for far‐red fluorogenic molecules.     

Near-infrared fluorescence activation probes based on disassembly-induced emission cyanine dye

Currently most of the fluorogenic probes are designed for the detection of enzymes which work by converting the non-fluorescence substrate into the fluorescence product via an enzymatic reaction. On the other hand, the design of fluorogenic probes for non-enzymatic proteins remains a great challenge. Herein, we report a general strategy to create near-IR fluorogenic probes, where a small molecule ligand is conjugated to a novel γ-phenyl-substituted Cy5 fluorophore, for the selective detection of proteins through a non-enzymatic process. Detail mechanistic studies reveal that the probes self-assemble to form fluorescence-quenched J-type aggregate. In the presence of target analyte, bright fluorescence in the near-IR region is emitted through the recognition-induced disassembly of the probe aggregate. This Cy5 fluorophore is a unique self-assembly/disassembly dye as it gives remarkable fluorescence enhancement. Based on the same design, three different fluorogenic probes were constructed and one of them was applied for the no-wash imaging of tumor cells for the detection of hypoxia-induced cancer-specific biomarker, transmembrane-type carbonic anhydrase IX.     

High-contrast and real-time visualization of membrane proteins in live cells with malachite green-based fluorogenic probes

Imaging dynamics of membrane proteins of live cells in a wash-free and real-time manner has been a challenging task. Herein, we report unprecedented applications of malachite green(MG), an organic dye widely used in pigment industry, as a switchable fluorophore to monitor membrane enzymes or noncatalytic proteins in live cells. Conformationally flexible MG is non-fluorescent in aqueous solution, yet covalent binding with endogenous proteins of cells significantly enhances its fluorescence at 670...     

Time-resolved fluorescence depolarization studies of rotational relaxation in viscous media

Rotational relaxation times (τ_roi) were measured for xanthene dyes in several n-alcohols, ethylene glycol and glycerol by following the fluorescence depolarization using a single photon counting technique. Additional studies were made of the fluidity of the hydrocarbon micellar interior using pyrene derivatives as fluorescent probes. While the correlation between τ_roi and viscosity for the smaller n-alcohols is good, as anticipated by the models of Stokes—Einstein—Debye and later Perrin, a saturation in this correlation is observed in more viscous systems in accordance with recent molecular dynamics calculations. The influence of molecular structure on both viscosity and rotational relaxation times is also discussed. Pyrene, 1-pyrene suphonic acid and 1-pyrene butyeric acid exhibit rapid reorientation τ_roi ? 10^?9 s, in glycerol and micellar systems.     

Interfacing Click Chemistry with Automated Oligonucleotide Synthesis for the Preparation of Fluorescent DNA Probes Containing Internal Xanthene and Cyanine Dyes

Double‐labeled oligonucleotide probes containing fluorophores interacting by energy‐transfer mechanisms are essential for modern bioanalysis, molecular diagnostics, and in vivo imaging techniques. Although bright xanthene and cyanine dyes are gaining increased prominence within these fields, little attention has thus far been paid to probes containing these dyes internally attached, a fact which is mainly due to the quite challenging synthesis of such oligonucleotide probes. Herein, by using 2′‐O‐propargyl uridine phosphoramidite and a series of xanthenes and cyanine azide derivatives, we have for the first time performed solid‐phase copper(I)‐catalyzed azide–alkyne cycloaddition (CuAAC) click labeling during the automated phosphoramidite oligonucleotide synthesis followed by postsynthetic click reactions in solution. We demonstrate that our novel strategy is rapid and efficient for the preparation of novel oligonucleotide probes containing internally positioned xanthene and cyanine dye pairs and thus represents a significant step forward for the preparation of advanced fluorescent oligonucleotide probes. Furthermore, we demonstrate that the novel xanthene and cyanine labeled probes display unusual and very promising photophysical properties resulting from energy‐transfer interactions between the fluorophores controlled by nucleic acid assembly. Potential benefits of using these novel fluorescent probes within, for example, molecular diagnostics and fluorescence microscopy include: Considerable Stokes shifts (40–110 nm), quenched fluorescence of single‐stranded probes accompanied by up to 7.7‐fold light‐up effect of emission upon target DNA/RNA binding, remarkable sensitivity to single‐nucleotide mismatches, generally high fluorescence brightness values (FB up to 26), and hence low limit of target detection values (LOD down to <5 nM ).     

[Et3NH][HSO4]-mediated efficient synthesis of novel xanthene derivatives and their biological evaluation

A series of novel 2-chloro quinoline incorporated xanthene derivatives were synthesized by using various 2-chloro 3-formyl quinoline, dimedone and triethylammonium hydrogen sulfate [Et₃NH][HSO₄] as a catalyst as well solvent to give good to excellent yields. All the xanthene compounds were investigated for their in vitro antimycobacterial activity against M. tuberculosis H37Ra (MTB) and M. bovis BCG strains. Among the synthesized compounds 3a, 3c, 3d, 3e, 3g, 3h and 3k were highly potent against both the strains. Most of the active compounds were non-cytotoxic against THP-1, HCT-116, A549 and MCF-7 cell lines. Most active compounds were having higher selectively index which suggested that these compound were highly potent.     

