Triarylmethane Fluorophores Resistant to Oxidative Photobluing

A palette of bridged bicycle-strengthened fluorophores

Organic fluorophores are the keystone of advanced biological imaging. The vast chemical space of fluorophores has been extensively explored in search of molecules with ideal properties. However, within the current molecular constraints, there appears to be a trade-off between high brightness, robust photostability, and tunable biochemical properties. Herein we report a general strategy to systematically boost the performance of donor-acceptor-type fluorophores, such as rhodamines, by leveraging SO2 and O-substituted azabicyclo[3.2.1] octane auxochromes. These bicyclic heterocycles give rise to a collection of 'bridged' dyes (BD) spanning the ultraviolet and visible range with top-notch quantum efficiencies, enhanced water solubility, and tunable cell-permeability. Notably, these azabicyclic fluorophores showed remarkable photostability compared to their tetramethyl or azetidine analogs while being completely resistant to oxidative photoblueing. Functionalized BD dyes are tailored for applications in single-molecule imaging, super-resolution imaging (STED and SIM) in fixed or live mammalian and plant cells, and live zebrafish imaging and chemogenetic voltage imaging.

Azetidinyl Malachite Green: a superior fluorogen-activating protein probe for live-cell and dynamic SIM imaging

Malachite Green (MG) and its fluorogen-activating protein (FAP) pair are valuable tools for live-cell and super-resolution fluorescence imaging due to their unique near-infrared absorption and signal enhancement. However, the low brightness and photostability of MG have limited its use in dynamic imaging. In this study, we introduce a novel derivative, azetidinly Malachite Green (Aze-MG), which enhances the brightness of the MG-FAP complex by 2.6-fold. This enhancement is achieved by replacing the N,N-dimethylamino group in MG with an azetidine group, which suppresses the twisted intramolecular charge transfer (TICT) effect, leading to improved quantum yield and photostability. Additionally, the reduced binding affinity of Aze-MG for FAP enables a buffering strategy, allowing the reversible exchange of photobleached fluorogens with free fluorogens, thereby ensuring stable fluorescence over time. This combination of improved brightness and buffering capability makes Aze-MG an ideal probe for live-cell and dynamic SIM imaging.

A Photoactivatable Plasma Membrane Probe Based on a Self-Triggered Photooxidation Cascade for Live Cell Super-Resolution Microscopy

Super-resolution imaging based on the localization of single emitters requires a spatio-temporal control of the ON and OFF states. To this end, photoactivatable fluorophores are adapted as they can be turned on upon light irradiation. Here, we present a concept called self-triggered photooxidation cascade (STPC) based on the photooxidation of a plasma membrane-targeted leuco-rhodamine (LRhod-PM), a non-fluorescent reduced form of a rhodamine probe. Upon visible light irradiation the small number of oxidized rhodamines, Rhod-PM, acts as a photosensitizer to generate singlet oxygen capable of oxidizing the OFF state LRhod-PM thereby switching it to its ON state. We showed that this phenomenon is kinetically favored by a high local concentration and propagates quickly when the probe is embedded in membrane bilayers. In addition, we showed that the close proximity of the dyes favors the photobleaching. At the single-molecule level, the concomitant activation/bleaching phenomena allow reaching a single-molecule blinking regime enabling single-molecule localization microscopy for super-resolution of live cellular membranes and their thin processes including filopodia and tuneling nanotubes.

Red Light Mediated Photoconversion of Silicon Rhodamines to Oxygen Rhodamines for Single-Molecule Microscopy

The rhodamine motif has been modified in myriad ways to produce probes with specific fluorescent and chemical properties optimal for a variety of fluorescence microscopy experiments. Recently, far-red (>640 nm) emitting silicon rhodamines have become popular in single-molecule localization microscopy (SMLM), since these dyes are membrane-permeable and can be used alongside red (570-640 nm) emitting fluorophores for two-color imaging. While this has expanded multicolor SMLM imaging capabilities, we demonstrate that silicon rhodamines can create previously unreported photoproducts with significantly blueshifted emissions, which appear as bright single-molecule crosstalk in the red emission channel. We show that this fluorescence is caused by the replacement of the central silicon group with oxygen after 640 nm illumination, turning far-red silicon rhodamines (JFX650, JF669, etc.) into their red oxygen rhodamine counterparts (JFX554, JF571, etc.). While this blueshifted population can cause artifacts in two-color SMLM data, we demonstrate up to 16-fold reduction in crosstalk using oxygen scavenging systems. We also leverage this far-red photoconversion to demonstrate UV-free photoactivated localization microscopy (PALM) without the need for additives, and with 5-fold higher efficiency than the Cy5 to Cy3 conversion. Finally, we demonstrate multiplexed pseudo two-color PALM in a single emission channel by separating localizations by their photoactivation wavelengths instead of their emission wavelengths.

Synthesis and Photophysical Properties of 4'-5' Disubstituted CinNapht Dyes Accessible through Double SNAr Late-Stage Functionalization

This article describes the synthesis of a difluorinated CinNapht derivative in the 4' and 5' positions allowing the easy access to two new families of fluorophores by late-stage functionalization using SNAr. The first one comprises derivatives incorporating hindered aromatic amines in the 4' and 5' positions, which show red-emission in apolar solvents. The second one is obtained through the use of dinucleophiles. Among them, Tetrahydroquinoxaline (THQ) and tetrahydrobenzodiazepine (THB) compounds show strongly redshifted emission. The photophysical properties of all the fluorophores in these two families are studied and rationalized by DFT and TDDFT calculations. The most promising compounds have been used to image living cells by confocal microscopy.

