Development of photo- and chemo-stable near-infrared-emitting dyes: linear-shape benzo-rosol and its derivatives as unique ratiometric bioimaging platforms

Microscopic imaging aided with fluorescent probes has revolutionized our understanding of biological systems. Organic fluorophores and probes thus continue to evolve for bioimaging applications. Fluorophores such as cyanines and hemicyanines emit in the near-infrared (NIR) region and thus allow deeper imaging with minimal autofluorescence; however, they show limited photo- and chemo-stability, demanding new robust NIR fluorophores. Such photo- and chemo-stable NIR fluorophores, linear-shape π-extended rosol and rosamine analogues, are disclosed here which provide bright fluorescence images in cells as well as in tissues by confocal laser-scanning microscopy. Furthermore, they offer unique ratiometric imaging platforms for activatable probes with dual excitation and dual emission capability, as demonstrated with a 2,4-dinitrophenyl ether derivative of benzo-rosol.

NIR-emitting benzo-rosol and -rosamine dyes offer novel ratiometric imaging platforms with high pohoto- and chemo-stability.     

Oxime as a general photocage for the design of visible light photo-activatable fluorophores

Photoactivatable fluorophores have been widely used for tracking molecular and cellular dynamics with subdiffraction resolution. In this work, we have prepared a series of photoactivatable probes using the oxime moiety as a new class of photolabile caging group in which the photoactivation process is mediated by a highly efficient photodeoximation reaction. Incorporation of the oxime caging group into fluorophores results in loss of fluorescence. Upon light irradiation in the presence of air, the oxime-caged fluorophores are oxidized to their carbonyl derivatives, restoring strong fluorophore fluorescence. To demonstrate the utility of these oxime-caged fluorophores, we have created probes that target different organelles for live-cell confocal imaging. We also carried out photoactivated localization microscopy (PALM) imaging under physiological conditions using low-power light activation in the absence of cytotoxic additives. Our studies show that oximes represent a new class of visible-light photocages that can be widely used for cellular imaging, sensing, and photo-controlled molecular release.

Photoactivatable fluorophores have been widely used for tracking molecular and cellular dynamics with subdiffraction resolution.     

Monolayer nanosheets formed by liquid exfoliation of charge-assisted hydrogen-bonded frameworks

Hydrogen-bonded organic frameworks (HOFs) are a diverse and tunable class of materials, but their potential as free-standing two-dimensional nanomaterials has yet to be explored. Here we report the self-assembly of two layered hydrogen-bonded frameworks based on strong, charge-assisted hydrogen-bonding between carboxylate and amidinium groups. Ultrasound-assisted liquid exfoliation of both materials readily produces monolayer hydrogen-bonded organic nanosheets (HONs) with micron-sized lateral dimensions. The HONs show remarkable stability and maintain their extended crystallinity and monolayer structures even after being suspended in water at 80 °C for three days. These systems also exhibit efficient fluorescence quenching of an organic dye in organic solvents, superior to the quenching ability of the bulk frameworks. We anticipate that this approach will provide a route towards a diverse new family of molecular two-dimensional materials.

We report the liquid-phase ultrasonic exfoliation of two layered hydrogen-bonded frameworks into monolayer, micron-sized, and water-stable nanosheets (HONs) connected purely by hydrogen-bonding interactions.     

A facile combinatorial approach to construct a ratiometric fluorescent sensor: application for the real-time sensing of cellular pH changes

Realtime monitoring of the cellular environment, such as the intracellular pH, in a defined cellular space provides a comprehensive understanding of the dynamics processes in a living cell. Considering the limitation of spatial resolution in conventional microscopy measurements, multiple types of fluorophores assembled within that space would behave as a single fluorescent probe molecule. Such a character of microscopic measurements enables a much more flexible combinatorial design strategy in developing fluorescent probes for given targets. Nanomaterials with sizes smaller than the microscopy spatial resolution provide a scaffold to assemble several types of fluorophores with a variety of optical characteristics, therefore providing a convenient strategy for designing fluorescent pH sensors. In this study, fluorescein (CF) and tetramethylrhodamine (CR) were assembled on a DNA nanostructure with controlling the number of each type of fluorophore. By taking advantage of the different responses of CF and CR emissions to the pH environment, an appropriate assembly of both CF and CR on DNA origami enabled a controlled intensity of fluorescence emission and ratiometric pH monitoring within the space defined by DNA origami. The CF and CR-assembled DNA origami was successfully applied for monitoring the intracellular pH changes.