2-Amino-3′-dialkylaminobiphenyl-based fluorescent intracellular probes for nitric oxide surrogate N2O3

Fluorescent probes for nitric oxide (NO), or more frequently for its oxidized surrogate dinitrogen trioxide (N₂O₃), have enabled scientists to study the contributions of this signaling molecule to many physiological processes. Seeking to improve upon limitations of other probes, we have developed a family of fluorescent probes based on a 2-amino-3′-dialkylaminobiphenyl core. This core condenses with N₂O₃ to form benzo[c]cinnoline structures, incorporating the analyte into the newly formed fluorophore, which results in product fluorescence with virtually no background contribution from the initial probe. We varied the substituents in the core in order to optimize both the reactivity of the probes with N₂O₃ and their cinnoline products'' fluorescence wavelengths and brightness. The top candidates were then applied to cultured cells to verify that they could respond to NO within cellular milieus, and the top performer, NO₅₃₀, was compared with a “gold standard” commercial probe, DAF-FM, in a macrophage-derived cell line, RAW 264.7, stimulated to produce NO. NO₅₃₀ demonstrated similar or better sensitivity and higher selectivity for NO than DAF, making it an attractive potential alternative for NO tracking in various applications.

A thorough structure-property relationship study has produced much-improved fluorescence probes for nitric oxide surrogate, e.g. N₂O₃, compared to the original NO₅₅₀.     

Development of xanthene dyes containing arylacetylenes: The role of acetylene linker and substituents on the aryl group

Fluorescent dyes possessing a variety of arylacetylenes at the 9-position of a xanthene skeleton were synthesized and their optical properties were investigated. The π system effectively expanded over the xanthene skeleton and the aryl group through the triple bond. Starting from the emission wavelength (λ_em) of 9-methyl xanthene 20 in basic DMSO solution at 536?nm, the emission wavelengths gradually shifted to the red region for methylacetylene 17 (λ_em?=?600?nm), phenylacetylene 5 (λ_em?=?636?nm), and p-CF₃-phenylacetylene 11 (λ_em?=?660?nm). On the basis of these data, we estimated the substituent effects for the red shift on the emission wavelength and rationally explained the results by DFT calculations. Furthermore, potential applicability of these fluorescent dyes to cell staining was exemplified.     

A general strategy for in situ assembly of light-up fluorophores via bioorthogonal Suzuki-Miyaura cross-coupling

Herein we presented a general strategy for in situ assembly of intramolecular charge-transfer (ICT)-based light-up fluorophores via bioorthogonal Suzuki-Miyaura cross-coupling reaction. By introducing iodo group at the appropriate position, five fluorophores with different scaffolds including naphthalimide, coumarin, naphthalene sulfonate, nitrobenzoxadiazole, and acetonaphthone, were designed as bioorthogonal multicolor fluorogenic probes, which could produce significant fluorescence enhancement and high fluorescence quantum yield after Suzuki-Miyaura reaction with aryl boronic acid or boronate. Manipulating the substituents and π scaffold in the fluorophores allows fine-tuning of their photophysical properties. With this strategy, we succeeded in peptide conjugation, no-wash fluorogenic protein labeling, and mitochondria-selective bioorthogonal imaging in live cells.     

Efficient [4+1]/[3+2+1] bis-cyclizations stereoselectively yielding unprecedented polyacyclic indeno-fused xanthenes

Concise and efficient [4+1]/[3+2+1] bis-cyclizations of o-phthalaldehyde with cyclic 1,3-dicarbonyls have been established for the stereoselective synthesis of unprecedented polycyclic indeno[2,1-l]xanthene derivatives. The multicomponent domino reaction (MDR, AB₂ type) is easy to perform by mixing inexpensive substrates in HOAc at room temperature. The present synthesis shows attractive properties such as the simple one-pot fashion, high bond-forming efficiency, and easy purifications. Up to two new rings and four sigma-bonds were achieved in these MDRs without using any metal catalysts.     

