Fluorescent dyes with large Stokes shifts for super-resolution optical microscopy of biological objects: a review

PyrAtes: Modular Organic Salts with Large Stokes Shifts for Fluo-rescence Microscopy

The deployment of small-molecule fluorescent agents plays an ever-growing role in medicine and drug development. Herein, we complement the portfolio of powerful fluorophores, reporting the serendipitous discovery and development of a novel class with an imidazo[1,2-a]pyridinium triflate core, which we term PyrAtes. These fluorophores are synthesized in a single step from readily available materials (>60 examples) and display Stokes shifts as large as 240 nm, while also reaching NIR-I emissions at λmax as long as 720 nm. Computational studies allow the development of a platform for the prediction of λmax and λEm. Furthermore, we demonstrate the compatibility of these novel fluorophores with live cell imaging in HEK293 cells, suggesting PyrAtes as potent intracellular markers.

Central Ring Puckering Enhances the Stokes Shift of Xanthene Dyes

Small-molecule dyes are generally designed based on well-understood electronic effects. However, steric hindrance can promote excited-state geometric relaxation, increasing the difference between the positions of absorption and emission bands (the Stokes shift). Accordingly, we hypothesized that sterically induced central ring puckering in xanthene dyes could be used to systematically increase their Stokes shift. Through a combined experimental/quantum-chemical approach, we screened a group of (9-acylimino)-pyronin dyes with a perturbed central ring geometry. Our results showed that an atom with sp3 hybridization in position 10 of (9-acylimino)-pyronins induces central ring puckering and facilitates excited-state geometric relaxation, thereby markedly enhancing their Stokes shifts (by up to ~2000 cm-1). Thus, we prepared fluorescent (9-acylimino)-pyronin pH sensors, which showed a Stokes shift disparity between acid and base forms of up to ~8700 cm-1. Moreover, the concept of ring puckering-enhanced Stokes shift can be applied to a wide range of xanthene analogues found in the literature. Therefore, central ring puckering may be reliably used as a strategy for enhancing Stokes shifts in the rational design of dyes.

Auxochrome Dimethyl-Dihydroacridine Improves Fluorophores for Prolonged Live-Cell Super-Resolution Imaging

Superior photostability, minimal phototoxicity, red-shifted absorption/emission wavelengths, high brightness, and an enlarged Stokes shift are essential characteristics of top-tier organic fluorophores, particularly for long-lasting super-resolution imaging in live cells (e.g., via stimulated emission depletion (STED) nanoscopy). However, few existing fluorophores possess all of these properties. In this study, we demonstrate a general approach for simultaneously enhancing these parameters through the introduction of 9,9-dimethyl-9,10-dihydroacridine (DMA) as an electron-donating auxochrome. DMA not only induces red shifts in emission wavelengths but also suppresses photooxidative reactions and prevents the formation of triplet states in DMA-based fluorophores, greatly improving photostability and remarkably minimizing phototoxicity. Moreover, the DMA group enhances the fluorophores' brightness and enlarges the Stokes shift. Importantly, the "universal" benefits of attaching the DMA auxochrome have been exemplified in various fluorophores including rhodamines, difluoride-boron complexes, and coumarin derivatives. The resulting fluorophores successfully enabled the STED imaging of organelles and HaloTag-labeled membrane proteins.

A novel near-infrared fluorescent probe for high-sensitivity detection of butyrylcholinesterase in various pathological states

Butyrylcholinesterase (BChE) is a crucial hydrolytic enzyme predominantly synthesized in the liver, playing a significant role in conditions like liver disorders, diabetes, Alzheimer's disease, and fat metabolism regulation. This study aims to address the current limitations in visualizing BChE activity in diseases at various states by introducing an ultra-sensitive near-infrared fluorescent probe, FDCM-BChE. The probe was engineered to have several properties, such as a large Stokes shift, rapid response time, high stability, excellent selectivity, and low detection limits. We validated the efficacy of FDCM-BChE in quantifying BChE activity in human serum and leveraged its low cytotoxicity for cellular imaging. The study revealed the downregulation of BChE activity in liver cancer and hepatic injury and the upregulation in diabetes. Thus, FDCM-BChE shows promise as a tool for specific applications, providing insights into diseases associated with BChE activity.

3, 5-Dihydroxy 4', 7-dimethoxyflavone-DNA interaction study for nucleic acid detection and differential cell staining

The present study is focused on application of a natural compound, 3, 5-dihydroxy 4', 7-dimethoxyflavone (DHDM) from a medicinal plant Alpinia nigra for nucleic acid detection and differential cell staining. DHDM was found to interact with nucleic acid and forms complex, which was investigated for various applications. It was successfully utilized to visualize plasmid, genomic, and ds-linear DNA in agarose gel electrophoresis without affecting the DNA mobility in the gel. Fluorescence of DHDM increased several fold upon binding to dsDNA. Photostability of the compound was assessed and showed photobleaching effect that decreased gradually over time. Application of the compound was further extended to differential cell staining. When observed in fluorescence microscope, DHDM stained the dead cells and differentiated them from live cells in the case of bacterial, yeast, and mammalian cells. Higher concentration of the compound was found to be less cytotoxic to cancerous cells. Nucleic acid staining dyes like Ethidium bromide (EtBr), Propidium iodide (PI), etc. are carcinogens and environmental pollutants and therefore DHDM a natural compound, is a major benefit and thus can serve as an alternative to the current dyes.

Rational Design and Biological Application of Hybrid Fluorophores

Fluorophores are considered powerful tools for not only enabling the visualization of cell structures, substructures, and biological processes, but also making for the quantitative and qualitative measurement of various analytes in living systems. However, most fluorophores do not meet the diverse requirements for biological applications in terms of their photophysical and biological properties. Hybridization is an important strategy in molecular engineering that provides fluorophores with complementarity and multifunctionality. This review summarizes the basic strategies of hybridization with four classes of fluorophores, including xanthene, cyanine, coumarin, and BODIPY with a focus on their structure-property relationship (SPR) and biological applications. This review aims to provide rational hybrid ideas for expanding the reservoir of knowledge regarding fluorophores and promoting the development of newly produced fluorophores for applications in the field of life sciences.

