Elimination of autofluorescence background from fluorescence tissue images by use of time-gated detection and the AzaDiOxaTriAngulenium (ADOTA) fluorophore

Control of the fluorescence lifetime in dye based nanoparticles

Fluorescent dye based nanoparticles (NPs) have received increased interest due to their high brightness and stability. In fluorescence microscopy and assays, high signal to background ratios and multiple channels of detection are highly coveted. To this end, time-resolved imaging offers suppression of background and temporal separation of spectrally overlapping signals. Although dye based NPs and time-resolved imaging are widely used individually, the combination of the two is uncommon. This is likely due to that dye based NPs in general display shortened and non-mono-exponential lifetimes. The lower quality of the lifetime signal from dyes in NPs is caused by aggregation caused quenching (ACQ) and energy migration to dark states in NPs. Here, we report a solution to this problem by the use of the small-molecule ionic isolation lattices (SMILES) concept to prevent ACQ. Additionally, incorporation of FRET pairs of dyes locks the exciton on the FRET acceptor providing control of the fluorescence lifetime. We demonstrate how SMILES NPs with a few percent rhodamine and diazaoxatriangulenium FRET acceptors imbedded with a cyanine donor dye give identical emission spectra and high quantum yields but very different fluorescence lifetimes of 3 ns and 26 ns, respectively. The two spectrally identical NPs are easily distinguished at the single particle level in fluorescence lifetime imaging. The doping approach for dye based NPs provides predictable fluorescence lifetimes and allows for these bright imaging reagents to be used in time-resolved imaging detection modalities.

Multi intercalators FRET enhanced detection of minute amounts of DNA

A novel approach is presented that increases sensitivity and specificity for detecting minimal traces of DNA in liquid and on solid samples. Förster Resonance Energy Transfer (FRET) from YOYO to Ethidium Bromide (EtBr) substantially increases the signal from DNA-bound EtBr highly enhancing sensitivity and specificity for DNA detection. The long fluorescence lifetime of the EtBr acceptor, when bound to DNA, allows for multi-pulse pumping with time gated (MPPTG) detection, which highly increases the detectable signal of DNA-bound EtBr. A straightforward spectra/image subtraction eliminates sample background and allows for a huge increase in the overall detection sensitivity. Using a combination of FRET and MPPTG detection an amount as small as 10 pg of DNA in a microliter sample can be detected without any additional sample purification/manipulation or use of amplification technologies. This amount of DNA is comparable to the DNA content of a one to two human cells. Such a detection method based on simple optics opens the potential for robust, highly sensitive DNA detection/imaging in the field, quick evaluation/sorting (i.e., triaging) of collected DNA samples, and can support various diagnostic assays.

Absolute quantification of protein number and dynamics in single cells

Quantitative characterization of protein abundance and interactions in live cells is necessary to understand and predict cellular behavior. The accurate determination of copy number for individual proteins and heterologous complexes in individual cells is critical because small changes in protein dosage, often less than two-fold, can have strong phenotypic consequences. Here, we review the merits and pitfalls of different quantitative fluorescence imaging methods for single-cell determination of protein abundance, localization, interactions, and dynamics. In particular, we discuss how scanning number and brightness (sN&B) and its variation, Raster scanning image correlation spectroscopy (RICS), exploit stochastic noise in small measurement volumes to quantify protein abundance, stoichiometry, and dynamics with high accuracy.

Investigating Design Rules for Photoinduced Electron Transfer Quenching in Triangulenium Probes

Fluorescent probes based on photoinduced electron transfer (PET) quenching of long lifetime triangulenium fluorophores have found multiple applications. For such probes a successful design relies on the right balance between the rate of PET quenching and fluorescence. In a series of ADOTA (A) and DAOTA (D) triangulenium fluorophores appended with aniline-like quencher moieties, we have investigated the rate of quenching and its relation to thermodynamic driving force, distance, and conjugation within the quencher moiety. Three different quenchers, a short (1), a long (2), and a long twisted (3), 4-aminophenyl, 4'-aminobiphenyl, and 2,2'-dimethyl-4'-aminobiphenyl, respectively were investigated. Steady-state spectroscopy and electrochemistry confirms that the quencher moieties are electronically decoupled from the dyes and have similar oxidation potentials and thus driving force for PET quenching, irrespectively of their different length and conjugation. Time-resolved fluorescence measurement was used to measure the fast PET quenching, with rate constant kPET ranging from >4×1011 to 2×109  s-1 . Interestingly, PET quenching is equally efficient/fast from 1 and 2, even with increase in distance between the donor and the acceptor. However, when twisting the biphenyl in 3, a 20-fold decrease in quenching is found. Even with this decrease in kPET, the quenching in 3 A/D is still highly efficient, with nearly 99 % quenching. The study show that long lifetime fluorophores can be efficiently switched even by relatively slow PET processes and that PET quencher moieties can be removed far from the fluorophore if conjugated linkers are applied.

Label-free fluorescence microscopy: revisiting the opportunities with autofluorescent molecules and harmonic generations as biosensors and biomarkers for quantitative biology

Over the past decade, the utilization of advanced fluorescence microscopy technologies has presented numerous opportunities to study or re-investigate autofluorescent molecules and harmonic generation signals as molecular biomarkers and biosensors for in vivo cell and tissue studies. The label-free approaches benefit from the endogenous fluorescent molecules within the cell and take advantage of their spectroscopy properties to address biological questions. Harmonic generation can be used as a tool to identify the occurrence of fibrillar or lipid deposits in tissues, by using second and third-harmonic generation microscopy. Combining autofluorescence with novel techniques and tools such as fluorescence lifetime imaging microscopy (FLIM) and hyperspectral imaging (HSI) with model-free analysis of phasor plots has revolutionized the understanding of molecular processes such as cellular metabolism. These tools provide quantitative information that is often hidden under classical intensity-based microscopy. In this short review, we aim to illustrate how some of these technologies and techniques may enable investigation without the need to add a foreign fluorescence molecule that can modify or affect the results. We address some of the most important autofluorescence molecules and their spectroscopic properties to illustrate the potential of these combined tools. We discuss using them as biomarkers and biosensors and, under the lens of this new technology, identify some of the challenges and potentials for future advances in the field.