A combinatorial assembly of two types of intensity-based fluorophores on a DNA nanostructure provided a ratiometric pH probe with high emission intensity for monitoring intracellular pH changes.     

Cyanine-based near infra-red organic photoredox catalysis

Direct metal-free near infra-red photoredox catalysis is applied to organic oxidation, photosensitization and reduction, involving cyanines as photocatalysts. This photocatalyst is competitive with conventional reactions catalyzed under visible light. Kinetic and quenching experiments are also reported. Interestingly, these systems are compatible with water media, opening perspective for various applications.

Direct metal-free near infra-red photoredox catalysis is applied to oxidation, reduction and photosensitization, involving cyanines as photocatalysts. Mechanistic insights through kinetic and quenching experiments are also reported.     

Persistent organic room temperature phosphorescence: what is the role of molecular dimers?

Molecular dimers have been frequently found to play an important role in room temperature phosphorescence (RTP), but its inherent working mechanism has remained unclear. Herein a series of unique characteristics, including singlet excimer emission and thermally activated delayed fluorescence, were successfully integrated into a new RTP luminogen of CS-2COOCH₃ to clearly reveal the excited-state process of RTP and the special role of molecular dimers in persistent RTP emission.

The first purely organic room temperature phosphorescence (RTP) luminogen, with singlet excimer emission and thermally activated delayed fluorescence (TADF) effect, was successfully developed.      

Effect of curvature and placement of donor and acceptor units in cycloparaphenylenes: a computational study

Cycloparaphenylenes have promise as novel fluorescent materials. However, shifting their fluorescence beyond 510 nm is difficult. Herein, we computationally explore the effect of incorporating electron accepting and electron donating units on CPP photophysical properties at the CAM-B3LYP/6-311G** level. We demonstrate that incorporation of donor and acceptor units may shift the CPP fluorescence as far as 1193 nm. This computational work directs the synthesis of bright red-emitting CPPs. Furthermore, the nanohoop architecture allows for interrogation of strain effects on common conjugated polymer donor and acceptor units. Strain results in a bathochromic shift versus linear variants, demonstrating the value of using strain to push the limits of low band gap materials.

Computational studies reveal near-IR emitting nanohoops and the effect of strain on donor and acceptor units used in conjugated polymers.     

Broadband fluorescence reveals mechanistic differences in excited-state proton transfer to protic and aprotic solvents

Excited-state proton transfer (ESPT) to solvent is often explained according to the two-step Eigen–Weller model including a contact ion pair (CIP*) as an intermediate, but general applicability of the model has not been thoroughly examined. Furthermore, examples of the spectral identification of CIP* are scarce. Here, we report on a detailed investigation of ESPT to protic (H₂O, D₂O, MeOH and EtOH) and aprotic (DMSO) solvents utilizing a broadband fluorescence technique with sub-200 fs time resolution. The time-resolved spectra are decomposed into contributions from the protonated and deprotonated species and a clear signature of CIP* is identified in DMSO and MeOH. Interestingly, the CIP* intermediate is not observable in aqueous environment although the dynamics in all solvents are multi-exponential. Global analysis based on the Eigen–Weller model is satisfactory in all solvents, but the marked mechanistic differences between aqueous and organic solvents cast doubt on the physical validity of the rate constants obtained.

Time-resolved broadband fluorescence facilitates direct observation of reaction intermediates in excited-state proton transfer to solvent in protic and aprotic solvents.     

Fluorogenic Trp(redBODIPY) cyclopeptide targeting keratin 1 for imaging of aggressive carcinomas

Keratin 1 (KRT1) is overexpressed in squamous carcinomas and associated with aggressive pathologies in breast cancer. Herein we report the design and preparation of the first Trp-based red fluorogenic amino acid, which is synthetically accessible in a few steps and displays excellent photophysical properties, and its application in a minimally-disruptive labelling strategy to prepare a new fluorogenic cyclopeptide for imaging of KRT1+ cells in whole intact tumour tissues.

Trp(redBODIPY) is the first red-emitting Trp-based amino acid for the preparation of fluorogenic peptides with retention of target binding affinity.     