Nanocrystals for Deep-Tissue In Vivo Luminescence Imaging in the Near-Infrared Region

In vivo imaging technologies have emerged as a powerful tool for both fundamental research and clinical practice. In particular, luminescence imaging in the tissue-transparent near-infrared (NIR, 700-1700 nm) region offers tremendous potential for visualizing biological architectures and pathophysiological events in living subjects with deep tissue penetration and high imaging contrast owing to the reduced light-tissue interactions of absorption, scattering, and autofluorescence. The distinctive quantum effects of nanocrystals have been harnessed to achieve exceptional photophysical properties, establishing them as a promising category of luminescent probes. In this comprehensive review, the interactions between light and biological tissues, as well as the advantages of NIR light for in vivo luminescence imaging, are initially elaborated. Subsequently, we focus on achieving deep tissue penetration and improved imaging contrast by optimizing the performance of nanocrystal fluorophores. The ingenious design strategies of NIR nanocrystal probes are discussed, along with their respective biomedical applications in versatile in vivo luminescence imaging modalities. Finally, thought-provoking reflections on the challenges and prospects for future clinical translation of nanocrystal-based in vivo luminescence imaging in the NIR region are wisely provided.

Heavy Atom Effect on the Intersystem Crossing of a Boron Difluoride Formazanate Complex-Based Photosensitizer: Experimental and Theoretical Studies

Photodynamic therapy (PDT) is a photochemical-based treatment approach that involves using light to activate photosensitizers (PSs). Attractively, PDT is one of the alternative cancer treatments due to its noninvasive technique. By utilizing the heavy atom effect, this work modified a class of formazan dyes to improve intersystem crossing (ISC) to improve reactive oxygen species (ROS) generation for PDT treatment. Two methods were used to observe the ROS generation enhanced by ISC of the synthesized complexes including, (1) recording DPBF decomposition caused by the ROS, and (2) calculating the potential energy curves for photophysical mechanisms of BF2 -formazanate dyes using the DFT and nudged elastic band (NEB) methods. The photophysical properties of the dyes were studied using spectroscopic techniques and X-ray crystallography, as well as DFT calculations. The experimental and theoretical results and in vitro cellular assays confirmed the potential use of the newly synthesized iodinated BF2 -formazanate dyes in PDT.

A pipeline for STED super-resolution imaging and Imaris analysis of nanoscale synapse organization in mouse cortical brain slices

Advances in super-resolution imaging enable us to delve into its intricate structural and functional complexities with unprecedented detail. Here, we present a pipeline to visualize and analyze the nanoscale organization of cortical layer 1 apical dendritic spines in the mouse prefrontal cortex. We describe steps for brain slice preparation, immunostaining, stimulated emission depletion super-resolution microscopy, and data analysis using the Imaris software package. This protocol allows the study of physiologically relevant brain circuits implicated in neuropsychiatric disorders.

Strongly emitting, centrosymmetric, ladder-type bis-coumarins with crankshaft architecture

Quadrupolar bis-coumarins bearing dialkylamino groups, prepared by a double Pechmann reaction and subsequent oxidation, strongly emit yellow-orange light. Comparison with non-substituted analogs reveals that, the photophysical properties of the conjugated bis-coumarins are controlled both by the dialkylamino substituents and by the π-system. Analogous but non-conjugated bis-coumarins emit blue light both in solution and in crystalline state. Unusually fast oxidation process in the crystalline state is responsible for the presence of two bands in their solid-state emission. Two-center, charge-transfer transition from an orbital delocalized on the entire molecule to the central benzene ring is responsible for photophysical properties.

Rational Design of Cost-Effective 4-Styrylcoumarin Fluorescent Derivatives for Biomolecule Labeling

Fluorescent labels are key tools in a wide range of modern scientific applications, such as fluorescence microscopy, flow cytometry, histochemistry, direct and indirect immunochemistry, and fluorescence in situ hybridization (FISH). Small fluorescent labels have important practical advantages as they allow maximizing the fluorescence signal by binding multiple fluorophores to a single biomolecule. At present, the most widely used fluorescent labels available present small Stokes shifts and are too costly to be used in routine applications. In this work we present four new coumarin derivatives, as promising and inexpensive fluorescent labels for biomolecules, obtained through a cost-effective, efficient, and straightforward synthetic strategy. Density functional theory and time-dependent density functional theory calculations of the electronic ground and lowest-lying singlet excited states were carried out in order to gain insights into the observed photophysical properties.

Conformation of the Ester Group Governs the Photophysics of Highly Polarized Benzo[g]coumarins

Photosensitizers that display "unusual" emission from upper electronically excited states offer possibilities for initiating higher-energy processes than what the governing Kasha's rule postulates. Achieving conditions for dual fluorescence from multiple states of the same species requires molecular design and conditions that favorably tune the excited-state dynamics. Herein, we switch the position of the electron-donating NMe₂ group around the core of benzo[g]coumarins (BgCoum) and tune the electronic coupling and the charge-transfer character of the fluorescent excited states. For solvents with intermediate polarity, three of the four regioisomers exhibit fluorescence from two different excited states with bands that are well separated in the visible and the near-infrared spectral regions. Computational analysis, employing ab initio methods, reveals that the orientation of an ester on the pyrone ring produces two conformers responsible for the observed dual fluorescence. Studies with solid solvating media, which restricts the conformational degrees of freedom, concur with the computational findings. These results demonstrate how "seemingly inconsequential" auxiliary substituents, such as the esters on the pyrone coumarin rings, can have profound effects leading to "anti-Kasha" photophysical behavior important for molecular photonics, materials engineering, and solar-energy science.