Imaging and detection of long-lived fluorescence probes in presence of highly emissive and scattering background

Optical biomedical imaging and diagnostics is a rapidly growing field that provides both structural and functional information with uses ranging from fundamental to practical clinical applications. Nevertheless, imaging/visualizing fluorescence objects with high spatial resolution in a highly scattering and emissive biological medium continues to be a significant challenge. A fundamental limiting factor for imaging technologies is the signal-to-background ratio (SBR). For a long time to improve the SBR, we tried to improve the brightness of fluorescence probes. Many novel fluorophores with improved brightness (almost reaching the theoretical limit), redshifted emission, highly improved photostability, and biocompatibility greatly helped advance fluorescence detection and imaging. However, autofluorescence, scattering of excitation light, and Raman scattering remain fundamental limiting problems that drastically limit detection sensitivity. Similarly, significant efforts were focused on reducing the background. High-quality sample purification eliminates the majority of autofluorescence background and in a limited confocal volume allows detection to reach the ultimate sensitivity to a single molecule. However, detection and imaging in physiological conditions does not allow for any sample (cells or tissue) purification, forcing us to face a fundamental limitation. A significant improvement in limiting background can be achieved when fluorophores with a long fluorescence lifetime are used, and time-gated detection is applied. However, all long-lived fluorophores present low brightness, limiting the potential improvement. We recently proposed to utilize multipulse excitation (burst of pulses) to enhance the relative signal of long-lived fluorophores and significantly improve the SBR. Herein, we present results obtained with multipulse excitation and compare them with standard single-pulse excitation. Subtraction of images obtained with a single pulse from those obtained with pulse burst (differential image) highly limits background and instrumental noise resulting in more specific/sensitive detection and allows to achieve greater imaging depth in highly scattering media, including skin and tissue.

Time-Resolved Luminescent Sensing and Imaging for Enzyme Catalytic Activity Based on Responsive Probes

Enzymes, as a kind of biomacromolecules, play an important role in many physiological processes and relate directly to various diseases. Developing an efficient detection method for enzyme activity is important to achieve early diagnosis of enzyme-relevant diseases and high throughput screening of potential enzyme-relevant drugs. Time-resolved luminescence assay provide a high accuracy and signal-to-noise ratios detection methods for enzyme activity, which has been widely used in high throughput screening of enzyme-relevant drugs and diagnosis of enzyme-relevant diseases. Inspired by these advantages, various responsive probes based on metal complexes and metal-free organic compounds have been developed for time-resolved bioimaging and biosensing of enzyme activity owing to their long luminescence lifetimes, high quantum yields and photostability. In this review, we comprehensively reviewed metal complex- and metal-free organic compound-based responsive probes applied to detect enzyme activity through time-resolved imaging, including their design strategies and sensing principles. Current challenges and future prospects in this rapidly growing field are also discussed.

Identification of cell types in multiplexed in situ images by combining protein expression and spatial information using CELESTA

Advances in multiplexed in situ imaging are revealing important insights in spatial biology. However, cell type identification remains a major challenge in imaging analysis, with most existing methods involving substantial manual assessment and subjective decisions for thousands of cells. We developed an unsupervised machine learning algorithm, CELESTA, which identifies the cell type of each cell, individually, using the cell's marker expression profile and, when needed, its spatial information. We demonstrate the performance of CELESTA on multiplexed immunofluorescence images of colorectal cancer and head and neck squamous cell carcinoma (HNSCC). Using the cell types identified by CELESTA, we identify tissue architecture associated with lymph node metastasis in HNSCC, and validate our findings in an independent cohort. By coupling our spatial analysis with single-cell RNA-sequencing data on proximal sections of the same specimens, we identify cell-cell crosstalk associated with lymph node metastasis, demonstrating the power of CELESTA to facilitate identification of clinically relevant interactions.

DeepSpot: A deep neural network for RNA spot enhancement in single-molecule fluorescence in-situ hybridization microscopy images

Detection of RNA spots in single-molecule fluorescence in-situ hybridization microscopy images remains a difficult task, especially when applied to large volumes of data. The variable intensity of RNA spots combined with the high noise level of the images often requires manual adjustment of the spot detection thresholds for each image. In this work, we introduce DeepSpot, a Deep Learning-based tool specifically designed for RNA spot enhancement that enables spot detection without the need to resort to image per image parameter tuning. We show how our method can enable downstream accurate spot detection. DeepSpot's architecture is inspired by small object detection approaches. It incorporates dilated convolutions into a module specifically designed for context aggregation for small object and uses Residual Convolutions to propagate this information along the network. This enables DeepSpot to enhance all RNA spots to the same intensity, and thus circumvents the need for parameter tuning. We evaluated how easily spots can be detected in images enhanced with our method by testing DeepSpot on 20 simulated and 3 experimental datasets, and showed that accuracy of more than 97% is achieved. Moreover, comparison with alternative deep learning approaches for mRNA spot detection (deepBlink) indicated that DeepSpot provides more precise mRNA detection. In addition, we generated single-molecule fluorescence in-situ hybridization images of mouse fibroblasts in a wound healing assay to evaluate whether DeepSpot enhancement can enable seamless mRNA spot detection and thus streamline studies of localized mRNA expression in cells.