Probing biotin receptors in cancer cells with rationally designed fluorogenic squaraine dimers

Fluorogenic probes enable imaging biomolecular targets with high sensitivity and maximal signal-to-background ratio under non-wash conditions. Here, we focus on the molecular design of biotinylated dimeric squaraines that undergo aggregation-caused quenching in aqueous media through intramolecular H-type dimerization, but turn on their fluorescence in apolar environment due to target-mediated disaggregation. Our structure–property study revealed that depending on the linkers used to connect the squaraine dyes, different aggregation patterns could be obtained (intramolecular dimerization versus intermolecular aggregation) leading to different probing efficiencies. Using a relatively short l-lysine linker we developed a bright fluorogenic probe, Sq2B, displaying only intramolecular dimerization-caused quenching properties in aqueous media. The latter was successfully applied for imaging biotin receptors, in particular sodium-dependent multivitamin transporter (SMVT), which are overexpressed at the surface of cancer cells. Competitive displacement with SMVT-targets, such as biotin, lipoic acid or sodium pantothenate, showed Sq2B targeting ability to SMVT. This fluorogenic probe for biotin receptors could distinguish cancer cells (HeLa and KB) from model non-cancer cell lines (NIH/3T3 and HEK293T). The obtained results provide guidelines for development of new dimerization-based fluorogenic probes and propose bright tools for imaging biotin receptors, which is particularly important for specific detection of cancer cells.

Rational design of self-quenched squaraine dimers bearing biotin yielded a bright fluorogenic probe that can distinguish cancerous from non-cancerous cells.     

A new pentacyclic pyrylium fluorescent probe that responds to pH imbalance during apoptosis

Efficient fluorophores with easy synthetic routes and fast responses are of great importance in clinical diagnostics. Herein, we report a new, rigid pentacyclic pyrylium fluorophore, PS-OMe, synthesised in a single step by a modified Vilsmeier–Haack reaction. Insights into the reaction mechanism facilitated a new reaction protocol for the efficient synthesis of PS-OMe which upon demethylation resulted in a “turn-on” pH sensor, PS-OH. This new fluorescent probe has been successfully used to monitor intracellular acidification at physiological pH. From the fluorescence image analysis, we were able to quantify the intracellular dynamic pH change during apoptosis. This new pH probe is a potential chemical tool for screening, drug discovery and dose determination in cancer therapy.

A modified Vilsmeier–Haack reaction resulted in the synthesis of a pyrylium based turn-on fluorescent pH probe. The probe can monitor minute acidification and dynamic pH variation in cells during apoptosis with therapeutic chemo drugs.     

Driving high quantum yield NIR emission through proquinoidal linkage motifs in conjugated supermolecular arrays

High quantum yield NIR fluorophores are rare. Factors that drive low emission quantum yields at long wavelength include the facts that radiative rate constants increase proportional to the cube of the emission energy, while nonradiative rate constants increase in an approximately exponentially with decreasing S₀–S₁ energy gaps (in accordance with the energy gap law). This work demonstrates how the proquinoidal BTD building blocks can be utilized to minimize the extent of excited-state structural relaxation relative to the ground-state conformation in highly conjugated porphyrin oligomers, and shows that 4-ethynylbenzo[c][1,2,5]thiadiazole (E-BTD) units that terminate meso-to-meso ethyne-bridged (porphinato)zinc (PZn_n) arrays, and 4,7-diethynylbenzo[c][1,2,5]thiadiazole (E-BTD-E) spacers that are integrated into the backbone of these compositions, elucidate new classes of impressive NIR fluorophores. We report the syntheses, electronic structural properties, and emissive characteristics of neoteric PZn-(BTD-PZn)_n, PZn₂-(BTD-PZn₂)_n, and BTD-PZn_n-BTD fluorophores. Absolute fluorescence quantum yield (ϕ_f) measurements, acquired using a calibrated integrating-sphere-based measurement system, demonstrate that these supermolecules display extraordinary ϕ_f values that range from 10–25% in THF solvent, and between 28–36% in toluene solvent over the 700–900 nm window of the NIR. These studies underscore how the regulation of proquinoidal conjugation motifs can be exploited to drive excited-state dynamical properties important for high quantum yield long-wavelength fluorescence emission.

Incorporation of proquinoidal BTD building blocks into conjugated porphyrin oligomers minimizes the extent of excited-state structural relaxation relative to the ground-state conformation, elucidating new classes of impressive NIR fluorophores.     