Incubation of protonated NADH or NADPH with ortho-aminobenzaldehyde generates a novel fluorescent nicotinamide dihydroquinazoline condensate

Incubation of reduced nicotinamide adenine dinucleotide (NADH) but not oxidized NAD+ with ortho-aminobenzaldehyde (oABA) generated an uncharacterized chromophore with an absorption peak characteristic of a dihydroquinazoline condensate. This chromophore is responsible for a non-specific signal in a diamine oxidase (DAO) activity assay based on the generation of fluorescent dihydroquinazoline structures directly from DAO substrates. Herein we show that at pH values below 3.0 the glycosidic bond of NADH/NADPH is broken releasing double protonated dihydro-nicotinamide (dihydro-NAM), which consequently condensates with oABA to a novel dihydroquinazoline chromophore and fluorophore, namely the 6- or 8-carbamoyl-5H,7H,8H,9H-10λ⁵-pyrido[2,1-b]quinazolin-10-ylium isomer (CMPQ). The second protonation event closely correlates with the pKa of the N1 nitrogen of C5-protonated dihydro-NAM and fluorophore stability. The fusion partner of oABA is likely the iminium of the primary acid product of dihydro-NAM after glycosidic bond hydrolysis and before irreversible cyclization. Trapping of protonated dihydro-NAM from NADH or NADPH with oABA allows quantification of these dinucleotides. Despite almost a century of research studying acid-catalyzed molecular rearrangements of NADH and NADPH, new and surprising details can be discovered.

Excitation dependent emissive multi stimuli responsive ESIPT organic luminogen for monitoring sea food freshness

Excited state intramolecular proton transfer (ESIPT) organic luminophores with excitation wavelength-dependent color tunability have drawn significant attention due to their exceptional photoluminescent properties in solution and solid state. A novel salicylaldehyde-based Schiff's base molecule, (E)-N'-(3,5-dibromo-2-hydroxybenzylidene)benzohydrazide (BHN) exhibited stimuli (excitation wavelength and pH) induced changes in fluorescence properties which was utilised for applications like trace level water sensing in organic solvents (THF, acetone and DMF), detection and quantification of biogenic amines and anticounterfeiting. In the solution state, BHN rendered a ratiometric detection and quantification of ammonia, diethylamine and trimethylamine, which is further supported by DFT studies. The photoluminescent response of BHN towards various biogenic amines was later utilised to monitor shrimp freshness. The investigation carried out highlights the potential versatility of ESIPT hydrazones, which renders multi stimuli responsive behaviour that can be utilised for water sensing, anticounterfeiting and the detection and quantification of biogenic amines.

Fluorescence-based super-resolution-microscopy strategies for chromatin studies

Super-resolution microscopy (SRM) is a prime tool to study chromatin organisation at near biomolecular resolution in the native cellular environment. With fluorescent labels DNA, chromatin-associated proteins and specific epigenetic states can be identified with high molecular specificity. The aim of this review is to introduce the field of diffraction-unlimited SRM to enable an informed selection of the most suitable SRM method for a specific chromatin-related research question. We will explain both diffraction-unlimited approaches (coordinate-targeted and stochastic-localisation-based) and list their characteristic spatio-temporal resolutions, live-cell compatibility, image-processing, and ability for multi-colour imaging. As the increase in resolution, compared to, e.g. confocal microscopy, leads to a central role of the sample quality, important considerations for sample preparation and concrete examples of labelling strategies applicable to chromatin research are discussed. To illustrate how SRM-based methods can significantly improve our understanding of chromatin functioning, and to serve as an inspiring starting point for future work, we conclude with examples of recent applications of SRM in chromatin research.

[1,3]-Dioxolo[4,5-f]benzodioxole (DBD) Fluorescent Dyes; Synthesis, Properties, and Applications

In this review we give an overview of the syntheses and photophysical properties of the new class of fluorescent dyes based on a [1,3]-dioxolo[4,5-f]benzodioxole core and their derivatives. Starting from commercially available reactants (e.g., sesamol, 1,2,4,5-tetrachlorobenzene) the core units can be prepared in a simple manner. Then, the benzene core can be derivatized via lithiation and their photophysical properties can be adjusted as desired. The obtained fluorophores have an absorption range of 403–520 nm and an emission range of 495–665 nm. This class of fluorescent dyes is also characterized by a long fluorescence lifetime, a high stability towards photobleaching, large Stokes shifts, and small size. Thus, the DBD dyes are optimally suited for optical sensing.

1 Introduction

2 Synthesis

3 Properties

4 Applications

Far Red-Shifted CdTe Quantum Dots for Multicolour Stimulated Emission Depletion Nanoscopy

Stimulated emission depletion (STED) nanoscopy is a widely used nanoscopy technique. Two-colour STED imaging in fixed and living cells is standardised today utilising both fluorescent dyes and fluorescent proteins. Solutions to image additional colours have been demonstrated using spectral unmixing, photobleaching steps, or long-Stokes-shift dyes. However, these approaches often compromise speed, spatial resolution, and image quality, and increase complexity. Here, we present multicolour STED nanoscopy with far red-shifted semiconductor CdTe quantum dots (QDs). STED imaging of the QDs is optimized to minimize blinking effects and maximize the number of detected photons. The far-red and compact emission spectra of the investigated QDs free spectral space for the simultaneous use of fluorescent dyes, enabling straightforward three-colour STED imaging with a single depletion beam. We use our method to study the internalization of QDs in cells, opening up the way for future super-resolution studies of particle uptake and internalization.

Highly emissions of TPA-linear based pyrazine derivatives with different mechanochromic luminosity

We designed the TPA-based linear pyrazine derivatives of PP-1 and PP-2, synthesized using the conventional Suzuki cross-linking reaction. It was followed by photophysical studies such as aprotic solvent (Haxene to DMF). A red-shift was observed from the non-polar aprotic solvent to the polar aprotic solvent, and the emission intensity was gradually decreased. In addition, the Aggregation-induced emission (AIE) effect has been studied against the DMF/water addition of linear pyrazine compounds. It showed a classic aggregation-caused quenching effect (ACQ) and red-shifted at an increase of (f_w) 0 to 40%. After this case, when the water fraction in these studies was increased by (fw) 50 to 90%, a blue shift and a mild AIE effect has occurred. And also, was investigated acidochromic effect of compounds PP-1 and PP-2 using TFA acid. Absorption and emission intensity were gradually reduced as the acid concentration increased for these studies, while the new peaks appeared red-shifted in the absorption spectrum. They were examined before and after exposure to UV light irradiation in the synthesized dye compounds.