Unique Properties of Surface-Functionalized Nanoparticles for Bio-Application: Functionalization Mechanisms and Importance in Application

This review tries to summarize the purpose of steadily developing surface-functionalized nanoparticles for various bio-applications and represents a fascinating and rapidly growing field of research. Due to their unique properties—such as novel optical, biodegradable, low-toxicity, biocompatibility, size, and highly catalytic features—these materials are considered superior, and it is thus vital to study these systems in a realistic and meaningful way. However, rapid aggregation, oxidation, and other problems are encountered with functionalized nanoparticles, inhibiting their subsequent utilization. Adequate surface modification of nanoparticles with organic and inorganic compounds results in improved physicochemical properties which can overcome these barriers. This review investigates and discusses the iron oxide nanoparticles, gold nanoparticles, platinum nanoparticles, silver nanoparticles, and silica-coated nanoparticles and how their unique properties after fabrication allow for their potential use in a wide range of bio-applications such as nano-based imaging, gene delivery, drug loading, and immunoassays. The different groups of nanoparticles and the advantages of surface functionalization and their applications are highlighted here. In recent years, surface-functionalized nanoparticles have become important materials for a broad range of bio-applications.

Utilizing Selective Chlorination to Synthesize New Triangulenium Dyes

Functionalization of new sites on the triangulenium structure has been achieved by early-stage chlorination with N-chlorosuccinimide (NCS), giving rise to two new triangulenium dyes (1 and 3). By introducing the chlorine functionalities in the acridinium precursor, positions complementary to those previously obtained by electrophilic aromatic substitution on the final dyes are accessed. The chlorination is selective, giving only one regioisomer for both mono- and dichlorination products. For the monochlorinated acridinium compound, a highly selective ring-closing reaction was discovered, generating a single regioisomer of the cationic [4]helicene product. Further investigations into the mechanism of the [4]helicene formation lead to the first isolation of the previously proposed intermediate of the two-step S_NAr reaction, key to all aza-bridged triangulenium and helicenium systems. Late-stage functionalization of DAOTA⁺ with NCS gave rise to a different dichlorinated compound (2). The fully ring closed chlorinated triangulenium dyes 1, 2, and 3 show a redshift in absorption and emission, while maintaining relatively high fluorescence quantum yields of 36%, 26%, and 41% and long fluorescence lifetimes of 15, 12.5, and 16 ns, respectively. Cyclic voltammetry shows that chlorination of the triangulenium dyes significantly lowers reduction potentials and thus allows for efficient tuning of redox and photoredox properties.

Out-of-Phase Imaging after Optical Modulation (OPIOM) for Multiplexed Fluorescence Imaging Under Adverse Optical Conditions

Fluorescence imaging has become a powerful tool for observations in biology. Yet it has also encountered limitations to overcome optical interferences of ambient light, autofluorescence, and spectrally interfering fluorophores. In this account, we first examine the current approaches which address these limitations. Then we more specifically report on Out-of-Phase Imaging after Optical Modulation (OPIOM), which has proved attractive for highly selective multiplexed fluorescence imaging even under adverse optical conditions. After exposing the OPIOM principle, we detail the protocols for successful OPIOM implementation.

Magnetoelectric effect: principles and applications in biology and medicine- a review

Magnetoelectric (ME) effect experimentally discovered about 60 years ago remains one of the promising research fields with the main applications in microelectronics and sensors. However, its applications to biology and medicine are still in their infancy. For the diagnosis and treatment of diseases at the intracellular level, it is necessary to develop a maximally non-invasive way of local stimulation of individual neurons, navigation, and distribution of biomolecules in damaged cells with relatively high efficiency and adequate spatial and temporal resolution. Recently developed ME materials (composites), which combine elastically coupled piezoelectric (PE) and magnetostrictive (MS) phases, have been shown to yield very strong ME effects even at room temperature. This makes them a promising toolbox for solving many problems of modern medicine. The main ME materials, processing technologies, as well as most prospective biomedical applications will be overviewed, and modern trends in using ME materials for future therapies, wireless power transfer, and optogenetics will be considered.

Luminescence lifetime imaging of three-dimensional biological objects

A major focus of current biological studies is to fill the knowledge gaps between cell, tissue and organism scales. To this end, a wide array of contemporary optical analytical tools enable multiparameter quantitative imaging of live and fixed cells, three-dimensional (3D) systems, tissues, organs and organisms in the context of their complex spatiotemporal biological and molecular features. In particular, the modalities of luminescence lifetime imaging, comprising fluorescence lifetime imaging (FLI) and phosphorescence lifetime imaging microscopy (PLIM), in synergy with Förster resonance energy transfer (FRET) assays, provide a wealth of information. On the application side, the luminescence lifetime of endogenous molecules inside cells and tissues, overexpressed fluorescent protein fusion biosensor constructs or probes delivered externally provide molecular insights at multiple scales into protein-protein interaction networks, cellular metabolism, dynamics of molecular oxygen and hypoxia, physiologically important ions, and other physical and physiological parameters. Luminescence lifetime imaging offers a unique window into the physiological and structural environment of cells and tissues, enabling a new level of functional and molecular analysis in addition to providing 3D spatially resolved and longitudinal measurements that can range from microscopic to macroscopic scale. We provide an overview of luminescence lifetime imaging and summarize key biological applications from cells and tissues to organisms.