Frontiers in fluorescence imaging: tools for the in situ sensing of disease biomarkers

Fluorescence imaging has been recognized as a powerful tool for the real-time detection and specific imaging of biomarkers within living systems, which is crucial for early diagnosis and treatment evaluation of major diseases. Over the years, significant advancements in this field have been achieved, particularly with the development of novel fluorescent probes and advanced imaging technologies such as NIR-II imaging, super-resolution imaging, and 3D imaging. These technologies have enabled deeper tissue penetration, higher image contrast, and more accurate detection of disease-related biomarkers. Despite these advancements, challenges such as improving probe specificity, enhancing imaging depth and resolution, and optimizing signal-to-noise ratios still remain. The emergence of artificial intelligence (AI) has injected new vitality into the designs and performances of fluorescent probes, offering new tools for more precise disease diagnosis. This review will not only discuss chemical modifications of classic fluorophores and in situ visualization of various biomarkers including metal ions, reactive species, and enzymes, but also share some breakthroughs in AI-driven fluorescence imaging, aiming to provide a comprehensive understanding of these advancements. Future prospects of fluorescence imaging for biomarkers including the potential impact of AI in this rapidly evolving field are also highlighted.

Investigating the photophysical properties of rhodamines using a spectroscopic single-molecule fluorescence method

The photophysical properties of rhodamine molecules play a critical role in their performance across various applications. The spectroscopic single-molecule fluorescence (sSMF) technique overcomes the limitations of conventional SMF by distinguishing individual fluorophores based on their emission spectra. This enables precise measurement and direct comparison of photophysical properties among distinct molecules under identical conditions, without requiring separation of molecules. In this study, using a custom sSMF instrument, we successfully identified individual rhodamine B molecules and their various N-dealkylated intermediates, allowing for simultaneous investigation of their photophysical properties. Notably, we observed that rhodamine B undergoing a single dealkylation step exhibited a striking enhancement in photostability compared to its fully intact counterparts and those undergoing two dealkylation steps. This enhancement persisted across various buffer conditions, including different pH levels and the presence or absence of an oxygen scavenger system (OSS). Despite these differences in photostability, time-dependent density functional theory (TD-DFT) calculations revealed that all these rhodamine molecules examined shared a similar energy gap (∼0.6 eV) between their first excited singlet and triplet states.

Gentle Rhodamines for Live-Cell Fluorescence Microscopy

Rhodamines have been continuously optimized in brightness, biocompatibility, and color to fulfill the demands of modern bioimaging. However, the problem of phototoxicity caused by the excited fluorophore under long-term illumination has been largely neglected, hampering their use in time-lapse imaging. Here we introduce cyclooctatetraene (COT) conjugated rhodamines that span the visible spectrum and exhibit significantly reduced phototoxicity. We identified a general strategy for the generation of Gentle Rhodamines, which preserved their outstanding spectroscopic properties and cell permeability while showing an efficient reduction of singlet-oxygen formation and diminished cellular photodamage. Paradoxically, their photobleaching kinetics do not go hand in hand with reduced phototoxicity. By combining COT-conjugated spirocyclization motifs with targeting moieties, these Gentle Rhodamines compose a toolkit for time-lapse imaging of mitochondria, DNA, and actin, and synergize with covalent and exchangeable HaloTag labeling of cellular proteins with less photodamage than their commonly used precursors. Taken together, the Gentle Rhodamines generally offer alleviated phototoxicity and allow advanced video recording applications, including voltage imaging.

Improved Sensitivity in a Modified Berkeley Red Sensor of Transmembrane Potential

Voltage imaging is an important complement to traditional methods for probing cellular physiology, such as electrode-based patch clamp techniques. Unlike the related Ca2+ imaging, voltage imaging provides a direct visualization of bioelectricity changes. We have been exploring the use of sulfonated silicon rhodamine dyes (Berkeley Red Sensor of Transmembrane potential, BeRST) for voltage imaging. In this study, we explore the effect of converting BeRST to diEt BeRST, by replacing the dimethyl aniline of BeRST with a diethyl aniline group. The new dye, diEt BeRST, has a voltage sensitivity of 40% ΔF/F per 100 mV, a 33% increase compared to the original BeRST dye, which has a sensitivity of 30% ΔF/F per 100 mV. In neurons, the cellular brightness of diEt BeRST is about 20% as bright as that of BeRST, which may be due to the lower solubility of diEt BeRST (300 μM) compared to that of BeRST (800 μM). Despite this lower cellular brightness, diEt BeRST is able to record spontaneous and evoked action potentials from multiple neurons simultaneously and in single trials. Far-red excitation and emission profiles enable diEt BeRST to be used alongside existing fluorescent indicators of cellular physiology, like Ca2+-sensitive Oregon Green BAPTA. In hippocampal neurons, simultaneous voltage and Ca2+ imaging reveals neuronal spiking patterns and frequencies that cannot be resolved with traditional Ca2+ imaging methods. This study represents a first step toward describing the structural features that define voltage sensitivity and brightness in silicon rhodamine-based BeRST indicators.

Ultrabright Dibenzofluoran-Based Polymer Dots with NIR-IIa Emission Maxima and Unusual Large Stokes Shifts for 3D Rotational Stereo Imaging

Emerging organic molecules with emissions in the second near-infrared (NIR-II) region are garnering significant attention. Unfortunately, achieving accountable organic emission intensity over the NIR-IIa (1300 nm) region faces challenges due to the intrinsic energy gap law. Up to the current stage, all reported organic NIR-IIa emitters belong to polymethine-based dyes with small Stokes shifts (<50 nm) and low quantum yield (QY; ≤0.015%). However, such polymethines have proved to cause self-absorption with constrained emission brightness, limiting advanced development in deep-tissue imaging. Here a new NIR-IIa scaffold based on rigid and highly conjugated dibenzofluoran core terminated by amino-containing moieties that reveal emission peaks of 1230-1305 nm is designed. The QY is at least 10 times higher than all synthesized or reported NIR-IIa polymethines with extraordinarily large Stokes shifts of 370-446 nm. DBF-BJ is further prepared as a polymer dot to demonstrate its in vivo 3D stereo imaging of mouse vasculature with a 1400 nm long-pass filter.