Photoactivatable Large Stokes Shift Fluorophores for Multicolor Nanoscopy

We designed caging-group-free photoactivatable live-cell permeant dyes with red fluorescence emission and ∼100 nm Stokes shifts based on a 1-vinyl-10-silaxanthone imine core structure. The proposed fluorophores undergo byproduct-free one- and two-photon activation, are suitable for multicolor fluorescence microscopy in fixed and living cells, and are compatible with super-resolution techniques such as STED (stimulated emission depletion) and PALM (photoactivated localization microscopy). Use of photoactivatable labels for strain-promoted tetrazine ligation and self-labeling protein tags (HaloTag, SNAP-tag), and duplexing of an imaging channel with another large Stokes shift dye have been demonstrated.

Theoretical insight on the saturated stimulated emission intensity of a squaraine dye for STED nanoscopy

Stimulated emission depletion nanoscopy (STED) is increasingly applied for the insights into the ultra-structures of organelles in live cells because of the bypassing of the Abbe's optical diffraction limit. Theoretically, with the increase of excitation and depletion laser power, the imaging resolution can be accordingly enhanced and even close to the infinity. Unfortunately, powerful laser illuminations usually produce severe phototoxicity and photobleaching, which will lead to more extra-interference with biological events in live cells and accelerate the decomposition of the fluorescent probes. In view of the trade-off of cell viability and imaging resolution, excellent probes with superior photophysical properties are great in demand. For a qualified STED probes, the saturated stimulated emission intensity (I_sat) is considered as a key evaluating factor. According to the formula, I_sat is inversely proportional to the stimulated emission cross section (σ_sti) of the fluorescent probe. However, the relationship between the σ_sti and chemical structure of the STED probe remain to be unclear. In this work, we explore the influence factors by theoretical calculations on a squaraine dye (MitoEsq-635) and a commercial dye (Atto647N). The results indicate that the increase of transition dipole moment (μ) are beneficial for the increase of σ_sti, thereafter reducing I_sat. Furthermore, we firstly proposed that stimulated emission depletion was qualitatively interpreted by the investigation on the potential energy surfaces of ground states (S₀) and the first excited states (S₁) of the dyes.

Fluorescent Pyranoindole Congeners: Synthesis and Photophysical Properties of Pyrano[3,2-f], [2,3-g], [2,3-f], and [2,3-e]Indoles

This paper reports the synthesis of four types of annulated pyranoindole congeners: pyrano[3,2-f]indole, pyrano[2,3-g]indole, pyrano[2,3-f]indole, and pyrano[2,3-e]indole and photophysical studies in this series. The synthesis of pyrano[3,2-f], [2,3-g], and [2,3-e]indoles involve a tandem of Bischler-Möhlau reaction of 3-aminophenol with benzoin to form 6-hydroxy- or 4-hydroxyindole followed by Pechmann condensation of these hydroxyindoles with β-ketoesters. Pyrano[2,3-f]indoles were synthesized through the Nenitzescu reaction of p-benzoquinone and ethyl aminocrotonates and subsequent Pechmann condensation of the obtained 5-hydroxyindole derivatives. Among the pyranoindoles studied, the most promising were pyrano[3,2-f] and [2,3-g]indoles. These compounds were characterized by moderate to high quantum yields (30-89%) and a large (9000-15,000 cm^-1) Stokes shift. More detailed photophysical studies were carried out for a series of the most promising derivatives of pyrano[3,2-f] and [2,3-g]indoles to demonstrate their positive solvatochromism, and the data collected was analyzed using Lippert-Mataga equation. Quantum chemical calculations were performed to deepen the knowledge of the absorption and emission properties of pyrano[3,2-f] and [2,3-g]indoles as well as to explain their unusual geometries and electronic structures.

Expansion microscopy of neutrophil nuclear structure and extracellular traps

Neutrophils are key players of the immune system and possess an arsenal of effector functions, including the ability to form and expel neutrophil extracellular traps (NETs) in a process termed NETosis. During NETosis, the nuclear DNA/chromatin expands until it fills the whole cell and is released into the extracellular space. NETs are composed of DNA decorated with histones, proteins, or peptides, and NETosis is implicated in many diseases. Resolving the structure of the nucleus in great detail is essential to understand the underlying processes, but so far, superresolution methods have not been applied. Here, we developed an expansion-microscopy-based method and determined the spatial distribution of chromatin/DNA, histone H1, and nucleophosmin with an over fourfold improved resolution (<40-50 nm) and increased information content. It allowed us to identify the punctate localization of nucleophosmin in the nucleus and histone-rich domains in NETotic cells with a size of 54-66 nm. The technique could also be applied to components of the nuclear envelope (lamins B1 and B2) and myeloperoxidase, providing a complete picture of nuclear composition and structure. In conclusion, expansion microscopy enables superresolved imaging of the highly dynamic structure of nuclei in immune cells.

Design of Smart Aggregates: Toward Rapid Clinical Diagnosis of Hyperlipidemia in Human Blood

Molecular aggregates with environmental responsive properties are desired for their wide practical applications such as bioprobes. Here, a series of smart near-infrared (NIR) luminogens for hyperlipidemia (HLP) diagnosis is reported. The aggregates of these molecules exhibit a twisted intramolecular charge-transfer effect in aqueous media, but aggregation-induced emission in highly viscous media due to the restriction of the intramolecular motion. These aggregates, which can autonomously respond to different environments via switching the aggregation state without changing their chemical structures are described, as "smart aggregates". Intriguingly, these luminogens demonstrate NIR-II and NIR-III luminescence with ultralarge Stokes shifts (>950 nm). Both in vitro detection and in vivo imaging of HLP can be realized in a mouse model. Linear relationships exist between the emission intensity and multiple pathological parameters in blood samples of HLP patients. Thus, the design of smart aggregate facilitates rapid and accurate detection of HLP and provides a promising attempt in aggregate science.