Three-Dimensional Imaging in Stem Cell-Based Researches

Stem cells have an important role in regenerative therapies, developmental biology studies and drug screening. Basic and translational research in stem cell technology needs more detailed imaging techniques. The possibility of cell-based therapeutic strategies has been validated in the stem cell field over recent years, a more detailed characterization of the properties of stem cells is needed for connectomics of large assemblies and structural analyses of these cells. The aim of stem cell imaging is the characterization of differentiation state, cellular function, purity and cell location. Recent progress in stem cell imaging field has included ultrasound-based technique to study living stem cells and florescence microscopy-based technique to investigate stem cell three-dimensional (3D) structures. Here, we summarized the fundamental characteristics of stem cells via 3D imaging methods and also discussed the emerging literatures on 3D imaging in stem cell research and the applications of both classical 2D imaging techniques and 3D methods on stem cells biology.

A fluorescent calix[4]arene with naphthalene units at the upper rim exhibits long fluorescence emission lifetime without fluorescence quenching

We synthesised a new compound with four naphthyl groups in the upper rims of calix[4]arene (1). Compared to the monomer unit, compound 1 has redshifted absorption and fluorescence, together with high fluorescence quantum yield and long fluorescence lifetime, which is extremely rare because long fluorescence lifetime emission tends to reduce the quantum yield. Single-crystal X-ray analysis and quantum calculations in the S1 state revealed π-π through-space interactions between naphthalene rings.

Optical Sensing and Imaging of pH Values: Spectroscopies, Materials, and Applications

This is the first comprehensive review on methods and materials for use in optical sensing of pH values and on applications of such sensors. The Review starts with an introduction that contains subsections on the definition of the pH value, a brief look back on optical methods for sensing of pH, on the effects of ionic strength on pH values and pKa values, on the selectivity, sensitivity, precision, dynamic ranges, and temperature dependence of such sensors. Commonly used optical sensing schemes are covered in a next main chapter, with subsections on methods based on absorptiometry, reflectometry, luminescence, refractive index, surface plasmon resonance, photonic crystals, turbidity, mechanical displacement, interferometry, and solvatochromism. This is followed by sections on absorptiometric and luminescent molecular probes for use pH in sensors. Further large sections cover polymeric hosts and supports, and methods for immobilization of indicator dyes. Further and more specific sections summarize the state of the art in materials with dual functionality (indicator and host), nanomaterials, sensors based on upconversion and 2-photon absorption, multiparameter sensors, imaging, and sensors for extreme pH values. A chapter on the many sensing formats has subsections on planar, fiber optic, evanescent wave, refractive index, surface plasmon resonance and holography based sensor designs, and on distributed sensing. Another section summarizes selected applications in areas, such as medicine, biology, oceanography, bioprocess monitoring, corrosion studies, on the use of pH sensors as transducers in biosensors and chemical sensors, and their integration into flow-injection analyzers, microfluidic devices, and lab-on-a-chip systems. An extra section is devoted to current challenges, with subsections on challenges of general nature and those of specific nature. A concluding section gives an outlook on potential future trends and perspectives.

What is Best Strategy for Water Soluble Fluorescence Dyes?-A Case Study Using Long Fluorescence Lifetime DAOTA Dyes*

The lipophilic nature of organic dyes complicates their effectiveness in aqueous solutions. In this work we investigate three different strategies for achieving water-solubility of the diazaoxatriangulenium (DAOTA⁺ ) chromophore: hydrophilic counter ions, aromatic sulfonation of the chromophore, and attachment of charged side chains. The long fluorescence lifetime (FLT, τ_f =20 ns) of DAOTA⁺ makes it a sensitive probe to analyze solvation and aggregation effects. Direct sulfonation of the chromophore was found to increase solubility drastically, but at the cost of greatly reduced quantum yields (QYs) due to enhanced non-radiative deactivation processes. The introduction of either cationic (4) or zwitterionic side chains (5), however, brings the FLT (τ_f =18 ns) and QY (ϕ_f =0.56) of the dye to the same level as the parent chromophore in acetonitrile. Time-resolved fluorescence spectroscopy also reveals a high resistance to aggregation and non-specific binding in a high loading of bovine serum albumin (BSA). The results clearly show that addition of charged flexible side chains is preferable to direct sulfonation of the chromophore core.

Lanthanide-Based Optical Probes of Biological Systems

The unique photophysical properties of lanthanides, such as europium, terbium, and ytterbium, make them versatile molecular probes of biological systems. In particular, their long-lived photoluminescence, narrow bandwidth emissions, and large Stokes shifts enable experiments that are infeasible with organic fluorophores and fluorescent proteins. The ability of these metal ions to undergo luminescence resonance energy transfer, and photon upconversion further expands the capabilities of lanthanide probes. In this review, we describe recent advances in the design of lanthanide luminophores and their application in biological research. We also summarize the latest detection systems that have been developed to fully exploit the optical properties of lanthanide luminophores. We conclude with a discussion of remaining challenges and new frontiers in lanthanide technologies. The unprecedented levels of sensitivity and multiplexing afforded by rare-earth elements illustrate how chemistry can enable new approaches in biology.