Effects and avoidance of photoconversion-induced artifacts in confocal and STED microscopy

Fluorescence microscopy is limited by photoconversion due to continuous illumination, which results in not only photobleaching but also conversion of fluorescent molecules into species of different spectral properties through photoblueing. Here, we determined different fluorescence parameters of photoconverted products for various fluorophores under standard confocal and stimulated emission depletion (STED) microscopy conditions. We observed changes in both fluorescence spectra and lifetimes that can cause artifacts in quantitative measurements, which can be avoided by using exchangeable dyes.

Targeted Photoconvertible BODIPYs Based on Directed Photooxidation-Induced Conversion for Applications in Photoconversion and Live Super-Resolution Imaging

Photomodulable fluorescent probes are drawing increasing attention due to their applications in advanced bioimaging. Whereas photoconvertible probes can be advantageously used in tracking, photoswitchable probes constitute key tools for single-molecule localization microscopy to perform super-resolution imaging. Herein, we shed light on a red and far-red BODIPY, namely, BDP-576 and BDP-650, which possess both properties of conversion and switching. Our study demonstrates that these pyrrolyl-BODIPYs convert into typical green- and red-emitting BODIPYs that are perfectly adapted to microscopy. We also showed that this pyrrolyl-BODIPYs undergo Directed Photooxidation Induced Conversion, a photoconversion mechanism that we recently introduced, where the pyrrole moiety plays a central role. These unique features were used to develop targeted photoconvertible probes toward different organelles or subcellular units (plasma membrane, mitochondria, nucleus, actin, Golgi apparatus, etc.) using chemical targeting moieties and a Halo tag. We notably showed that BDP-650 could be used to track intracellular vesicles over more than 20 min in two-color imagings with laser scanning confocal microscopy, demonstrating its robustness. The switching properties of these photoconverters were studied at the single-molecule level and were then successfully used in live single-molecule localization microscopy in epithelial cells and neurons. Both membrane- and mitochondria- targeted probes could be used to decipher membrane 3D architecture and mitochondrial dynamics at the nanoscale. This study builds a bridge between the photoconversion and photoswitching properties of probes undergoing directed photooxidation and shows the versatility and efficacy of this mechanism in advanced live imaging.

Dimethyl Dihydrophenazine: A Highly Conjugated Auxochrome in Fluorophores to Improve Photostability, Red-Shift Wavelength, and Enlarge Stokes Shift

5,10-Dimethyl-5,10-dihydrophenazine (MP) is utilized as an effective auxochrome, leveraging its highly conjugated structure to enhance the photophysical and photochemical properties of fluorophores. As illustrated in the difluoride-boron complex and coumarin fluorophores, the extensive conjugation of MP auxochrome substantially red-shifts the absorption/emission wavelengths and increases Stokes shift due to the intensified intramolecular charge transfer effect; notably, MP auxochrome effectively improves fluorophores' photostability by mitigating photooxidative reactions through enhanced electron density delocalization on nitrogen atoms and increased ionization potential. Importantly, MP-based fluorophores demonstrate applicability in stimulated emission depletion nanomicroscopy, showcasing their utility in lipid droplet labeling.

Excited-State Conjugation/De-Conjugation Driven Nonradiative Thermal Deactivation for Developing Fluorogenic Probes to Diagnose Cancers

Fluorogenic probes have shown great potential in imaging biological species as well as in diagnosing diseases, especially cancers. However, the fluorogenic mechanisms are largely limited to a few photophysical processes to date, typically including photoinduced electron transfer (PeT), fluorescence resonant energy transfer (FRET), and intramolecular charge transfer (ICT). Herein, by calculations and experiments, we set forth that the inhibition of the excited-state π-conjugation in meso-ester Si-rhodamine SiR-COOM or the de-π-conjugation in meso-ester cyanine 5 Cy5-COOM via the "ester-to-carboxylate" conversion can operate as a general fluorogenic mechanism to fabricate fluorogenic probes. Based on the mechanism and considering the higher chemical stability of Cy5-COOM than that of SiR-COOM, we developed, as a proof-of-concept, three fluorogenic probes Cy5-APN, Cy5-GGT, and Cy5-NTR on the basis of the Cy5-COOM platform for sensing cancer biomarkers aminopeptidase N (APN), γ-glutamyltranspeptidase (GGT), and nitroreductase (NTR), respectively, and demonstrated their outstanding performances in distinguishing between cancerous and normal tissues with the high tumor-to-normal tissue ratios in the range of 9-14.

Effect of photoconversion conditions on the spectral and cytotoxic properties of photoconvertible fluorescent polymer markers

Fluorescence labeling of cells is a versatile tool used to study cell behavior, which is of significant importance in biomedical sciences. Fluorescent photoconvertible markers based on polymer microcapsules have been recently considered as efficient and perspective ones for long-term tracking of individual cells. However, the dependence of photoconversion conditions on the polymeric capsule structure is still not sufficiently clear. Here, we have studied the structural and spectral properties of fluorescent photoconvertible polymeric microcapsules doped with Rhodamine B and irradiated using a pulsed laser in various regimes, and shown the dependence between the photoconversion degree and laser irradiation intensity. The effect of microcapsule composition on the photoconversion process was studied by monitoring structural changes in the initial and photoconverted microcapsules using X-ray diffraction analysis with synchrotron radiation source, and Fourier transform infrared, Raman and fluorescence spectroscopy. We demonstrated good biocompatibility of free-administered initial and photoconverted microcapsules through long-term monitoring of the RAW 264.7 monocyte/macrophage cells with unchanged viability. These data open new perspectives for using the developed markers as safe and precise cell labels with switchable fluorescent properties.

