Masked red-emitting carbopyronine dyes with photosensitive 2-diazo-1-indanone caging group

Caged near-IR emitting fluorescent dyes are in high demand in optical microscopy but up to now were unavailable. We discovered that the combination of a carbopyronine dye core and a photosensitive 2-diazo-1-indanone residue leads to masked near-IR emitting fluorescent dyes. Illumination of these caged dyes with either UV or visible light (λ < 420 nm) efficiently generates fluorescent compounds with absorption and emission at 635 nm and 660 nm, respectively. A high-yielding synthetic route with attractive possibilities for further dye design is described in detail. Good photostability, high contrast, and a large fluorescence quantum yield after uncaging are the most important features of the new compounds for non-invasive imaging in high-resolution optical microscopy. For use in immunolabelling the caged dyes were decorated with a (hydrophilic) linker and an (activated) carboxyl group.     

Advances in the chemistry of small molecule fluorescent probes

Small molecule fluorophores are essential tools for chemical biology. A benefit of synthetic dyes is the ability to employ chemical approaches to control the properties and direct the position of the fluorophore. Applying modern synthetic organic chemistry strategies enables efficient tailoring of the chemical structure to obtain probes for specific biological experiments. Chemistry can also be used to activate fluorophores; new fluorogenic enzyme substrates and photoactivatable compounds with improved properties have been prepared that facilitate advanced imaging experiments with low background fluorescence. Finally, chemical reactions in live cells can be used to direct the spatial distribution of the fluorophore, allowing labeling of defined cellular regions with synthetic dyes.     

Synthesis of New Styrylquinoline Cellular Dyes,Fluorescent Properties,Cellular Localization and Cytotoxic Behavior

New styrylquinoline derivatives with their photophysical constants are described. The synthesis was achieved via Sonogashira coupling using the newly developed heterogeneous nano-Pd/Cu catalyst system, which provides an efficient synthesis of high purity products. The compounds were tested in preliminary fluorescent microscopy studies to in order to identify their preferable cellular localization, which appeared to be in the lipid cellular organelles. The spectroscopic properties of the compounds were measured and theoretical TD-DFT calculations were performed. A biological analysis of the quinolines that were tested consisted of cytotoxicity assays against normal human fibroblasts and colon adenocarcinoma cells. All of the compounds that were studied appeared to be safe and indifferent to cells in a high concentration range. The presented results suggest that the quinoline compounds that were investigated in this study may be valuable structures for development as fluorescent dyes that could have biological applications.     

Immunofluorescent labeling of cancer marker Her2 and other cellular targets with semiconductor quantum dots

Semiconductor quantum dots (QDs) are among the most promising emerging fluorescent labels for cellular imaging. However, it is unclear whether QDs, which are nanoparticles rather than small molecules, can specifically and effectively label molecular targets at a subcellular level. Here we have used QDs linked to immunoglobulin G (IgG) and streptavidin to label the breast cancer marker Her2 on the surface of fixed and live cancer cells, to stain actin and microtubule fibers in the cytoplasm, and to detect nuclear antigens inside the nucleus. All labeling signals are specific for the intended targets and are brighter and considerably more photostable than comparable organic dyes. Using QDs with different emission spectra conjugated to IgG and streptavidin, we simultaneously detected two cellular targets with one excitation wavelength. The results indicate that QD-based probes can be very effective in cellular imaging and offer substantial advantages over organic dyes in multiplex target detection.     

High-throughput screens for fluorescent dye discovery

A recent screen of a combinatorial library of fluorescent compounds discovered fluorescent dyes that were able to distinguish myoblasts from differentiated myotubes. New fluorescent dyes that respond to biologically relevant changes in cell state or type are useful as stains in a wide variety of biological experiments, including high-throughput screens for chemical and genetic regulators. Combining this approach with microscopy imaging is likely to be even more powerful and might lead to the discovery of new dyes with interesting and useful properties.     

Binding of cationic dyes to DNA: distinguishing intercalation and groove binding mechanisms using simple experimental and numerical models

Abstract

Simple methods for predicting intercalation or groove binding of dyes and analogous compounds with double stranded DNA are described. The methods are based on a quantitative assessment of the aspect (width to length) ratio of the dyes. The procedures were validated using a set of 38 cationic dyes of varied chemical structures binding to well oriented DNA fibers and assessing binding orientation by linear dichroism and polarized fluorescence. We demonstrated that low aspect ratio dyes bound by intercalation, whereas more rod-like dyes were groove binders. Some problems that result and possible applications are discussed briefly.     