Quenching autofluorescence in the alimentary canal tissues of Bactericera cockerelli (Hemiptera: Triozidae) for immunofluorescence labeling

Immunofluorescence has been widely used to localize microbes or specific molecules in insect tissues or cells. However, significant autofluorescence is frequently observed in tissues which can interfere with the fluorescent identification of target antigens, leading to inaccurate or even false positive fluorescent labeling. The alimentary canal of the potato psyllid, Bactericera cockerelli Šulc, exhibits intense autofluorescence, hindering the application of immunolocalization for the detection and localization of the economically important pathogen transmitted by this insect, "Candidatus Liberibacter solanacearum" (Lso). In the present study, we tested the use of irradiation, hydrogen peroxide (H₂ O₂ ) and Sudan black B (SBB) treatments to reduce the autofluorescence in the B. cockerelli alimentary canal tissues. Furthermore, we assessed the compatibility of the above-mentioned treatments with Lso immunolocalization and actin staining using phalloidin. Our results showed that the autofluorescence in the alimentary canal was reduced by irradiation, H₂ O₂ , or SBB treatments. The compatibility assays indicated that irradiation and H₂ O₂ treatment both greatly reduced the fluorescent signal associated with Lso and actin. However, the SBB incubation preserved those target signals, while efficiently eliminating autofluorescence in the psyllid alimentary canal. Therefore, herein we propose a robust method for reducing the autofluorescence in the B. cockerelli alimentary canal with SBB treatment, which may improve the use of immunofluorescence labeling in this organism. This method may also have a wide range of uses by reducing the autofluorescence in other arthropod species.

Long fluorescence lifetime triangulenium dyes in imaging and fluorescence polarization assay

The development of new fluorescent dyes-new fluorochromes-has a large potential to improve the established methods in enzymology, by empowering both detection capability and the scope of the individual method. Unfortunately, there are huge barriers when adopting new improved fluorescent dyes in established methods. The dyes have to be generally available, protocols for labeling and analysis must be in place, and the field has to be aware how the new improved dye can enhance their method of choice. In this chapter, we will address these issues for the triangulenium dyes. A class of dyes that has a long fluorescence lifetime and emission in the red. A unique combination that opens up new possibilities for the study of protein rotational motion, when developing fluorescence polarization (FP) assays, and for all time-resolved imaging or analysis platforms. To make these dyes generally available, the features of the long fluorescence lifetime triangulenium dyes are described and an optimized labelling protocol are reported.

Dynamic contrast with reversibly photoswitchable fluorescent labels for imaging living cells

Interrogating living cells requires sensitive imaging of a large number of components in real time. The state-of-the-art of multiplexed imaging is usually limited to a few components. This review reports on the promise and the challenges of dynamic contrast to overcome this limitation.

Facile autofluorescence suppression enabling tracking of single viruses in live cells

Live cell fluorescence imaging is the method of choice for studying dynamic processes, such as nuclear transport, vesicular trafficking, and virus entry and egress. However, endogenous cellular autofluorescence masks a useful fluorescence signal, limiting the ability to reliably visualize low-abundance fluorescent proteins. Here, we employed synchronously amplified fluorescence image recovery (SAFIRe), which optically alters ground versus photophysical dark state populations within fluorescent proteins to modulate and selectively detect their background-free emission. Using a photoswitchable rsFastLime fluorescent protein combined with a simple illumination and image-processing scheme, we demonstrate the utility of this approach for suppressing undesirable, unmodulatable fluorescence background. Significantly, we adapted this technique to different commercial wide-field and spinning-disk confocal microscopes, obtaining >10-fold improvements in signal to background. SAFIRe allowed visualization of rsFastLime targeted to mitochondria by efficiently suppressing endogenous autofluorescence or overexpressed cytosolic unmodulatable EGFP. Suppression of the overlapping EGFP signal provided a means to perform multiplexed imaging of rsFastLime and spectrally overlapping fluorophores. Importantly, we used SAFIRe to reliably visualize and track single rsFastLime-labeled HIV-1 particles in living cells exhibiting high and uneven autofluorescence signals. Time-lapse SAFIRe imaging can be performed for an extended period of time to visualize HIV-1 entry into cells. SAFIRe should be broadly applicable for imaging live cell dynamics with commercial microscopes, even in strongly autofluorescent cells or cells expressing spectrally overlapping fluorescent proteins.

Optical imaging spectroscopy for plant research: more than a colorful picture

Optical imaging is a routine and indispensable tool in plant research. Here we review different emerging spectrally resolved optical imaging approaches and the wealth of information they can be used to obtain pertaining to the underlying chemistry, structure and mechanics of plants.

Synthesis and properties of sulfur-functionalized triarylmethylium, acridinium and triangulenium dyes

Triangulenium dyes functionalized with one, two or three ethylthiol functionalities were synthesized and their optical properties were studied. The sulfur functionalities were introduced by aromatic nucleophilic substitution of methoxy groups in triarylmethylium cations with ethanethiol followed by partial or full ring closure of the ortho positions with nitrogen or oxygen bridges leading to sulfur-functionalized acridinium, xanthenium or triangulenium dyes. For all the dye classes the sulfur functionalities are found to lead to intensely absorbing dyes in the visible range (470 to 515 nm), quite similar to known analogous dye systems with dialkylamino donor groups in place of the ethylthiol substituents. For the triangulenium derivatives significant fluorescence was observed (Φ_f = 0.1 to Φ_f = 0.3).

Background autofluorescence induced by plant extracts in human lymphocytes: A flow cytometric analysis of a critical bias

The presence of background autofluorescence sources is considered as an important problem when performing fluorometric methods, due to the possible spectral overlap between it and the fluorescence emission of probes. Regarding that, we evaluated the presence of background autofluorescence in human lymphocytes after the treatment with extracts from three medicinal plants, including ethanolic extract from aerial parts of Ageratum fastigiatum, ethanolic extract from aerial parts of Eriosema campestre and the ethanolic extract from stem of Pseudobrickellia brasiliensis. Human peripheral blood mononuclear cells were treated with each extract in vitro during 24 h, followed by flow cytometric analysis. Additionally, the fluorescence emission of plant extracts was evaluated by fluorometry, using the same concentrations used in cell cultures. We identified that plant extracts treatment on lymphocytes induced background autofluorescence detectable in several wavelength ranges. Isolated extracts showed no expressive fluorescence emission in fluorometric analyses, suggesting that background autofluorescence was induced in lymphocytes by interactions between cellular components and extracts compounds. Here we discuss the importance to perform previous tests to evaluate a possible background autofluorescence induction after cell treatments with plant extracts or any other substance. In spite of being mandatory, background autofluorescence analysis of cells after treatments and stimulations is still underestimated on literature. In summary, following the precautions herein established should help to reduce the incidence of false positive results.