Fluorogenic Squaraine Dendrimers for Background-Free Imaging of Integrin Receptors in Cancer Cells

To overcome the limited brightness of existing fluorogenic molecular probes for biomolecular targets, we introduce a concept of fluorogenic dendrimer probe, which undergoes polarity-dependent switching due to intramolecular aggregation-caused quenching of its fluorophores. Based on a rational design of dendrimers with four and eight squaraine dyes, we found that octamer bearing dyes through a sufficiently long PEG(8) linker displays >400-fold fluorescence enhancement from water to non-polar dioxane. High extinction coefficient (≈2,300,000 m ⁻¹ cm⁻¹) resulted from eight squaraine dyes and quantum yield (≈25 %) make this octamer the brightest environment-sensitive fluorogenic molecule reported to date. Its conjugate with cyclic RGD used at low concentration (3 nm ) enables integrin-specific fluorescence imaging of cancer cells with high signal-to-background ratio. The developed dendrimer probe is a “golden middle” between molecular probes and nanoparticles, combining small size, turn-on response and high brightness, important for bioimaging.     

New Chemodosimetric Reagents as Ratiometric Probes for Cysteine and Homocysteine and Possible Detection in Living Cells and in Blood Plasma

In this work, we have rationally designed and synthesized two new reagents ( L₁ and L₂ ), each bearing a pendant aldehyde functionality. This aldehyde group can take part in cyclization reactions with β‐ or γ‐amino thiols to yield the corresponding thiazolidine and thiazinane derivatives, respectively. The intramolecular charge‐transfer (ICT) bands of these thiazolidine and thiazinane derivatives are distinctly different from those of the molecular probes ( L₁ and L₂ ). Such changes could serve as a potential platform for using L₁ and L₂ as new colorimetric/fluorogenic as well as ratiometric sensors for cysteine (Cys) and homocysteine (Hcy) under physiological conditions. Both reagents proved to be specific towards Cys and Hcy even in the presence of various amino acids, glucose, and DNA. Importantly, these two chemodosimetric reagents could be used for the quantitative detection of Cys present in blood plasma by using a pre‐column HPLC technique. Such examples are not common in contemporary literature. MTT assay studies have revealed that these probes have low cytotoxicity. Confocal laser scanning micrographs of cells demonstrated that these probes could penetrate cell membranes and could be used to detect intracellular Cys/Hcy present within living cells. Thus, the results presented in this article not only demonstrate the efficiency and specificity of two ratiometric chemodosimeter molecules for the quantitative detection of Cys and Hcy, but also provide a strategy for developing reagents for analysis of these vital amino acids in biological samples.     

Ultrafluorogenic Monochromophore-Type BODIPY-Tetrazine Series for Dual-Color Bioorthogonal Imaging with a Single Probe

Various fluorogenic probes utilizing tetrazine (Tz) as a fluorescence quencher and bioorthogonal reaction partner have been extensively studied over the past few decades. Herein, we synthesized a series of boron-dipyrromethene (BODIPY)-Tz probes using monochromophoric design strategy for bioorthogonal cellular imaging. The BODIPY-Tz probes exhibited excellent bicyclo[6.1.0]nonyne (BCN)-selective fluorogenicity with three- to four-digit-fold enhancements in fluorescence over a wide range of emission wavelengths, including the far-red region. Furthermore, we demonstrated the applicability of BODIPY-Tz probes in bioorthogonal fluorescence imaging of cellular organelles without washing steps. We also elucidated the aromatized pyridazine moiety as the origin of BCN-selective fluorogenic behavior. Additionally, we discovered that the fluorescence of the trans-cyclooctene (TCO) adducts was quenched in aqueous media via photoinduced electron transfer (PeT) process. Interestingly, we observed a distinctive recovery of the initially quenched fluorescence of BODIPY-Tz-TCO upon exposure to hydrophobic media, accompanied by a significant bathochromic shift of its emission wavelength relative to that exhibited by the corresponding BODIPY-Tz-BCN. Leveraging this finding, for the first time, we achieved dual-color bioorthogonal cellular imaging with a single BODIPY-Tz probe.     

Saturable absorption dynamics in the triplet system and triplet excitation induced singlet fluorescence of some organic molecules

The triplet saturable absorption behaviour of the xanthene dyes eosin Y, erythrosin B, and rose bengal and of the fullerene molecule C₇₀ is studied. The molecules are excited to the S₁-state by intense picosecond pulses (wavelength λ_P=527 nm). They relax dominantly to the triplet system by intersystem crossing. The triplet–triplet saturable absorption is investigated with time-delayed intense picosecond pulses (wavelength λ_L=1054 nm) in the transparency region of the molecules in the singlet ground state. Higher excited-state triplet absorption cross-sections and higher excited-state triplet relaxation times are determined by numerical simulation of the experimental results. Time-resolved fluorescence measurements reveal higher excited-state triplet to singlet back-intersystem-crossing and multi-step triplet photoionization. Additionally the two-photon absorption cross-sections at λ_L=1054 nm are determined by measurement of the fundamental pulse two-photon induced fluorescence relative to the second-harmonic pulse single-photon induced fluorescence.     