Biology and medicine in the landscape of quantum advantages

Quantum computing holds substantial potential for applications in biology and medicine, spanning from the simulation of biomolecules to machine learning methods for subtyping cancers on the basis of clinical features. This potential is encapsulated by the concept of a quantum advantage, which is contingent on a reduction in the consumption of a computational resource, such as time, space or data. Here, we distill the concept of a quantum advantage into a simple framework to aid researchers in biology and medicine pursuing the development of quantum applications. We then apply this framework to a wide variety of computational problems relevant to these domains in an effort to (i) assess the potential of practical advantages in specific application areas and (ii) identify gaps that may be addressed with novel quantum approaches. In doing so, we provide an extensive survey of the intersection of biology and medicine with the current landscape of quantum algorithms and their potential advantages. While we endeavour to identify specific computational problems that may admit practical advantages throughout this work, the rapid pace of change in the fields of quantum computing, classical algorithms and biological research implies that this intersection will remain highly dynamic for the foreseeable future.

Stimulated emission depletion microscopy with a single depletion laser using five fluorochromes and fluorescence lifetime phasor separation

Stimulated emission depletion (STED) microscopy achieves super-resolution by exciting a diffraction-limited volume and then suppressing fluorescence in its outer parts by depletion. Multiple depletion lasers may introduce misalignment and bleaching. Hence, a single depletion wavelength is preferable for multi-color analyses. However, this limits the number of usable spectral channels. Using cultured cells, common staining protocols, and commercially available fluorochromes and microscopes we exploit that the number of fluorochromes in STED or confocal microscopy can be increased by phasor based fluorescence lifetime separation of two dyes with similar emission spectra but different fluorescent lifetimes. In our multi-color FLIM-STED approach two fluorochromes in the near red (exc. 594 nm, em. 600–630) and two in the far red channel (633/641–680), supplemented by a single further redshifted fluorochrome (670/701–750) were all depleted with a single laser at 775 nm thus avoiding potential alignment issues. Generally, this approach doubles the number of fully distinguishable colors in laser scanning microscopy. We provide evidence that eight color FLIM-STED with a single depletion laser would be possible if suitable fluorochromes were identified and we confirm that a fluorochrome may have different lifetimes depending on the molecules to which it is coupled.

Inactivation of Competitive Decay Channels Leads to Enhanced Coumarin Photochemistry

In the development of photolabile protecting groups, it is of high interest to selectively modify photochemical properties with structural changes as simple as possible. In this work, knowledge of fluorophore optimization was adopted and used to design new coumarin‐ based photocages. Photolysis efficiency was selectively modulated by inactivating competitive decay channels, such as twisted intramolecular charge transfer (TICT) or hydrogen‐bonding, and the photolytic release of the neurotransmitter serotonin was demonstrated. Structural modifications inspired by the fluorophore ATTO 390 led to a significant increase in the uncaging cross section that can be further improved by the simple addition of a double bond. Ultrafast transient absorption spectroscopy gave insights into the underlying solvent‐dependent photophysical dynamics. The chromophores presented here are excellently suited as new photocages in the visible wavelength range due to their simple synthesis and their superior photochemical properties.

Developing FRET Networks for Sensing

Förster resonance energy transfer (FRET) is a widely used fluorescence-based sensing mechanism. To date, most implementations of FRET sensors have relied on a discrete donor-acceptor pair for detection of each analytical target. FRET networks are an emerging concept in which target recognition perturbs a set of interconnected FRET pathways between multiple emitters. Here, we review the energy transfer topologies and scaffold materials for FRET networks, propose a general nomenclature, and qualitatively summarize the dynamics of the competitive, sequential, homoFRET, and heteroFRET pathways that constitute FRET networks. Implementations of FRET networks for sensing are also described, including concentric FRET probes, other single-vector multiplexing, and logic gates and switches. Unresolved questions and future research directions for current systems are discussed, as are potential but currently unexplored applications of FRET networks in sensing.

Single-Particle Resolution Fluorescence Microscopy of Nanoplastics

Understanding of nanoplastic prevalence and toxicology is limited by imaging challenges resulting from their small size. Fluorescence microscopy is widely applied to track and identify microplastics in laboratory studies and environmental samples. However, conventional fluorescence microscopy, due to diffraction, lacks the resolution to precisely localize nanoplastics in tissues, distinguish them from free dye, or quantify them in environmental samples. To address these limitations, we developed techniques to label nanoplastics for imaging with stimulated emission depletion (STED) microscopy to achieve resolution at an order of magnitude superior to conventional fluorescence microscopy. These techniques include (1) passive sorption; (2) swell incorporation; and (3) covalent coupling of STED-compatible fluorescence dyes to nanoplastics. We demonstrate that our labeling techniques, combined with STED microscopy, can be used to resolve nanoplastics of different shapes and compositions as small as 50 nm. The longevity of dye labeling is demonstrated in different media and conditions of biological and environmental relevance. We also test STED imaging of nanoplastics in exposure experiments with the model worm Caenorhabditis elegans. Our work shows the value of the method for detection and localization of nanoplastics as small as 50 nm in a whole animal without disruption of the tissue. These techniques will allow more precise localization and quantification of nanoplastics in complex matrices such as biological tissues in exposure studies.

A synergistic strategy to develop photostable and bright dyes with long Stokes shift for nanoscopy

The quality and application of super-resolution fluorescence imaging greatly lie in the dyes’ properties, including photostability, brightness, and Stokes shift. Here we report a synergistic strategy to simultaneously improve such properties of regular fluorophores. Introduction of quinoxaline motif with fine-tuned electron density to conventional rhodamines generates new dyes with vibration structure and inhibited twisted-intramolecular-charge-transfer (TICT) formation synchronously, thus increasing the brightness and photostability while enlarging Stokes shift. The new fluorophore YL578 exhibits around twofold greater brightness and Stokes shift than its parental fluorophore, Rhodamine B. Importantly, in Stimulated Emission Depletion (STED) microscopy, YL578 derived probe possesses a superior photostability and thus renders threefold more frames than carbopyronine based probes (CPY-Halo and 580CP-Halo), known as photostable fluorophores for STED imaging. Furthermore, the strategy is well generalized to offer a new class of bright and photostable fluorescent probes with long Stokes shift (up to 136 nm) for bioimaging and biosensing.