Recent advances of AIE light-up probes for photodynamic therapy

As a new non-invasive treatment method, photodynamic therapy (PDT) has attracted great attention in biomedical applications. The advantages of possessing fluorescence for photosensitizers have made it possible to combine imaging and diagnosis together with PDT. The unique features of aggregation-induced emission (AIE) fluorogens provide new opportunities for facile design of light-up probes with high signal-to-noise ratios and improved theranostic accuracy and efficacy for image-guided PDT. In this review, we summarize the recent advances of AIE light-up probes for PDT. The strategies and principles to design AIE photosensitizers and light-up probes are firstly introduced. The application of AIE light-up probes in photodynamic antitumor and antibacterial applications is further elaborated in detail, from binding/targeting-mediated, reaction-mediated, and external stimuli-mediated light-up aspects. The challenges and future perspectives of AIE light-up probes in the PDT field are also presented with the hope to encourage more promising developments of AIE materials for phototheranostic applications and translational research.

AIE fluorogens provide new opportunities for the development of light-up probes for photodynamic therapy.     

Carbon nanodots revised: the thermal citric acid/urea reaction

Luminescent compounds obtained from the thermal reaction of citric acid and urea have been studied and utilized in different applications in the past few years. The identified reaction products range from carbon nitrides over graphitic carbon to distinct molecular fluorophores. On the other hand, the solid, non-fluorescent reaction product produced at higher temperatures has been found to be a valuable precursor for the CO₂-laser-assisted carbonization reaction in carbon laser-patterning. This work addresses the question of structural identification of both, the fluorescent and non-fluorescent reaction products obtained in the thermal reaction of citric acid and urea. The reaction products produced during autoclave–microwave reactions in the melt were thoroughly investigated as a function of the reaction temperature and the reaction products were subsequently separated by a series of solvent extractions and column chromatography. The evolution of a green molecular fluorophore, namely HPPT, was confirmed and a full characterization study on its structure and photophysical properties was conducted. The additional blue fluorescence is attributed to oligomeric ureas, which was confirmed by complementary optical and structural characterization. These two components form strong hydrogen-bond networks which eventually react to form solid, semi-crystalline particles with a size of ∼7 nm and an elemental composition of 46% C, 22% N, and 29% O. The structural features and properties of all three main components were investigated in a comprehensive characterization study.

Products of the thermal reaction of citric acid and urea have been identified as a complex mixture of fluorophores and particles.     

Fluorescent small organic probes for biosensing

Small-molecule based fluorescent probes are increasingly important for the detection and imaging of biological signaling molecules due to their simplicity, high selectivity and sensitivity, whilst being non-invasive, and suitable for real-time analysis of living systems. With this perspective we highlight sensing mechanisms including Förster resonance energy transfer (FRET), intramolecular charge transfer (ICT), photoinduced electron transfer (PeT), excited state intramolecular proton transfer (ESIPT), aggregation induced emission (AIE) and multiple modality fluorescence approaches including dual/triple sensing mechanisms (DSM or TSM). Throughout the perspective we highlight the remaining challenges and suggest potential directions for development towards improved small-molecule fluorescent probes suitable for biosensing.

Small-molecule based fluorescent probes are increasingly important for the detection and imaging of biological signaling molecules due to their simplicity, high selectivity and sensitivity, whilst being non-invasive, and suitable for real-time analysis of living systems.     

J-dimer emission in interwoven metal–organic frameworks

J-dimer emission is an emergent property that occurs when pairs of ground state fluorophores associate, typically in a dilute solution medium. The resulting fluorescence is shifted with respect to the monomer. J-dimer emission, however, has never been observed in concentrated dispersions or in the solid state. We posited that multivariate (MTV) MOFs with double interwoven structures would help to isolate these dimers within their crystalline matrix. Using this strategy, J-aggregate density was controlled during crystallization by following a substitutional solid solution approach. Here, we identified the presence of J-dimers over the entire composition range for interwoven PIZOF-2/NNU-28 structures with variable amounts of a diethynyl-anthracene aggregate-forming link. We produced bulk crystals that systematically shifted their fluorescence from green to red with lifetimes (up to 13 ns) and quantum yields (up to 76%) characteristic of π–π stacked aggregates. Photophysical studies also revealed an equilibrium constant of dimerization, K_D = 1.5 ± 0.3 M⁻¹, enabling the first thermodynamic quantification of link–link interactions that occur during MOF assembly. Our findings elucidate the role that supramolecular effects play during crystallization of MTV MOFs, opening pathways for the preparation of solid-state materials with solution-like properties by design.

J-dimer emission is an emergent property that occurs when pairs of ground-state fluorophores associate within multivariate MOFs producing tunable red shifted emission.     