On the mechanism of visible-light sensitized photosulfoxidation of toluidine blue O

We report on the formation of toluidine blue O (TBO) sulfoxide by a self-sensitized photooxidation of TBO. Here, the photosulfoxidation process was studied by mass spectrometry (MS) and discussed in the context of photodemethylation processes which both contribute to TBO consumption over time. Analysis of solvent effects with D2O, H2O, and CH3CN along with product yields and MS fragmentation patterns provided mechanistic insight into TBO sulfoxide's formation. The formation of TBO sulfoxide is minor and detectable up to 12% after irradiation of 3 h. The photosulfoxidation process is dependent on oxygen wherein instead of a type II (singlet oxygen, 1O2) reaction, a type I reaction involving TBO to reach the TBO sulfoxide is consistent with the results. Density functional theory results point to the formation of the TBO sulfoxide by the oxidation of TBO via transiently formed peroxyl radical or thiadioxirane intermediates. We discover that the TBO photosulfoxidation arises competitively with TBO photodemethylation with the latter leading to formaldehyde formation.

Lumos maxima - How robust fluorophores resist photobleaching?

Fluorescent dyes synergize with advanced microscopy for researchers to investigate the location and dynamic processes of biomacromolecules with high spatial and temporal resolution. However, the instability of fluorescent dyes, including photobleaching and photoconversion, represent fundamental limits for super-resolution and time-lapse imaging. In this review, we discuss the latest advances in improving the photostability of fluorescent dyes. We summarize the primary photobleaching processes of cyanine and rhodamine dyes and highlight a range of strategies developed in recent years to strengthen these fluorophores. Additionally, we discuss the influence of protein microenvironments and labeling methods on the photostability of fluorophores. We aim to inspire next-generation robust and bright fluorophores that ultimately enable the routine practice of time-lapse super-resolution imaging of live cells.

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.

Chemical Approaches to Optimize the Properties of Organic Fluorophores for Imaging and Sensing

Organic fluorophores are indispensable tools in cells, tissue and in vivo imaging, and have enabled much progress in the wide range of biological and biomedical fields. However, many available dyes suffer from insufficient performances, such as short absorption and emission wavelength, low brightness, poor stability, small Stokes shift, and unsuitable permeability, restricting their application in advanced imaging technology and complex imaging. Over the past two decades, many efforts have been made to improve these performances of fluorophores. Starting with the luminescence principle of fluorophores, this review clarifies the mechanisms of the insufficient performance for traditional fluorophores to a certain extent, systematically summarizes the modified approaches of optimizing properties, highlights the typical applications of the improved fluorophores in imaging and sensing, and indicates existing problems and challenges in this area. This progress not only proves the significance of improving fluorophores properties, but also provide a theoretical guidance for the development of high-performance fluorophores.

Structure-property-function relationships of stabilized and persistent C- and N-based triaryl radicals

Structurally similar C- and N-based triaryl radicals are among the most commonly used structural motifs in stable, open-shell, organic molecules. The application of such species is associated with their stability, properties and structural design. This study summarizes the basic stabilization and persistence principles of C- and N-based triaryl radicals and highlights recent advances in design strategies of radicals tailored for specific applications.

Bluer Phototruncation: Retro-Diels-Alder of Heptamethine Cyanine to Trimethine Cyanine through an Allene Hydroperoxide Intermediate

The photoconversion of heptamethine to pentamethine cyanines and of pentamethine to trimethine cyanines was recently reported. Here, we report mechanistic studies and initial experimental evidence for a previously unexplored 4-carbon truncation reaction that converts the simplest heptamethine cyanine to the corresponding trimethine cyanine. We propose a DFT-supported model describing a singlet oxygen (1O2)-mediated formation of an allene hydroperoxide intermediate and subsequent 4-carbon loss through a retro-Diels-Alder process. Fluorescence and mass spectrometry measurements provide evidence of this direct conversion process. This 4-carbon truncation reaction adds to a growing body of cyanine reactivity and may provide an optical tool leading to a substantial blue-shift (Δλem) of ∼200 nm.

Valkyrie Probes: A Novel Class of Enzyme-Activatable Photosensitizers based on Sulfur- and Seleno-Rosamines with Pyridinium Unit

The rational design of activatable photosensitizers (aPSs) uncaged by specific disease biomarkers is currently booming due to their positive attributes to achieve targeted photodynamic therapy (PDT). In this context, we present here the synthesis and detailed photophysical characterization of a novel class of hetero-rosamine dyes bearing sulfur or selenium as bridging heavy atom and 4-pyridyl meso-substituent as optically tunable group. The main feature of such photoactive platforms is the spectacular change of their spectral properties depending on the caging/decaging status of their 4-pyridyl moiety (cationic pyridinium vs. neutral pyridine). The preparation of two alkaline phosphatase (ALP)-responsive probes (named Valkyrie probes) was achieved through formal N-quaternarization with 4-phosphoryloxybenzyl, the traditional recognition moiety for this important diagnostic enzyme. Bio-analytical validations including fluorescence/singlet oxygen phosphorescence enzyme assays and RP-HPLC-fluorescence/-MS analyses have enabled us to demonstrate the viability and effectiveness of this novel photosensitizer activation strategy. Since sulfur-containing Valkyrie probe also retains high fluorogenicity in the orange-red spectral range, this study highlights meso-pyridyl-substituted S-pyronin scaffolds as valuable candidates for the rapid construction of molecular phototheranostic platforms suitable for combined fluorescence diagnosis and PDT.