Super-resolution microscopy is a powerful tool for cellular studies but requires bright and stable fluorescent probes. Here, the authors report on a strategy to introduce quinoxaline motifs to conventional probes to make them brighter, more photostable, larger Stokes shift, and demonstrate the probes for biosensing applications.

Polarized, V-Shaped, and Conjoined Biscoumarins: From Lack of Dipole Moment Alignment to High Brightness

Eleven conjoined coumarins possessing a chromeno[3,4-c]chromene-6,7-dione skeleton have been synthesized via the reaction of electron-rich phenols with esters of coumarin-3-carboxylic acids, catalyzed by either Lewis acids or 4-dimethylaminopyridine. Furthermore, Michael-type addition to angular benzo[f]coumarins is possible, leading to conjugated helical systems. Arrangement of the electron-donating amino groups at diverse positions on this heterocyclic skeleton makes it possible to obtain π-expanded coumarins with emission either sensitive to, or entirely independent of, solvent polarity with large Stokes shifts. Computational studies have provided a rationale for moderate solvatochromic effects unveiling the lack of collinearity of the dipole moments in the ground and excited states. Depending on the functional groups present, the obtained dyes are highly polarized with dipole moments of ∼14 D in the ground state and ∼20–25 D in the excited state. Strong emission in nonpolar solvents, in spite of the inclusion of a NO₂ group, is rationalized by the fact that the intramolecular charge transfer introduced into these molecules is strong enough to suppress intersystem crossing yet weak enough to prevent the formation of dark twisted intramolecular charge transfer states. Photochemical transformation of the dye possessing a chromeno[3,4-c]pyridine-4,5-dione scaffold led to the formation of a spirocyclic benzo[g]coumarin.

Bleaching-Resistant Super-Resolution Fluorescence Microscopy

Photobleaching is the permanent loss of fluorescence after extended exposure to light and is a major limiting factor in super-resolution microscopy (SRM) that restricts spatiotemporal resolution and observation time. Strategies for preventing or overcoming photobleaching in SRM are reviewed developing new probes and chemical environments. Photostabilization strategies are introduced first, which are borrowed from conventional fluorescence microscopy, that are employed in SRM. SRM-specific strategies are then highlighted that exploit the on-off transitions of fluorescence, which is the key mechanism for achieving super-resolution, which are becoming new routes to address photobleaching in SRM. Off states can serve as a shelter from excitation by light or an exit to release a damaged probe and replace it with a fresh one. Such efforts in overcoming the photobleaching limits are anticipated to enhance resolution to molecular scales and to extend the observation time to physiological lifespans.

An Efficient Aequorea victoria Green Fluorescent Protein for Stimulated Emission Depletion Super-Resolution Microscopy

In spite of their value as genetically encodable reporters for imaging in living systems, fluorescent proteins have been used sporadically for stimulated emission depletion (STED) super-resolution imaging, owing to their moderate photophysical resistance, which does not enable reaching resolutions as high as for synthetic dyes. By a rational approach combining steady-state and ultrafast spectroscopy with gated STED imaging in living and fixed cells, we here demonstrate that F99S/M153T/V163A GFP (c3GFP) represents an efficient genetic reporter for STED, on account of no excited state absorption at depletion wavelengths <600 nm and a long emission lifetime. This makes c3GFP a valuable alternative to more common, but less photostable, EGFP and YFP/Citrine mutants for STED imaging studies targeting the green-yellow region of the optical spectrum.

New Red-Shifted 4-Styrylcoumarin Derivatives as Potential Fluorescent Labels for Biomolecules

Important scientific areas, such as cellular biology, medicine, pharmacy, and environmental sciences, are dependent on very sensitive analytical techniques to track and detect biomolecules. In this work, we develop a simple, low-cost and effective synthetic strategy to produce new red-shifted 4-styrylcoumarin derivatives as promising inexpensive fluorescent labels for biomolecules. The extension of the delocalized π-electron system results in bathochromic shifts in these new coumarin derivatives, which also present large Stokes shifts. In addition, density functional theory and time-dependent density functional theory calculations helped to rationalize the photophysical properties observed by the experimental results.

Coumarin-pyridine push-pull fluorophores: Synthesis and photophysical studies

A series of coumarin-pyridine-based push-pull fluorophores were prepared starting from 1,2,4-triazines by using direct C-H functionalization (S_N^H-reaction)-Diels-Alder-retro Diels-Alder domino reaction sequence. This efficient synthetic strategy allowed to obtain a series of 19 coumarin-pyridine fluorophores. Their photophysical properties were studied. While pyridine-substituted derivatives of 4-alkylcoumarins may be considered as alternative to coumarin dyes characterized by emission maxima mainly in a visible region with wavelengths of 402-415 nm, absorption in the UV range at 210-307 nm, and good photoluminescence quantum yields of 6-19%, all the derivatives of 4-phenylcoumarin did not exhibit any noticeable fluorescence. More detailed photophysical studies were carried out for two the most representative derivatives of 4-alkyl-coumarin-pyridines to demonstrate their positive solvatochromism, and the collected data were analyzed by using Lippert-Mataga equation, as well as Kosower and Dimroth/Reichardt scales. The obtained results demonstrate that the combining two chromophore systems, such as 2,5-diarylpyridine and coumarin ones, is promising in terms of improving the photophysical properties of the new coumarin-pyridine hybrid compounds.

Development of new 2-piperidinium-4-styrylcoumarin derivatives with large Stokes shifts as potential fluorescent labels for biomolecules

New 2-piperidinium-4-styrylcoumarin derivatives, with large Stokes shifts and high fluorescence quantum yields, as potential fluorescent labels for biomolecules.

Bioorthogonal Ligation-Activated Fluorogenic FRET Dyads

An energy transfer‐based signal amplification relay concept enabling transmission of bioorthogonally activatable fluorogenicity of blue‐excitable coumarins to yellow/red emitting cyanine frames is presented. Such relay mechanism resulted in improved cyanine fluorogenicities together with increased photostabilities and large apparent Stokes‐shifts allowing lower background fluorescence even in no‐wash bioorthogonal fluorogenic labeling schemes of intracellular structures in live cells. These energy transfer dyads sharing the same donor moiety together with their parent donor molecule allowed three‐color imaging of intracellular targets using one single excitation source with separate emission windows. Sub‐diffraction imaging of intracellular structures using the bioorthogonally activatable FRET dyads by STED microscopy is also presented.