Chiral exciplex dyes showing circularly polarized luminescence: extension of the excimer chirality rule

A series of axially chiral binaphthyls and quaternaphthyls possessing two kinds of aromatic fluorophores, such as pyrenyl, perylenyl, and 4-(dimethylamino)phenyl groups, arranged alternately were synthesized by a divergent method. In the excited state, the fluorophores selectively formed a unidirectionally twisted exciplex (excited heterodimer) by a cumulative steric effect and exhibited circularly polarized luminescence (CPL). They are the first examples of a monomolecular exciplex CPL dye. This versatile method for producing exciplex CPL dyes also improved fluorescence intensity, and the CPL properties were not very sensitive to the solvent or to the temperature owing to the conformationally rigid exciplex. This systematic study allowed us to confirm that the excimer chirality rule can be applied to the exciplex dyes: left- and right-handed exciplexes with a twist angle of less than 90° exhibit (−)- and (+)-CPL, respectively.

Axially chiral binaphthyls and quaternaphthyls possessing two kinds of fluorophores were synthesized. In the excited state, the fluorophores formed a twisted exciplex and exhibited CPL. This study gave us named the exciplex chirality rule.     

Development and application of ubiquitin-based chemical probes

Protein ubiquitination regulates almost every process in eukaryotic cells. The study of the many enzymes involved in the ubiquitination system and the development of ubiquitination-associated therapeutics are important areas of current research. Synthetic tools such as ubiquitin-based chemical probes have been making an increasing contribution to deciphering various biochemical components involved in ubiquitin conjugation, recruitment, signaling, and deconjugation. In the present minireview, we summarize the progress of ubiquitin-based chemical probes with an emphasis on their various structures and chemical synthesis. We discuss the utility of the ubiquitin-based chemical probes for discovering and profiling ubiquitin-dependent signaling systems, as well as the monitoring and visualization of ubiquitin-related enzymatic machinery. We also show how the probes can serve to elucidate the molecular mechanism of recognition and catalysis. Collectively, the development and application of ubiquitin-based chemical probes emphasizes the importance and utility of chemical protein synthesis in modern chemical biology.

This article reviews the design, synthesis, and application of different classes of Ub-based chemical probes.     

The chronological evolution of small organic molecular fluorescent probes for thiols

Abnormal concentrations of biothiols such as cysteine, homocysteine and glutathione are associated with various major diseases. In biological systems, the structural similarity and functional distinction of these three small molecular thiols has not only required rigorous molecular design of the fluorescent probes used to detect each thiol specifically, but it has also inspired scientists to uncover the ambiguous biological relationships between these bio-thiols. In this minireview, we will discuss the evolution of small organic molecular fluorescent probes for the detection of thiols over the past 60 years, highlighting the potent methodologies used in the design of thiol probes and their particular applications in the semi-quantification of cellular thiols and real-time labelling. At the same time, the present challenges that limit their further application will be discussed. We hope that this minireview will promote future research to enable deeper insight into the crucial role of thiols in biological systems.

The chronological evolution of small organic molecular fluorescent probes for thiols: from separation dependency analysis to cellular specific analysis, what''s next?     

Multiplexed droplet loop-mediated isothermal amplification with scorpion-shaped probes and fluorescence microscopic counting for digital quantification of virus RNAs

Highly sensitive digital nucleic acid techniques are of great significance for the prevention and control of epidemic diseases. Here we report the development of multiplexed droplet loop-mediated isothermal amplification (multiplexed dLAMP) with scorpion-shaped probes (SPs) and fluorescence microscopic counting for simultaneous quantification of multiple targets. A set of target-specific fluorescence-activable SPs are designed, which allows establishment of a novel multiplexed LAMP strategy for simultaneous detection of multiple cDNA targets. The digital multiplexed LAMP assay is thus developed by implementing the LAMP reaction using a droplet microfluidic chip coupled to a droplet counting microwell chip. The droplet counting system allows rapid and accurate counting of the numbers of total droplets and the positive droplets by collecting multi-color fluorescence images of the droplets in a microwell. The multiplexed dLAMP assay was successfully demonstrated for the quantification of HCV and HIV cDNA with high precision and detection limits as low as 4 copies per reaction. We also verified its potential for simultaneous digital assay of HCV and HIV RNA in clinical plasma samples. This multiplexed dLAMP technique can afford a useful platform for highly sensitive and specific detection of nucleic acids of viruses and other pathogens, enabling rapid diagnosis and prevention of infectious diseases.

The development of multiplexed dLAMP with scorpion-shaped probes and fluorescence microscopic counting affords simultaneous digital quantification of multiple virus RNAs.