Extended Triangulenium Ions: Syntheses and Characterization of Benzo-Bridged Dioxa- and Diazatriangulenium Dyes

The very limited class of fluorophores, with a long fluorescence lifetime (>10 ns) and fluorescence beyond 550 nm, has been expanded with two benzo-fused triangulenium derivatives and two cationic [5]-helicene salts. The syntheses of the benzo-bridged dioxa- and diazatriangulenium derivatives (BDOTA⁺ and BDATA⁺, respectively) required two different synthetic approaches, which reflect the structural and physiochemical impact on the reactivity of [5]-helicenium precursors. Spectroscopic investigations show that the introduction of the benzo bridge into the triangulenium chromophore significantly redshifts the absorption and emission while maintaining fluorescence lifetimes above 10 ns. The combination of a high quantum yield, long fluorescence lifetime, and emission above 600 nm is possible only if the structural aspects of the triangulenium framework are perfectly harmonized to secure a low rate of nonradiative deactivation. The new benzo bridge may be a general motif to obtain red-shifted derivatives of other dye classes.

Background-Free Fluorescence-Decay-Time Sensing and Imaging of pH with Highly Photostable Diazaoxotriangulenium Dyes

Novel fluorescent diazaoxatriangulenium (DAOTA) pH indicators for lifetime-based self-referenced pH sensing are reported. The DAOTA dyes were decorated with phenolic-receptor groups inducing fluorescence quenching via a photoinduced-electron-transfer mechanism. Electron-withdrawing chlorine substituents ensure response in the most relevant pH range (apparent p K_a^' values of ∼5 and 7.5 for the p, p-dichlorophenol- and p-chlorophenol-substituted dyes, respectively). The dyes feature long fluorescence lifetimes (17-20 ns), high quantum yields (∼60%), and high photostabilities. Planar optodes are prepared upon immobilization of the dyes into polyurethane hydrogel D4. Apart from the response in the fluorescence intensity, the optodes show pH-dependent lifetime behavior, which makes them suitable for studying 2D pH distributions with the help of fluorescence-lifetime-imaging techniques. The lifetime response is particularly pronounced for the sensors with high dye concentrations (0.5-1 wt % with respect to the polymer) and is attributed to the efficient homo-FRET mechanism.

Design, synthesis, and time-gated cell imaging of carbon-bridged triangulenium dyes with long fluorescence lifetime and red emission

Time-resolved fluorescence offers many advantages over normal steady-state detection and becomes increasingly important in bioimaging. However, only very few fluorophores with emission in the visible range and fluorescence lifetimes above 5 ns are available. In this work, we prepare a series of new aza/oxa-triangulenium dyes where one of the usual oxa or aza bridges is replaced by an isopropyl bridge. This leads to a significant redshift of fluorescence with only moderate reductions of quantum yields and a unique long fluorescence lifetime. The fluorescence of the isopropyl bridged diazatriangulenium derivative CDATA+ is red-shifted by 50 nm (1400 cm-1) as compared to the oxygen-bridged DAOTA+ chromophore and has intense emission in the red region (600-700 nm) with a quantum yield of 61%, and a fluorescence lifetime of 15.8 ns in apolar solution. When the CDATA+ dye is used as cell stain, high photostability and efficient time-gated cell imaging is demonstrated.

Monitoring intracellular nanomolar calcium using fluorescence lifetime imaging

Nanomolar-range fluctuations of intracellular [Ca2+] are critical for brain cell function but remain difficult to measure. We have advanced a microscopy technique to monitor intracellular [Ca2+] in individual cells in acute brain slices (also applicable in vivo) using fluorescence lifetime imaging (FLIM) of the Ca2+-sensitive fluorescent indicator Oregon Green BAPTA1 (OGB-1). The OGB-1 fluorescence lifetime is sensitive to [Ca2+] within the 10-500 nM range but not to other factors such as viscosity, temperature, or pH. This protocol describes the requirements, setup, and calibration of the FLIM system required for OGB-1 imaging. We provide a step-by-step procedure for whole-cell OGB-1 loading and two-photon FLIM. We also describe how to analyze the obtained FLIM data using total photon count and gated-intensity record, a ratiometric photon-counting approach that provides a highly improved signal-to-noise ratio and greater sensitivity of absolute [Ca2+] readout. We demonstrate our technique in nerve cells in situ, and it is adaptable to other cell types and fluorescent indicators. This protocol requires a basic understanding of FLIM and experience in single-cell electrophysiology and cell imaging. Setting up the FLIM system takes ∼2 d, and OGB-1 loading, imaging, and data analysis take 2 d.

Enhanced DNA detection using a multiple pulse pumping scheme with time-gating (MPPTG)

Fluorescence signal enhancement induced by the binding of intercalators to DNA has been broadly utilized in various DNA detection methods.