Basic and applied aspects in the microbial degradation of azo dyes

Azo dyes are the most important group of synthetic colorants. They are generally considered as xenobiotic compounds that are very recalcitrant against biodegradative processes. Nevertheless, during the last few years it has been demonstrated that several microorganisms are able, under certain environmental conditions, to transform azo dyes to non-colored products or even to completely mineralize them. Thus, various lignolytic fungi were shown to decolorize azo dyes using ligninases, manganese peroxidases or laccases. For some model dyes, the degradative pathways have been investigated and a true mineralization to carbon dioxide has been shown. The bacterial metabolism of azo dyes is initiated in most cases by a reductive cleavage of the azo bond, which results in the formation of (usually colorless) amines. These reductive processes have been described for some aerobic bacteria, which can grow with (rather simple) azo compounds. These specifically adapted microorganisms synthesize true azoreductases, which reductively cleave the azo group in the presence of molecular oxygen. Much more common is the reductive cleavage of azo dyes under anaerobic conditions. These reactions usually occur with rather low specific activities but are extremely unspecific with regard to the organisms involved and the dyes converted. In these unspecific anaerobic processes, low-molecular weight redox mediators (e.g. flavins or quinones) which are enzymatically reduced by the cells (or chemically by bulk reductants in the environment) are very often involved. These reduced mediator compounds reduce the azo group in a purely chemical reaction. The (sulfonated) amines that are formed in the course of these reactions may be degraded aerobically. Therefore, several (laboratory-scale) continuous anaerobic/aerobic processes for the treatment of wastewaters containing azo dyes have recently been described.     

Concentration,cellular exposure and specificity of organelle selective fluorescent dyes in fungal cell biology

This technical focus article discusses the importance of concentration, cellular exposure and specificity for the application of organelle selective fluorescent dyes in fungi using DNA, membrane and cell wall stains as examples. Nonetheless, the presented considerations are generally applicable to all fluorescent dyes applied to living cells.The association of a fluorescent dye with its target molecule generally impairs molecule and consequently organelle function. Effective dye concentration, cellular exposure time and specificity to the target molecule are key factors that influence the biocompatibility of any fluorescent dye. Prominent molecules frequently used as fluorescent staining targets in fungal cell biology are: (i) DNA for nuclear labelling, (ii) α-/β-glucans and chitin for cell wall labelling, and (iii) phospholipids for plasma membrane and endomembrane labelling. In combination with live-cell imaging settings that reduce light stress, i.e. excitation intensities and exposure times set to the minimum that still achieves good signal-to-noise ratios, is the low dosage application of fluorescent markers as so called “vital dyes” essential for visualising cellular processes in an artefact-free fashion.     

Flow cytometric analysis of cell cycle-dependent changes in cell thiol level by combining a new laser dye with Hoechst 33342.

By halogenation of methylfluorescein-diacetate (MFDA) or eosin-diacetate, two new dyes for cellular thiol compatible with visible laser excitation have become available. These probes circumvent the use of an ultraviolet (UV)-excitation system as required by bimane-based dyes and allow combination with probes for other cellular parameters. The thiol dyes attain maximal staining after 10 min at 37 degrees C, and fluorescence is sensitive to pretreatment with diethylmaleate but not to buthionine sulfoximine. In a dual-laser system, analysis of the cellular thiol level as a function of cell cycle distribution can be achieved in viable cells by simultaneous staining with the bisbenzimidazole dye Hoechst 33342 and one of the halogenated dyes. Using this approach, we were able to show that cells in the G2 phase of the cell cycle were more sensitive to thiol depletion with diethylmaleate than were cells in the G1 compartment. The new thiol dyes allow a more flexible selection of wavelengths of excitation and emission for assessing changes in cellular thiol (glutathione and other thiol compounds) and allow this parameter to be examined as a function of cell cycle position.     

Facile synthesis of symmetric, monofunctional cyanine dyes for imaging applications

Efficient syntheses of several members of a new class of symmetric, monocarboxylate-functionalized cyanine dyes have been developed. The synthesis is a simple two-step method, typically with greater than 60% yield and easy final product purification. The new monocarboxylate-functionalized cyanine dyes exhibit excellent water solubility and similar excitation and emission properties to those of Cy5 and Alexa Fluor 647. The application of the new dyes in cellular imaging has been demonstrated through direct conjugating of the dye with an antibody, then imaging of microtubules inside cells, visualized by near-infrared fluorescence microscopy.     