Engineering of a fluorescent chemogenetic reporter with tunable color for advanced live-cell imaging

Biocompatible fluorescent reporters with spectral properties spanning the entire visible spectrum are indispensable tools for imaging the biochemistry of living cells and organisms in real time. Here, we report the engineering of a fluorescent chemogenetic reporter with tunable optical and spectral properties. A collection of fluorogenic chromophores with various electronic properties enables to generate bimolecular fluorescent assemblies that cover the visible spectrum from blue to red using a single protein tag engineered and optimized by directed evolution and rational design. The ability to tune the fluorescence color and properties through simple molecular modulation provides a broad experimental versatility for imaging proteins in live cells, including neurons, and in multicellular organisms, and opens avenues for optimizing Förster resonance energy transfer (FRET) biosensors in live cells. The ability to tune the spectral properties and fluorescence performance enables furthermore to match the specifications and requirements of advanced super-resolution imaging techniques.

Ultrahigh-Throughput Detection of Enzymatic Alcohol Dehydrogenase Activity in Microfluidic Droplets with a Direct Fluorogenic Assay

The exploration of large DNA libraries of metagenomic or synthetic origin is greatly facilitated by ultrahigh‐throughput assays that use monodisperse water‐in‐oil emulsion droplets as sequestered reaction compartments. Millions of samples can be generated and analysed in microfluidic devices at kHz speeds, requiring only micrograms of reagents. The scope of this powerful platform for the discovery of new sequence space is, however, hampered by the limited availability of assay substrates, restricting the functions and reaction types that can be investigated. Here, we broaden the scope of detectable biochemical transformations in droplet microfluidics by introducing the first fluorogenic assay for alcohol dehydrogenases (ADHs) in this format. We have synthesized substrates that release a pyranine fluorophore (8‐hydroxy‐1,3,6‐pyrenetrisulfonic acid, HPTS) when enzymatic turnover occurs. Pyranine is well retained in droplets for >6 weeks (i. e. 14‐times longer than fluorescein), avoiding product leakage and ensuring excellent assay sensitivity. Product concentrations as low as 100 nM were successfully detected, corresponding to less than one turnover per enzyme molecule on average. The potential of our substrate design was demonstrated by efficient recovery of a bona fide ADH with an >800‐fold enrichment. The repertoire of droplet screening is enlarged by this sensitive and direct fluorogenic assay to identify dehydrogenases for biocatalytic applications.

Coumarin luciferins and mutant luciferases for robust multi-component bioluminescence imaging

Multi-component bioluminescence imaging requires an expanded collection of luciferase-luciferin pairs that emit far-red or near-infrared light. Toward this end, we prepared a new class of luciferins based on a red-shifted coumarin scaffold. These probes (CouLuc-1s) were accessed in a two-step sequence via direct modification of commercial dyes. The bioluminescent properties of the CouLuc-1 analogs were also characterized, and complementary luciferase enzymes were identified using a two-pronged screening strategy. The optimized enzyme-substrate pairs displayed robust photon outputs and emitted a significant portion of near-infrared light. The CouLuc-1 scaffolds are also structurally distinct from existing probes, enabling rapid multi-component imaging. Collectively, this work provides novel bioluminescent tools along with a blueprint for crafting additional fluorophore-derived probes for multiplexed imaging.

Fluorescent chameleon labels for bioconjugation and imaging of proteins, nucleic acids, biogenic amines and surface amino groups. a review

Chameleon labels (ChLs) possess the unique property of changing (visible) color and fluorescence on binding to amino groups of biomolecules. MostChLs react with primary aliphatic amino groups such as those in lysine or with amino groups artificially introduced into polynucleic acids or saccharides, but someothers also react with secondary amino groups. Under controlled circumstances, the reactions are fairly specific. The review is subdivided into the following sections: (1) An introduction and classification of fluorescent labels; (2) pyrylium labels that undergo shortwave color changes upon labelling, typically from blue to red; (3) polymethine type of labels (that also undergo shortwave color changes, typically from green to blue; (4) various other (less common) chromogenic and fluorogenic systems; (5) hemicyanine labels that undergolongwavecolor changes, typically from yellow to purple; (6) the application of ChLs to labeling of proteins and oligonucleotides; (7) applications to fluorometric assays and sensing; (8) applications to fluorescence imaging of biomolecules; (9) applications in studies on affinity interactions (receptor-ligand binding); (10) applications in surface and interface chemistry; and (11) applications in chromatography, electrophoresis and isotachophoresis of biomolecules.

Tunable NIR AIE-active optical materials for lipid droplet imaging in typical model organisms and photodynamic therapy

Near infrared (NIR) luminescent materials with aggregation-induced emission (AIE) features have attracted enormous attention in the areas of medical imaging and diagnostic therapeutics because of their low background fluorescence and strong tissue penetration. This study reports a series of easily synthesized AIEgen molecules that feature NIR emission. These molecules have a donor-donor-π-acceptor (D1-D2-π-A) structure with intramolecular charge transfer (ICT) character. The nature of charge transfer transition can be modified by different structures of D2, i.e. phenyl, thiophene, and furan ring. These AIEgens have high selectivity towards lipid droplets (LDs) in vitro and in vivo, such as zebrafish, Caenorhabditis elegans, and oil crop tissue. In addition, the effect of photodynamic therapy (PDT) on SMMC-7721 cells was investigated, and the results indicate that these AIEgens have potential application for PDT on cancer cells with white light illumination. This study reveals that these triphenylamine (TPA)-based AIEgens have great potential for biological imaging and preclinical applications of PDT.