Green and Red Fluorescent Dyes for Translational Applications in Imaging and Sensing Analytes: A Dual-Color Flag

Red and green are two of the most-preferred colors from the entire chromatic spectrum, and red and green dyes are widely used in biochemistry, immunohistochemistry, immune-staining, and nanochemistry applications. Selective dyes with green and red excitable chromophores can be used in biological environments, such as tissues and cells, and can be irradiated with visible light without cell damage. This critical review, covering a period of five years, provides an overview of the most-relevant results on the use of red and green fluorescent dyes in the fields of bio-, chemo- and nanoscience. The review focuses on fluorescent dyes containing chromophores such as fluorescein, rhodamine, cyanine, boron-dipyrromethene (BODIPY), 7-nitobenz-2-oxa-1,3-diazole-4-yl, naphthalimide, acridine orange, perylene diimides, coumarins, rosamine, Nile red, naphthalene diimide, distyrylpyridinium, benzophosphole P-oxide, benzoresorufins, and tetrapyrrolic macrocycles. Metal complexes and nanomaterials with these dyes are also discussed.

Anti-Stokes fluorescence microscopy using direct and indirect dark state formation

Optically activated delayed fluorescence and upconversion fluorescence allow removing unwanted auto-fluorescence.

Creating infinite contrast in fluorescence microscopy by using lanthanide centered emission

The popularity of fluorescence microscopy arises from the inherent mode of action, where the fluorescence emission from probes is used to visualize selected features on a presumed dark background. However, the background is rarely truly dark, and image processing and analysis is needed to enhance the fluorescent signal that is ascribed to the selected feature. The image acquisition is facilitated by using considerable illumination, bright probes at a relatively high concentration in order to make the fluorescent signal significantly more intense than the background signal. Here, we present two methods for completely removing the background signal in spectrally resolved fluorescence microscopy. The methodology is applicable for all probes with narrow and well-defined emission bands (Full width half-maximum < 20 nm). Here, we use two lanthanide based probes exploiting the narrow emission lines of europium(III) and terbium(III) ions. We used a model system with zeolites doped with lanthanides immobilized in a polymer stained with several fluorescent dyes regularly used in bioimaging. After smoothing the spectral data recorded in each pixel, they are differentiated. Method I is based on the direct sum of the gradient, while method II resolves the fluorescent signal by subtracting a background calculated via the gradient. Both methods improve signal-to-background ratio significantly and we suggest that spectral imaging of lanthanide-centered emission can be used as a tool to obtain absolute contrast in bioimaging.

Investigating dye performance and crosstalk in fluorescence enabled bioimaging using a model system

Detailed imaging of biological structures, often smaller than the diffraction limit, is possible in fluorescence microscopy due to the molecular size and photophysical properties of fluorescent probes. Advances in hardware and multiple providers of high-end bioimaging makes comparing images between studies and between research groups very difficult. Therefore, we suggest a model system to benchmark instrumentation, methods and staining procedures. The system we introduce is based on doped zeolites in stained polyvinyl alcohol (PVA) films: a highly accessible model system which has the properties needed to act as a benchmark in bioimaging experiments. Rather than comparing molecular probes and imaging methods in complicated biological systems, we demonstrate that the model system can emulate this complexity and can be used to probe the effect of concentration, brightness, and cross-talk of fluorophores on the detected fluorescence signal. The described model system comprises of lanthanide (III) ion doped Linde Type A zeolites dispersed in a PVA film stained with fluorophores. We tested: F18, MitoTracker Red and ATTO647N. This model system allowed comparing performance of the fluorophores in experimental conditions. Importantly, we here report considerable cross-talk of the dyes when exchanging excitation and emission settings. Additionally, bleaching was quantified. The proposed model makes it possible to test and benchmark staining procedures before these dyes are applied to more complex biological systems.

Azadioxatriangulenium and Diazaoxatriangulenium: Quantum Yields and Fundamental Photophysical Properties

Over the last decade, we have investigated and exploited the photophysical properties of triangulenium dyes. Azadioxatriangulenium (ADOTA) and diazaoxatriangulenium (DAOTA), in particular, have features that make them useful in various fluorescence-based technologies (e.g., bioimaging). Through our work with ADOTA and DAOTA, we became aware that the reported fluorescence quantum yields (ϕ_fl) for these dyes are lower than their actual values. We thus set out to further investigate the fundamental structure-property relationships in these unique conjugated cationic systems. The nonradiative processes in the systems were explored using transient absorption spectroscopy and time-resolved emission spectroscopy in combination with computational chemistry. The influence of molecular oxygen on the fluorescence properties was explored, and the singlet oxygen sensitization efficiencies of ADOTA and DAOTA were determined. We conclude that, for these dyes, the amount of nonradiative deactivation of the first excited singlet state (S₁) of the azaoxa-triangulenium fluorophores is low, that the rate of such deactivation is slower than what is observed in common cationic dyes, that there are no observable radiative transitions occurring from the first excited triplet state (T₁) of these dyes, and that the efficiency of sensitized singlet oxygen production is low (ϕ_Δ ≤ 10%). These photophysical results provide a solid base upon which technological applications of these fluorescent dyes can be built.