Photoinduced Ring-Opening and Phototoxicity of an Indolin-3-one Derivative

The study of a fluorescent indolin-3-one derivative is reported that, as opposed to its previously described congeners, selectively undergoes photoactivated ring-opening in apolar solvents. The excited state involved in this photoisomerization was partially deactivated by the formation of singlet oxygen. Cell studies revealed lipid droplet accumulation and efficient light-induced cytotoxicity.

Bioorthogonal Caging-Group-Free Photoactivatable Probes for Minimal-Linkage-Error Nanoscopy

Here we describe highly compact, click compatible, and photoactivatable dyes for super-resolution fluorescence microscopy (nanoscopy). By combining the photoactivatable xanthone (PaX) core with a tetrazine group, we achieve minimally sized and highly sensitive molecular dyads for the selective labeling of unnatural amino acids introduced by genetic code expansion. We exploit the excited state quenching properties of the tetrazine group to attenuate the photoactivation rates of the PaX, and further reduce the overall fluorescence emission of the photogenerated fluorophore, providing two mechanisms of selectivity to reduce the off-target signal. Coupled with MINFLUX nanoscopy, we employ our dyads in the minimal-linkage-error imaging of vimentin filaments, demonstrating molecular-scale precision in fluorophore positioning.

Rejuvenating old fluorophores with new chemistry

The field of organic chemistry began with 19th century scientists identifying and then expanding upon synthetic dye molecules for textiles. In the 20th century, dye chemistry continued with the aim of developing photographic sensitizers and laser dyes. Now, in the 21st century, the rapid evolution of biological imaging techniques provides a new driving force for dye chemistry. Of the extant collection of synthetic fluorescent dyes for biological imaging, two classes reign supreme: rhodamines and cyanines. Here, we provide an overview of recent examples where modern chemistry is used to build these old-but-venerable classes of optically responsive molecules. These new synthetic methods access new fluorophores, which then enable sophisticated imaging experiments leading to new biological insights.

Non-adiabatic dynamics simulations of the S1 excited-state relaxation of diacetyl phenylenediamine

The small molecule built around the benzene ring, diacetyl phenylenediamine (DAPA), has attracted much attention due to its synthesis accessibility, large Stokes shift, etc. However, its meta structure m-DAPA does not fluoresce. In a previous investigation, it was found that such a property is due to the fact that it undergoes an energy-reasonable double proton transfer conical intersection during the deactivation of the S₁ excited-state, then returns to the ground state by a nonradiative relaxation process eventually. However, our static electronic structure calculations and non-adiabatic dynamics analysis results indicate that only one reasonable non-adiabatic deactivation channel exists: after being excited to the S₁ state, m-DAPA undergoes an ultrafast and barrierless ESIPT process and reaches the single-proton-transfer conical intersection. Subsequently, the system either returns to the keto-form S₀ state minimum with proton reversion or returns to the single-proton-transfer S₀ minimum after undergoing a slight twist of the acetyl group. The dynamics results show that the S₁ excited-state lifetime of m-DAPA is 139 fs. In other words, we propose an efficient single-proton-transfer non-adiabatic deactivation channel of m-DAPA that is different from previous work, which can provide important mechanistic information of similar fluorescent materials.

Unprecedented perspectives on the application of CinNapht fluorophores provided by a "late-stage" functionalization strategy

A simple and easy-to-implement process based on a nucleophilic aromatic substitution reaction with a wide variety of nucleophiles on a fluorinated CinNapht is described. This process has the key advantage of introducing multiple functionalities at a very late stage, thus providing access to new applications including the synthesis of photostable and bioconjugatable large Stokes shift red emitting dyes and selective organelle imaging agents, as well as AIEE-based wash-free lipid droplet imaging in live cells with high signal-to-noise ratio. The synthesis of bench-stable CinNapht-F has been optimized and can be reproduced on a large scale, making it an easy-to-store starting material that can be used at will to prepare new molecular imaging tools.

Cyclic Dichalcogenides Extend the Reach of Bioreductive Prodrugs to Harness Thiol/Disulfide Oxidoreductases: Applications to seco-Duocarmycins Targeting the Thioredoxin System

Small-molecule prodrug approaches that can activate cancer therapeutics selectively in tumors are urgently needed. Here, we developed the first antitumor prodrugs designed for activation by thiol-manifold oxidoreductases, targeting the thioredoxin (Trx) system. The Trx system is a critical cellular redox axis that is tightly linked to dysregulated redox/metabolic states in cancer, yet it cannot be addressed by current bioreductive prodrugs, which mainly cluster around oxidized nitrogen species. We instead harnessed Trx/TrxR-specific artificial dichalcogenides to gate the bioactivity of 10 "off-to-on" reduction-activated duocarmycin prodrugs. The prodrugs were tested for cell-free and cellular reductase-dependent activity in 177 cell lines, establishing broad trends for redox-based cellular bioactivity of the dichalcogenides. They were well tolerated in vivo in mice, indicating low systemic release of their duocarmycin cargo, and in vivo anti-tumor efficacy trials in mouse models of breast and pancreatic cancer gave promising indications of effective tumoral drug release, presumably by in situ bioreductive activation. This work therefore presents a chemically novel class of bioreductive prodrugs against a previously unaddressed reductase chemotype, validates its ability to access in vivo-compatible small-molecule prodrugs even of potently cumulative toxins, and so introduces carefully tuned dichalcogenides as a platform strategy for specific bioreduction-based release.