Quantitative imaging of membrane lipid order in cells and organisms

It is now recognized that lipids and proteins in cellular membranes are not homogenously distributed. A high degree of membrane order is the biophysical hallmark of cholesterol-enriched lipid rafts, which may induce the lateral sorting of proteins within the membrane. Here we describe a quantitative fluorescence microscopy technique for imaging localized lipid environments and measuring membrane lipid order in live and fixed cells, as well as in intact tissues. The method is based on the spectral ratiometric imaging of the polarity-sensitive membrane dyes Laurdan and di-4-ANEPPDHQ. Laurdan typically requires multiphoton excitation, making it suitable for the imaging of tissues such as whole, living zebrafish embryos, whereas di-4-ANEPPDHQ imaging can be achieved with standard confocal microscopes. This approach, which takes around 4 h, directly examines the organization of cellular membranes and is distinct from alternative approaches that infer membrane order by measuring probe partitioning or dynamics.     

Imaging calcium dynamics in living plant cells and tissues

The central role of Ca²⁺ signalling in plants is now well established. Much of our recent research has been based on the premise that the direct demonstration of signal-response coupling via Ca²⁺ requires the imaging or measurement of cytosolic free Ca²⁺ in living cells. Methods (confocal microscopy, fluorescence ratio imaging and photon counting imaging) which we use for imaging Ca²⁺ with fluorescent dyes or recombinant aequorin, are described. Approaches for using dyes are now routine for many plant cells. However, the imaging Ca²⁺ in whole tissues of plants genetically transformed with the aequorin gene is a very new development. We predict that this method, first employed in our laboratory, will bring about a revolution in our understanding of Ca²⁺ signalling at the multicellular level.     

Show your true color: Mammalian cell surface staining for tracking cellular identity in multiplexing and beyond

Fluorescence microscopy revolutionized cell biology and changed requirements for dyes towards higher brightness, novel capacities, and specific targets. With the need for multiplexing assays in high-throughput methodologies, surface staining gained particular interest because it allows rapid application of exogenous stains to track cellular identity in mixed populations. Indeed, the last decade has enriched the toolbox of general lipid stains, fluorescent lipid analogues, sugar-binding lectins, and protein-specific antibodies enabling the first rationally designed plasma membrane-specific dyes. Still, multiple challenges exist, and the unique properties of each dye must be considered when selecting a staining approach for a specific application. Recent advances are also promising that future dyes will provide ultimate brightness and photostability in diverse colors and reduced sizes for high-resolution imaging.     

Sequential Superresolution Imaging of Multiple Targets Using a Single Fluorophore

Fluorescence superresolution (SR) microscopy, or fluorescence nanoscopy, provides nanometer scale detail of cellular structures and allows for imaging of biological processes at the molecular level. Specific SR imaging methods, such as localization-based imaging, rely on stochastic transitions between on (fluorescent) and off (dark) states of fluorophores. Imaging multiple cellular structures using multi-color imaging is complicated and limited by the differing properties of various organic dyes including their fluorescent state duty cycle, photons per switching event, number of fluorescent cycles before irreversible photobleaching, and overall sensitivity to buffer conditions. In addition, multiple color imaging requires consideration of multiple optical paths or chromatic aberration that can lead to differential aberrations that are important at the nanometer scale. Here, we report a method for sequential labeling and imaging that allows for SR imaging of multiple targets using a single fluorophore with negligible cross-talk between images. Using brightfield image correlation to register and overlay multiple image acquisitions with ~10 nm overlay precision in the x-y imaging plane, we have exploited the optimal properties of AlexaFluor647 for dSTORM to image four distinct cellular proteins. We also visualize the changes in co-localization of the epidermal growth factor (EGF) receptor and clathrin upon EGF addition that are consistent with clathrin-mediated endocytosis. These results are the first to demonstrate sequential SR (s-SR) imaging using direct stochastic reconstruction microscopy (dSTORM), and this method for sequential imaging can be applied to any superresolution technique.     