Triple-Color STED Nanoscopy: Sampling Absorption Spectra Differences for Efficient Linear Species Unmixing

Stimulated emission depletion (STED) in confocal fluorescence microscopy enables a visualization of biological structures within cells far below the optical diffraction limit. To meet the demand in the field for simultaneous investigations of multiple species within a cell, a couple of different STED techniques have been proposed, each with their own challenges. By systemically exploiting spectral differences in the absorption of fluorescent labels, we present a novel, beneficial approach to multispecies STED nanoscopy. By using three excitation wavelengths in nanosecond pulsed interleaved excitation (PIE) mode, we probe quasi simultaneously multiple species with fluorescent labels having absorption maxima as close as 13 nm. The acquired image is decomposed into its single species contributions by application of a linear unmixing algorithm based on present reference patterns. For multispecies images containing single species regions, we introduce the image correlation map (ICM). Here, the single species regions easily can be identified in order to generate the necessary single species reference patterns. This avoids the otherwise cumbersome and artifact prone preparation and recording of additional reference samples. The power of the proposed imaging scheme persists in species separation quality at high speed shown for up to three species with established reference samples and dyes commonly used for cellular STED imaging.

Heterocyclic Schiff Bases of 3-Aminobenzanthrone and Their Reduced Analogues: Synthesis, Properties and Spectroscopy

New substituted azomethines of benzanthrone with heterocyclic substituents were synthesized by condensation reaction of 3-aminobenzo[de]anthracen-7-one with appropriate aromatic aldehydes. The resulting imines were reduced with sodium borohydride to the corresponding amines, the luminescence of which is more pronounced in comparison with the initial azomethines. The novel benzanthrone derivatives were characterized by NMR, IR, MS, UV/Vis, and fluorescence spectroscopy. The structure of three dyes was studied by the X-ray single crystal structure analysis. The solvent effect on photophysical behaviors of synthesized imines and amines was investigated. The obtained compounds absorb at 420–525 nm, have relatively large Stokes shifts (up to 150 nm in ethanol), and emit at 500–660 nm. The results testify that emission of the studied compounds is sensitive to the solvent polarity, exhibiting negative fluorosolvatochromism for the synthesized azomethines and positive fluorosolvatochromism for the obtained amines. The results obtained indicate that the synthesized compounds are promising as luminescent dyes.

Organic Nanoparticles-Assisted Low-Power STED Nanoscopy

Stimulated emission depletion (STED) nanoscopy plays a key role in achieving sub-50 nm high spatial resolution for subcellular live-cell imaging. To avoid re-excitation, the STED wavelength has to be tuned at the red tail of the emission spectrum of fluorescent probes, leading to high depletion laser power that might damage the cell viability and functionality. Herein, with the highly emissive silica-coated core-shell organic nanoparticles (CSONPs) enabling a giant Stokes shift of 150 nm, ultralow power STED is achieved by shifting the STED wavelength to the emission maximum at 660 nm. The stimulated emission cross section is increased by ∼20-fold compared to that at the emission red tail. The measured saturation intensity and lateral resolution of our CSONP are 0.0085 MW cm^-2 and 25 nm, respectively. More importantly, long-term (>3 min) dynamic super-resolution imaging of the lysosomal fusion-fission processes in living cells is performed with a resolution of 37 nm.

Comparison of the Benzanthrone Luminophores: They Are Not Equal for Rapid Examination of Parafasciolopsis fasciolaemorpha (Trematoda: Digenea)

Luminescent derivatives of benzanthrone are becoming more useful based on their light-absorbing and fluorescent-emitting properties. Our previous studies showed that luminescent staining properties of the same benzanthrone dye differ for variable parasite samples. Therefore, two types of benzanthrone dyes were prepared. One has a strongly basic amidine group and a halogen atom, and the other has an amide moiety and a tertiary amine group. Trematoda Parafasciolopsis fasciolaemorpha is a liver fluke of a moose (Alces alces) and has a significant influence on the health and abundance of the moose population. Staining protocols for parasite P. fasciolaemorpha specific organ or organ systems imaging are mostly time-consuming and labor-intensive. The study aimed to compare the fixation technique and the staining protocol by synthesized benzanthrone luminescent dyes to determine detailed morphology, anatomical arrangement of the organ systems and gross organization of the muscle layers of P. fasciolaemorpha using confocal laser scanning microscopy. Luminophores were tested for samples fixed in different fixatives. Developed dyes and staining protocol resulting in imaging of all parts of trematode without additional sample preparation procedures, which usually are required for parasite examination. Obtained results confirmed that the most qualitative results could be reached using 3-N-(2-piperidinylacetamido)benzanthrone dye which has amide moiety and a tertiary amine group. Based on obtained results, 3-N-(2-piperidinylacetamido)benzanthrone gave more qualitative parasite visualization than 2-bromo-3-N-(N′,N′-dimethylformamidino)benzanthrone.

White light employing luminescent engineered large (mega) Stokes shift molecules: a review

Large (mega) Stokes shift molecules have shown great potential in white light emission for optoelectronic applications, such as flat panel display technology, light-emitting diodes, photosensitizers, molecular probes, cellular and bioimaging, and other applications. This review aims to summarize recent developments of white light generation that incorporate a large Stokes shift component, key approaches to designing large Stokes shift molecules, perspectives on future opportunities, and remaining challenges confronting this emerging research field. After a brief introduction of feasible pathways in generating white light, exemplifications of large Stokes shift molecules as white light candidates from organic and inorganic-based materials are illustrated. Various possible ways to design such molecules have been revealed by integrating the photophysical mechanisms that are essential to produce red-shifted emission upon photoexcitation, such as excited state intramolecular proton transfer (ESIPT), intramolecular charge transfer (ICT), excited state geometrical relaxation or structural deformation, aggregation-induced emission (AIE) alongside the different formations of aggregates, interplay between monomer and excimer emission, host-guest interaction, and lastly metal to ligand charge transfer (MLCT) via harvesting triplet state. Furthermore, previously reported fluorescent materials are described and categorized based on luminescence behaviors on account of the Stokes shifts value. This review will serve as a rationalized introduction and reference for researchers who are interested in exploring large or mega Stokes shift molecules, and will motivate new strategies along with instigation of persistent efforts in this prominent subject area with great avenues.