Recruiting Rate Determines the Blinking Propensity of Rhodamine Fluorophores for Super-Resolution Imaging

Live-cell single-molecule localization microscopy has advanced with the development of self-blinking rhodamines. A pK_cycling of <6 is recognized as the criterion for self-blinking, yet a few rhodamines matching the standard fail for super-resolution reconstruction. To resolve this controversy, we constructed two classic rhodamines (pK_cycling < 6) and four sulfonamide rhodamines with three exhibited exceptional larger pK_cycling characteristics (6.91-7.34). A kinetic study uncovered slow equilibrium rates, and limited switch numbers resulted in the reconstruction failure of some rhodamines. From the kinetic disparity, a recruiting rate was first abstracted to reveal the natural switching frequency of spirocycling equilibrium. The new parameter independent from applying a laser satisfactorily explained the imaging failure, efficacious for determining the propensity of self-blinking from a kinetic perspective. Following the prediction from this parameter, the sulfonamide rhodamines enabled live-cell super-resolution imaging of various organelles through Halo-tag technology. It is determined that the recruiting rate would be a practical indicator of self-blinking and imaging performance.

Accelerated MINFLUX Nanoscopy, through Spontaneously Fast-Blinking Fluorophores

The introduction of MINFLUX nanoscopy allows single molecules to be localized with one nanometer precision in as little as one millisecond. However, current applications have so far focused on increasing this precision by optimizing photon collection, rather than minimizing the localization time. Concurrently, commonly used fluorescent switches are specifically designed for stochastic methods (e.g., STORM), optimized for a high photon yield and rather long on-times (tens of milliseconds). Here, accelerated MINFLUX nanoscopy with up to a 30-fold gain in localization speed is presented. The improvement is attained by designing spontaneously blinking fluorescent markers with remarkably fast on-times, down to 1-3 ms, matching the iterative localization process used in a MINFLUX microscope. This design utilizes a silicon rhodamine amide core, shifting the spirocyclization equilibrium toward an uncharged closed form at physiological conditions and imparting intact live cell permeability, modified with a fused (benzo)thiophene spirolactam fragment. The best candidate for MINFLUX microscopy (also suitable for STORM imaging) is selected through detailed characterization of the blinking behavior of single fluorophores, bound to different protein tags. Finally, optimization of the localization routines, customized to the fast blinking times, renders a significant speed improvement on a commercial MINFLUX microscope.

Subtle Structural Translation Magically Modulates the Super-Resolution Imaging of Self-Blinking Rhodamines

The evolution of super-resolution imaging techniques is benefited from the ongoing competition for optimal rhodamine fluorophores. Yet, it seems blind to construct the desired rhodamine molecule matching the imaging need without the knowledge on imaging impact of even the minimum structural translation. Herein, we have designed a pair of self-blinking sulforhodamines (STMR and SRhB) with the bare distinction of methyl or ethyl substituents and engineered them with Halo protein ligands. Although the two possess similar spectral properties (λ_ab, λ_fl, ϕ, etc.), they demonstrated unique single-molecule characteristics preferring to individual imaging applications. Experimentally, STMR with high emissive rates was qualified for imaging structures with rapid dynamics (endoplasmic reticulum, and mitochondria), and SRhB with prolonged on-times and photostability was suited for relatively "static" nuclei and microtubules. Using this new knowledge, the mitochondrial morphology during apoptosis and ferroptosis was first super-resolved by STMR. Our study highlights the significance of even the smallest structural modification to the modulation of super-resolution imaging performance and would provide insights for future fluorophore design.

Experimentally Calibrated Computational Prediction Enables Accurate Fine-Tuning of Near-Infrared Rhodamines for Multiplexing

A significant barrier inhibiting multiplexed imaging in the near-infrared (NIR) is the extensive trial and error associated with fine-tuning NIR dyes. In particular, the need to synthesize and experimentally evaluate dye derivatives in order to empirically identify those that can be used in multiplexing applications, requires a large investment of time. While coarse-tuning efforts benefit from computational prediction that can be used to identify target dye structures for synthetic campaigns, errors in computational prediction remain too large to accurately parse modifications aimed at fine-tuning changes in dye absorbance and emission. To address this issue, we screened different levels of theory and identified a time-dependent density functional theory (TD-DFT) approach that can rapidly, as opposed to synthesis and experimental evaluation, estimate absorbance and emission. By calibrating these computational estimations of absorbance and emission to experimentally determined parameters for a panel of existing NIR dyes, we obtain calibration curves that can be used to accurately predict the effect of fine-tuning modifications in new dyes. We demonstrate the predictive power of this calibrated dataset using seven previously unreported dyes, obtaining mean percent errors in absorbance and emission of 2.2 and 2.8 %, respectively. This approach provides a significant timesavings, relative to synthesis and evaluation of dye derivatives, and can be used to focus synthetic campaigns on the most promising dye structures. The new dyes described herein can be utilized for multiplexed imaging, and the experimentally calibrated dataset will provide the dye chemistry community with a means to rapidly identify fine-tuned NIR dyes in silico to guide subsequent synthetic campaigns.

Room-Temperature ZnBr2 -Catalyzed Regioselective 1,6-Hydroarylation of Electron-Rich Arenes to para-Quinone Methides: Synthesis of Unsymmetrical Triarylmethanes

A mild and efficient Zn(II)-catalyzed regioselective 1,6-hydroarylation of para-quinone methides (p-QMs) with electron-rich arenes protocol is reported. A variety of electron-rich arenes and para-quinone methides are well tolerated under mild conditions, delivering a broad range of triarylmethanes in good to excellent yields. The present method also works well for the hydroarylation of p-QMs with other nucleophiles, such as aniline, indole and phenol derivatives, offering the corresponding triarylmethanes with good yields under the standard conditions. The possible mechanism for the formation of C(sp³ )-C(sp² ) bonds in hydroarylation reactions has been explored by step-by-step control experiments, and the reaction may follow a second-order manner in a chemical kinetic study.