Imaging proteins inside cells with fluorescent tags

Watching biological molecules provides clues to their function and regulation. Some of the most powerful methods of labeling proteins for imaging use genetically encoded fluorescent fusion tags. There are four standard genetic methods of covalently tagging a protein with a fluorescent probe for cellular imaging. These use (i) autofluorescent proteins, (ii) self-labeling enzymes, (iii) enzymes that catalyze the attachment of a probe to a target sequence, and (iv) biarsenical dyes that target tetracysteine motifs. Each of these techniques has advantages and disadvantages. In this review, we cover new developments in these methods and discuss practical considerations for their use in imaging proteins inside living cells.     

Near infrared active heptacyanine dyes with unique cancer-imaging and cytotoxic properties

Three near-infrared fluorescent heptacarbocyanine dyes have been synthesized using a facile one-pot synthetic approach. The reaction methodology afforded a mixture of three symmetric and unsymmetric heptacyanines containing various N-indolenine substituents, a dicarbocyclic acid (DA), a monoester (ME), and a diester (DE). These compounds were isolated, purified, characterized and biologically investigated for tumor cell cytotoxicity and uptake selectivity. Using cell viability and in vitro proliferation assays, we found that the esterified dyes (monoester, ME and diester, DE) were selectively cytotoxic to cancer cells and spared normal fibroblast cells. Additionally, confocal fluorescence imaging confirmed selective uptake of these dyes in cancer cells, thus suggesting tumor cell targeting.     

Epigenetic effectiveness of complete carcinogens: specific interactions of polycyclic aromatic hydrocarbons and aminoazo dyes with cholesterol and apolipoprotein A-I

During a co-precipitation of cholesterol (Chol) and slight amounts of polycyclic aromatic hydrocarbons (PAHs) or aminoazo dyes (AZOs) in aqueous albumin solution, complex particles are formed; on their surfaces apolipoproteins with an amphipathic alpha-helix (e.g. apoA-I) are more or less firmly adsorbed. An efficacy index can be calculated from the strength of the hydrophobic interactions between apoA-I and the [Chol/PAH]- or [Chol/AZO]-complex, and the solubility of the PAH or AZO in an aqueous medium, which correlates to the carcinogenicity of these compounds. A short-term test for PAHs and AZOs is described, in which the efficacy index can be determined in the simplest manner without any great expenditure on equipment. The previous results suggest that the parent compounds of the PAHs and AZOs can be involved in a specific interaction with cholesterol-domains of the plasma membrane of a cell. The changes in membrane fluidity and architecture caused by these specific interactions could modulate the distribution and/or activity of membrane proteins which are critical to the regulation of cellular proliferation.     

Motmot, an open-source toolkit for realtime video acquisition and analysis

Background  

Video cameras sense passively from a distance, offer a rich information stream, and provide intuitively meaningful raw data. Camera-based imaging has thus proven critical for many advances in neuroscience and biology, with applications ranging from cellular imaging of fluorescent dyes to tracking of whole-animal behavior at ecologically relevant spatial scales.     

Quinolizinium as a new fluorescent lysosomotropic probe

We have synthesized a collection of quinolizinium fluorescent dyes for the purpose of cell imaging. Preliminary biological studies in human U2OS osteosarcoma cancer cells have shown that different functional groups appended to the cationic quinolizinium scaffold efficiently modulate photophysical properties but also cellular distribution. While quinolizinium probes are known nuclear staining reagents, we have identified a particular quinolizinium derivative salt that targets the lysosomal compartment. This finding raises the question of predictability of specific organelle targeting from structural features of small molecules.     

β-amyloid PET neuroimaging: A review of radiopharmaceutical development

Alzheimer's disease (AD) is a neurodegenerative disease characterized by deposition of amyloid-β plaques that occurs even before symptoms of brain failure are clinically detectable. Whereas previously the diagnosis of AD was only routinely based on clinical assessment, an improvement over the past few years in imaging biomarkers has now led to reconsider the core of the AD diagnostic pathway. Therefore, positron emission tomography (PET) radiotracers for the in vivo imaging of amyloid plaques have been the focus of intense research. Many chemical compounds, mostly derived from the chemistry of amyloid histological staining dyes, have permitted to obtain promising brain amyloid radiopharmaceuticals. Three of them have been approved by the FDA and European regulatory bodies. The present review focuses on the development of these compounds not only as a suitable imaging biomarker to improve AD diagnosis, but also to evaluate new potential therapy.