Fluorescence of Eu3+-doped InF3-based optical glasses

This paper reports physical, absorption and photoluminescence spectral properties of Eu³⁺-doped indium trifluoride-based optical glasses of the following formulae: 48 InF₃-24 BaF₂-7 AlF₃-20 RF, where RF is the alkali content (LiF, NaF and KF). From fluorescence characteristics of these Eu³⁺-doped glasses, it is found that Glass-A with 20 M% LiF as the network modifier shows a better trend in its optical behaviour. A red emission from these glasses has been noticed upon illumination with the UV lamp. The lifetimes of the lasing transition (⁵D₀→⁷F₂) have been measured both at 300 and 77K with an Ar⁺ laser (487.9 nm) as the source of excitation. Four additional fluorescent levels at 580, 592, 598 and 653 nm have also been measured.     

A Far-Red Molecular Rotor Fluorogenic Trehalose Probe for Live Mycobacteria Detection and Drug-Susceptibility Testing

Increasing the speed, specificity, sensitivity, and accessibility of mycobacteria detection tools are important challenges for tuberculosis (TB) research and diagnosis. In this regard, previously reported fluorogenic trehalose analogues have shown potential, but their green-emitting dyes may limit sensitivity and applications in complex settings. Here, we describe a trehalose-based fluorogenic probe featuring a molecular rotor turn-on fluorophore with bright far-red emission (RMR-Tre). RMR-Tre, which exploits the unique biosynthetic enzymes and environment of the mycobacterial outer membrane to achieve fluorescence activation, enables fast, no-wash, low-background fluorescence detection of live mycobacteria. Aided by the red-shifted molecular rotor fluorophore, RMR-Tre exhibited up to a 100-fold enhancement in M. tuberculosis labeling compared to existing fluorogenic trehalose probes. We show that RMR-Tre reports on M. tuberculosis drug resistance in a facile assay, demonstrating its potential as a TB diagnostic tool.     

3‐Formyl‐BODIPY Phenylhydrazone as a Chromo‐Fluorogenic Probe for Selective Detection of NO2 (g)

A new colorimetric and fluorogenic probe, based on a 3‐formyl boron dipyrromethene (BODIPY) phenylhydrazone, for the sensitive and selective detection NO₂ (g) has been prepared. The probe in solution experiences a remarkable hypsochromic shift of its absorption and fluorescence emission bands in the presence gaseous NO₂ (g), leading to limits of detection of few ppb. The probe also works in the solid phase, adsorbed on filter paper strips, or chemically immobilized on the surface of silica nanoparticles, with limits of detection to the naked eye of about 0.5 ppm.     

In Situ Localization of Enzyme Activity in Live Cells by a Molecular Probe Releasing a Precipitating Fluorochrome

Current enzyme‐responsive, fluorogenic probes fail to provide in situ information because the released fluorophores tend to diffuse away from the reaction sites. The problem of diffusive signal dilution can be addressed by designing a probe that upon enzyme conversion releases a fluorophore that precipitates. An excited‐state intramolecular proton transfer (ESIPT)‐based solid‐state fluorophore HTPQ was developed that is strictly insoluble in water and emits intense fluorescence in the solid state, with λ _ex/em=410/550 nm, thus making it far better suited to use with a commercial confocal microscope. HTPQ was further utilized in the design of an enzyme‐responsive, fluorogenic probe (HTPQA), targeting alkaline phosphatase (ALP) as a model enzyme. HTPQA makes possible diffusion‐resistant in situ detection of endogenous ALP in live cells. It was also employed in the visualizing of different levels of ALP in osteosarcoma cells and tissue, thus demonstrating its interest for the diagnosis of this type of cancer.     

Clicking of organelle-enriched probes for fluorogenic imaging of autophagic and endocytic fluxes

Autophagy and endocytosis are essential in regulating cellular homeostasis and cancer immunotherapeutic responses. Existing methods for autophagy and endocytosis imaging are susceptible to cellular micro-environmental changes, and direct fluorogenic visualization of their fluxes remains challenging. We develop a novel strategy via clicking of organelle-enriched probes (COP), which comprises a pair of trans-cyclooctenol (TCO) and tetrazine probes separately enriched in lysosomes and mitochondria (in autophagy) or plasma membrane (in endocytosis). These paired probes are merged and boost a fluorogenic click reaction in response to autophagic or endocytic flux that ultimately fuses mitochondria or plasma membrane into lysosomes. We demonstrate that this strategy enables direct visualization of autophagic and endocytic fluxes, and confer insight into correlation of autophagic or endocytic flux to cell surface expression of immunotherapeutic targets such as MHC-I and PD-L1. The COP strategy provides a new paradigm for imaging autophagic and endocytic fluxes, and affords potential for improved cancer immunotherapy using autophagy or endocytosis inhibitors.

A new strategy is developed for direct fluorogenic imaging of autophagic and endocytic fluxes via clicking of organelle-enriched trans-cyclooctenol and tetrazine derived probes.