Tuning Directed Photooxidation-Induced Conversion of Pyrrole-Based Styryl Coumarin Dual-Color Photoconverters

Dual-emissive photoconvertible fluorophores (DPCFs) are powerful tools to unambiguously track labeled cells in bioimaging. We recently introduced a new rational mechanism called directed photooxidation-induced conversion (DPIC) enabling efficient DPCFs to be obtained by conjugating a coumarin to aromatic singlet-oxygen reactive moieties (ASORMs). Pyrrole was found to be a suitable ASORM as it provided a high hypsochromic shift along with a fast and efficient conversion. By synthesizing various pyrrole-based styryl coumarin dyes, we showed that the photoconversion properties, including the quantum yield of photoconversion and the chemical yield of conversion can be tuned by chemical modification of the pyrrole. These modifications led to an improved dual emissive converter, SCP-Boc, which displayed a high brightness and an enhanced photoconversion yield of 63 %. SCP-Boc was successfully used to sequentially photoconvert cells by laser scanning confocal microscopy.

Dual-Color Photoconvertible Fluorescent Probes Based on Directed Photooxidation Induced Conversion for Bioimaging

We herein present a new concept to produce dual-color photoconvertible probes based on a mechanism called Directed Photooxidation Induced Conversion (DPIC). As a support of this mechanism, styryl-coumarins (SCs) bearing Aromatic Singlet Oxygen Reactive Moieties (ASORMs) like furan and pyrrole have been synthesized. SCs are bright fluorophores, which undergo a hypsochromic conversion upon visible light irradiation due to directed photooxidation of the ASORM that leads to the disruption of conjugation. SC-P, a yellow emitting probe bearing a pyrrole moiety, converts to a stable blue emitting coumarin with a 68 nm shift allowing the photoconversion and tracking of lipid droplet in live cells. This new approach might pave the way to a new generation of photoconvertible dyes for advanced bioimaging applications.

Photochemical Mechanisms of Fluorophores Employed in Single-Molecule Localization Microscopy

Decoding cellular processes requires visualization of the spatial distribution and dynamic interactions of biomolecules. It is therefore not surprising that innovations in imaging technologies have facilitated advances in biomedical research. The advent of super-resolution imaging technologies has empowered biomedical researchers with the ability to answer long-standing questions about cellular processes at an entirely new level. Fluorescent probes greatly enhance the specificity and resolution of super-resolution imaging experiments. Here, we introduce key super-resolution imaging technologies, with a brief discussion on single-molecule localization microscopy (SMLM). We evaluate the chemistry and photochemical mechanisms of fluorescent probes employed in SMLM. This Review provides guidance on the identification and adoption of fluorescent probes in single molecule localization microscopy to inspire the design of next-generation fluorescent probes amenable to single-molecule imaging.

Transition-Metal-Free Synthesis of Polyfluoro-Polyarylmethanes via Direct Cross-Coupling of Polyfluoroarenes and Benzyl Chlorides

The transition-metal-free direct cross-coupling between polyfluoroarenes and benzyl chlorides is reported. In this strategy, a variety of polyfluoro di-, tri- and tetra-arylmethanes was efficiently prepared with good to excellent yields in the presence of Mg turnings via a one-pot procedure. Significantly, this method provides a general approach for the synthesis of polyfluorinated polyarylmethanes.

Anticancer Agents as Design Archetypes: Insights into the Structure-Property Relationships of Ionic Liquids with a Triarylmethyl Moiety

A fundamental challenge underlying the design principles of ionic liquids (ILs) entails a lack of understanding into how tailored properties arise from the molecular framework of the constituent ions. Herein, we present detailed analyses of novel functional ILs containing a triarylmethyl (trityl) motif. Combining an empirically driven molecular design, thermophysical analysis, X-ray crystallography, and computational modeling, we achieved an in-depth understanding of structure-property relationships, establishing a coherent correlation with distinct trends between the thermophysical properties and functional diversity of the compound library. We observe a coherent relationship between melting (T _m) and glass transition (T _g) temperatures and the location and type of chemical modification of the cation. Furthermore, there is an inverse correlation between the simulated dipole moment and the T _m/T _g of the salts. Specifically, chlorination of the ILs both reduces and reorients the dipole moment, a key property controlling intermolecular interactions, thus allowing for control over T _m/T _g values. The observed trends are particularly apparent when comparing the phase transitions and dipole moments, allowing for the development of predictive models. Ultimately, trends in structural features and characterized properties align with established studies in physicochemical relationships for ILs, underpinning the formation and stability of these new lipophilic, low-melting salts.

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.

Nickel-Catalyzed C-N Cross-Coupling of 4-Chloro-1,8-naphthalimides and Bulky, Primary Alkylamines at Room Temperature

4-Amino-1,8-naphthalimides, potentially useful fluorescent probes in biological applications, are prepared via Ni(cod)₂/IPr-catalyzed cross-couplings between 4-chloro-1,8-naphthalimide electrophiles and α,α,α-trisubstituted, primary alkylamines at room temperature. This method represents the first synthesis of 4-amino-1,8-naphthalimides using Ni-catalyzed C-N cross-coupling and provides the first examples of 4-amino-1,8-naphthalimides incorporating such bulky primary alkylamines, thereby highlighting the utility of Ni-catalyzed processes in synthesizing naphthalimide scaffolds that were inaccessible using established methods (S_NAr; Pd or Cu catalysis).

Photostable fluorescent probes based on multifunctional group substituted naphthalimide dyes for imaging of lipid droplets in live cells

We designed and synthesized multifunctional group substituted naphthalimide (MFGNI) dyes by introducing glycine ethyl ester and azetidine on 1,8-naphthalimide. With different azetidine substituents, the emission of the MFGNI dyes was shifted from blue to green. These MFGNI dyes exhibited high photoluminescence quantum yields (61% to 85%) and large Stokes shifts (67 nm). The amides and hydroxyl groups improved the photostability of the MFGNI dyes. Due to the small molecular weight and lipophilic properties, these MFGNI dyes specifically stained lipid droplets in living cells.