Wide-field time-gated photoluminescence microscopy for fast ultrahigh-sensitivity imaging of photoluminescent probes

Fluorescence microscopy is a fundamental technique for the life sciences, where biocompatible and photostable photoluminescence probes in combination with fast and sensitive imaging systems are continually transforming this field. A wide-field time-gated photoluminescence microscopy system customised for ultrasensitive imaging of unique nanoruby probes with long photoluminescence lifetime is described. The detection sensitivity derived from the long photoluminescence lifetime of the nanoruby makes it possible to discriminate signals from unwanted autofluorescence background and laser backscatter by employing a time-gated image acquisition mode. This mode enabled several-fold improvement of the photoluminescence imaging contrast of discrete nanorubies dispersed on a coverslip. It enabled recovery of the photoluminescence signal emanating from discrete nanorubies when covered by a layer of an organic fluorescent dye, which were otherwise invisible without the use of spectral filtering approaches. Time-gated imaging also facilitated high sensitivity detection of nanorubies in a biological environment of cultured cells. Finally, we monitor the binding kinetics of nanorubies to a functionalised substrate, which exemplified a real-time assay in biological fluids. 3D-pseudo colour images of nanorubies immersed in a highly fluorescent dye solution. Nanoruby photoluminescence is subdued by that of the dye in continuous excitation/imaging (left), however it can be recovered by time-gated imaging (right). At the bottom is schematic diagram of nanoruby assay in a biological fluid.

Heterocyclic Nanographenes and Other Polycyclic Heteroaromatic Compounds: Synthetic Routes, Properties, and Applications

Two-dimensionally extended, polycyclic heteroaromatic molecules (heterocyclic nanographenes) are a highly versatile class of organic materials, applicable as functional chromophores and organic semiconductors. In this Review, we discuss the rich chemistry of large heteroaromatics, focusing on their synthesis, electronic properties, and applications in materials science. This Review summarizes the historical development and current state of the art in this rapidly expanding field of research, which has become one of the key exploration areas of modern heterocyclic chemistry.

A Macrocyclic Fluorophore Dimer with Flexible Linkers: Bright Excimer Emission with a Long Fluorescence Lifetime

Bright fluorescent molecules with long fluorescence lifetimes are important for the development of lifetime-based fluorescence imaging techniques. Herein, a molecular design is described for simultaneously attaining long fluorescence lifetime (τ) and high brightness (ΦF ×ɛ) in a system that features macrocyclic dimerization of fluorescent π-conjugated skeletons with flexible linkers. An alkylene-linked macrocyclic dimer of bis(thienylethynyl)anthracene was found to show excimer emission with a long fluorescence lifetime (τ≈19 ns) in solution, while maintaining high brightness. A comparison with various relevant derivatives revealed that the macrocyclic structure and the length of the alkylene chains play crucial roles in attaining these properties. In vitro time-gated imaging experiments were conducted as a proof-of-principle for the superiority of this macrocyclic fluorophore relative to the commercial fluorescent dye Alexa Fluor 488.

Azadioxatriangulenium: exploring the effect of a 20 ns fluorescence lifetime in fluorescence anisotropy measurements

Azaoxatriangulenium (ADOTA) has been shown to be highly emissive despite a moderate molar absorption coefficient of the primary electronic transition. As a result, the fluorescence lifetime is ~20 ns, longer than all commonly used red fluorescent organic probes. The electronic transitions in ADOTA are highly polarised (r ₀  =  0.38), which in combination with the long fluorescence lifetime extents the size-range of biomolecular weights that can be detected in fluorescence polarisation-based experiments. Here, the rotational dynamics of bovine serum albumin (BSA) are monitored with three different ADOTA derivatives, differing only in constitution of the reactive linker. A detailed study of the degree of labelling, the steady-state anisotropy, and the time-resolved anisotropy of the three different ADOTA-BSA conjugates are reported. The fluorescence quantum yields (ϕ _fl) of the free dyes in PBS solution are determined to be ~55%, which is reduced to ~20% in the ADOTA-BSA conjugates. Despite the reduction in ϕ _fl, a ~20 ns intensity averaged lifetime is maintained, allowing for the rotational dynamics of BSA to be monitored for up to 100 ns. Thus, ADOTA can be used in fluorescence polarisation assays to fill the gap between commonly used organic dyes and the long luminescence lifetime transition metal complexes. This allows for efficient steady-state fluorescence polarisation assays for detecting binding of analytes with molecular weights of up to 100 kDa.

Azadioxatriangulenium: Synthesis and Photophysical Properties of Reactive Dyes for Bioconjugation

Azadioxatriangulenium (ADOTA) is a fluorescent triangulenium dye with a long fluorescence lifetime, highly polarized transitions and emission in the red part of the visible spectrum. These properties make the chromophore suited for application in fluorescence polarization/anisotropy assay. To be useful for these applications, reactive forms of the dyes must be available in significant quantities. Here, the synthesis and photophysical properties of amine-reactive NHS esters and a thiol-reactive maleimide derivate of ADOTA are reported. The synthesis involves two steps of nucleophilic bridge forming reactions starting from tris(2,6-dimethoxyphenyl) methylium tetrafluoroborate, which can readily be made on 100 gram scale. In the third and final step the reactive NHS or maleimide groups are formed. The beneficial photophysical properties of the ADOTA chromophore are maintained in these derivatives, and we conclude that these systems are ideal to study protein motion and protein-protein interactions for systems of up towards 1000 kDa.

Physicochemical properties of potential porphyrin photosensitizers for photodynamic therapy

This research evaluated the suitability of synthetic photosensitizers for their use as potential photosensitizers in photodynamic therapy using steady state and time-resolved spectroscopic techniques. Four tetraphenylporphyrin derivatives were studied in ethanol and dimethyl sulfoxide. The spectroscopic properties namely electronic absorption and emission spectra, ability to generate singlet oxygen, lifetimes of the triplet state, as well as their fluorescence quantum yield were determined. Also time-correlated single photon counting method was used to precisely determine fluorescence lifetimes for all four compounds. Tested compounds exhibit high generation of singlet oxygen, low generation of fluorescence and they are chemical stable during irradiation. The studies show that the tested porphyrins satisfy the conditions of a potential drug in terms of physicochemical properties.