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.

Caveat fluorophore: an insiders' guide to small-molecule fluorescent labels

The last three decades have brought a revolution in fluorescence microscopy. The development of new microscopes, fluorescent labels and analysis techniques has pushed the frontiers of biological imaging forward, moving from fixed to live cells, from diffraction-limited to super-resolution imaging and from simple cell culture systems to experiments in vivo. The large and ever-evolving collection of tools can be daunting for biologists, who must invest substantial time and effort in adopting new technologies to answer their specific questions. This is particularly relevant when working with small-molecule fluorescent labels, where users must navigate the jargon, idiosyncrasies and caveats of chemistry. Here, we present an overview of chemical dyes used in biology and provide frank advice from a chemist's perspective.

Visible Light Chemical Micropatterning Using a Digital Light Processing Fluorescence Microscope

Patterning chemical reactivity with a high spatiotemporal resolution and chemical versatility is critically important for advancing revolutionary emergent technologies, including nanorobotics, bioprinting, and photopharmacology. Current methods are complex and costly, necessitating novel techniques that are easy to use and compatible with a wide range of chemical functionalities. This study reports the development of a digital light processing (DLP) fluorescence microscope that enables the structuring of visible light (465-625 nm) for high-resolution photochemical patterning and simultaneous fluorescence imaging of patterned samples. A range of visible-light-driven photochemical systems, including thiol-ene photoclick reactions, Wolff rearrangements of diazoketones, and photopolymerizations, are shown to be compatible with this system. Patterning the chemical functionality onto microscopic polymer beads and films is accomplished with photographic quality and resolutions as high as 2.1 μm for Wolff rearrangement chemistry and 5 μm for thiol-ene chemistry. Photoactivation of molecules in living cells is demonstrated with single-cell resolution, and microscale 3D printing is achieved using a polymer resin with a 20 μm xy-resolution and a 100 μm z-resolution. Altogether, this work debuts a powerful and easy-to-use platform that will facilitate next-generation nanorobotic, 3D printing, and metamaterial technologies.

N-Cyanorhodamines: cell-permeant, photostable and bathochromically shifted analogues of fluoresceins

Fluorescein and its analogues have found only limited use in biological imaging because of the poor photostability and cell membrane impermeability of their O-unprotected forms. Herein, we report rationally designed N-cyanorhodamines as orange- to red-emitting, photostable and cell-permeant fluorescent labels negatively charged at physiological pH values and thus devoid of off-targeting artifacts often observed for cationic fluorophores. In combination with well-established fluorescent labels, self-labelling protein (HaloTag, SNAP-tag) ligands derived from N-cyanorhodamines permit up to four-colour confocal and super-resolution STED imaging in living cells.

N-Cyanorhodamines – photostable, cell-permeant analogues of fluoresceins – provide fast labelling kinetics with the HaloTag protein and background-free images in multicolour super-resolution microscopy.

Fluorescence sensors for imaging membrane lipid domains and cholesterol

Lipid membrane domains are supramolecular lateral heterogeneities of biological membranes. Of nanoscopic dimensions, they constitute specialized hubs used by the cell as transient signaling platforms for a great variety of biologically important mechanisms. Their property to form and dissolve in the bulk lipid bilayer endow them with the ability to engage in highly dynamic processes, and temporarily recruit subpopulations of membrane proteins in reduced nanometric compartments that can coalesce to form larger mesoscale assemblies. Cholesterol is an essential component of these lipid domains; its unique molecular structure is suitable for interacting intricately with crevices and cavities of transmembrane protein surfaces through its rough β face while "talking" to fatty acid acyl chains of glycerophospholipids and sphingolipids via its smooth α face. Progress in the field of membrane domains has been closely associated with innovative improvements in fluorescence microscopy and new fluorescence sensors. These advances enabled the exploration of the biophysical properties of lipids and their supramolecular platforms. Here I review the rationale behind the use of biosensors over the last few decades and their contributions towards elucidation of the in-plane and transbilayer topography of cholesterol-enriched lipid domains and their molecular constituents. The challenges introduced by super-resolution optical microscopy are discussed, as well as possible scenarios for future developments in the field, including virtual ("no staining") staining.

Molecular Design of Monochromophore-Based Bifunctional Photosensitizers for Simultaneous Ratiometric Oxygen Reporting and Photodynamic Cancer Therapy

Monitoring the tumor oxygen level when implementing photodynamic therapy (PDT) on malignant cancer has vital significance but remains challenging yet. Herein, by structurally manipulating a 2,4-dimethylpyrrole-engineered asymmetric BODIPY scaffold with different kinds, numbers, and positions of halogen atoms, we rationally designed several monochromophore-based bifunctional photosensitizers, named BDPs (BDP-I, BDP-II, and BDP-III), with self-sensitized photooxidation characteristics for accurate oxygen reporting and photodynamic tumor ablation. We show that different ways of halogen regulation allow available tuning of BDPs' oxygen-dependent ratiometric fluorescence turn-ons upon light irradiation as well as type-II PDT efficiencies before and after self-sensitized photooxidation. Encouragingly, measuring the specific ratiometric signals of the most promising BDP-II enabled the direct observation of initial oxygen concentration in both living 4T1 cells and a tumor-bearing mice model, affording an alternative way for evaluating oxygen supplementation strategies. Meanwhile, the "always on" PDT effect of BDP-II ensured efficient tumor ablation via apoptosis. Our research was thus believed to be of instructive significance for future application of oxygen-related auxiliary strategies and the design of unimolecular multifunctional PDT agents for cancer precision therapy.