Optimized Red-Absorbing Dyes for Imaging and Sensing

Matrix-designed bright near-infrared fluorophores for precision peripheral nerve imaging

The FDA's recent approval of pafolacianine, the first molecular targeted contrast agent for fluorescence-guided surgery (FGS), signifies a remarkable milestone in precision medicine. This advance offers new hope for cancer patients by enabling guided removal of cancerous tissues, where completed surgical removal remains a consistent challenge without real-time intraoperative guidance. For optimal surgical outcomes, delicate nerve tissues must be preserved to maintain patient quality of life. Despite advances in the clinical translation pipeline, the development of clinically viable nerve-specific contrast agents for FGS remains a significant challenge. Herein, a medicinal chemistry-based matrix design strategy was applied to effectively generate a synthetic roadmap permitting management of nerve-specificity within the near-infrared (NIR) oxazine fluorophore family. Many of these newly developed fluorophores demonstrated robust nerve-specificity and superior safety profiles, while also offering spectral profiles that are compatible with the clinical surgical FGS infrastructure. Notably, improving observed brightness in vivo enabled exceptional visibility of buried nerve tissue, a priority during surgical procedures. Critically, the lead probe showed a large dosage safety window capable of generating substantial contrast at doses 100x lower than the maximum tolerated dose. Following clinical translation, such NIR nerve-specific fluorophores stand poised to significantly improve outcomes for surgical patients by improving identification and visualization of surface and buried nerve tissues in real time within the surgical arena.

Selective Lower-Occupied Through-Bond Interactions for Efficient Organic Phosphorescence Enabling High-Resolution Long-Wavelength Afterglow

Persistent organic room-temperature phosphorescence (RTP) enables high-resolution afterglow bioimaging, independent of autofluorescence. However, the yield of organic RTP in the long-wavelength region is generally low, which limits the high-resolution information that can be obtained from the long-wavelength region. Moreover, this makes it impossible to obtain multicolor and high-resolution afterglow images. This report describes a molecule containing no atoms from the fourth or higher period that exhibits efficient red RTP in high yield. A molecule with red phosphorescent chromophores substituted with multiple phenylthio groups reached an RTP yield of 46.3% and an RTP lifetime of 0.43 s in an appropriate crystalline host medium. The selective lower-occupied through-bond or through-space interactions among molecules significantly enhance the phosphorescence in the long-wavelength region. The highly efficient and bright red persistent RTP induces a red afterglow from individual nanoparticles. Tuning the selective lower-occupied through-bond or through-space interactions allows for the design of high-performance RTP dyes and offers a novel approach to explore high-resolution full-color afterglow imaging.

Acoustic loudness factor as an experimental parameter for benchmarking small molecule photoacoustic probes

Photoacoustic imaging (PAI) is an emerging biomedical imaging modality with promise as a point-of-care diagnostic. This imaging modality relies on optical excitation of an absorber followed by production of ultrasound through the photoacoustic effect, resulting in high spatial resolution with imaging depths in the centimeter range. Herein, we disclose the discovery of the first benchmarking parameter for small molecule dye performance in PAI, which we term the acoustic loudness factor (ALF). ALF can predict dye performance in PAI without the need for access to photoacoustic instrumentation and can be used to guide the systematic evaluation of design strategies to enhance photoacoustic signal. Lastly, we demonstrate that enhancements in ALF can be translated to in vivo PAI. Akin to the use of fluorescence brightness in fluorophore design and evaluation for fluorescence imaging, we anticipate that ALF will guide the design and evaluation of improved probes for PAI.

Mapping Dynamic Protein Clustering with AIEgen-Active Chemigenetic Probe

Protein clustering/disassembling is a fundamental process in biomolecular condensates, playing a crucial role in cell fate decision and cellular homeostasis. However, the inherent features of protein clustering, especially for its reversible behavior and subtle microenvironment variation, present significant hurdles in probe chemistry for tracking protein clustering dynamics. Herein, we report a bilateral-tailored chemigenetic probe, in which an "amphiphilic" aggregate-induced emission luminogen (AIEgen) QMSO3Cl is covalently conjugated to a protein tag that is genetically fused to protein-of-interest (POI). Prior to target POI, the "amphiphilic" AIE-active QMSO3Cl achieves a completely dark state in both aqueous biological environment and lipophilic organelles, thereby ensuring an ultra-low intrinsic background interference. Upon reaching POI, the combination of synthetic molecule and genetically encoded protein allows for protein clustering-dependent ultra-sensitive response, with a substantial lighting-up fluorescence (67.5-fold) as protein transitions from disassembling to clustering state. Such ultra-high signal-to-noise ratio enables to monitor the dynamic and fate of inositol requiring enzyme 1 (IRE1) clustering/disassembling under both acute and chronic endoplasmic reticulum (ER) stress in living cells. For the first time, we have demonstrated the use of chemigenetic probe to reveal therapy-induced ER stress and screen drugs in a three-dimensional scenario: microviscosity change, clustering dynamic, and cluster morphology. This chemigenetic probe design strategy would greatly facilitate the advancement of mapping protein dynamics in cell homeostasis and medicine research.

Confining Spirocyclic Fluorescein in an Asymmetric Solid-State Nanochannel: A Simple and Versatile Design Concept for Fabricating Integrated Nanofluidic Diodes with Adjustable Surface Chemistry

Using small molecules to integrate multifunctional surfaces within a nanopore is an effective way to endow smart responsibilities of nanofluidic diodes. However, the complex synthesis of the small molecules hinders their further application in achieving multifunctional surfaces. Here, a simple and versatile design concept is reported for fabricating bioinspired integrated nanofluidic diodes with adjustable surface chemistry by confining a spirocyclic fluorescein derivative, 6-aminofluorescein (6-AF), within an asymmetric track-etched nanopore. The pH-dependent open-close of lactone ring in 6-AF allows facile fabrication of a pH-gated nanofluidic diode, confirmed with finite element simulations. This pH-gated nanofluidic diode also shows high specificity for sensing 3-nitropropionic acid (3-NPA), indicating its potential applications in food safety. Moreover, three functional nanofluidic diodes are successfully constructed via a regioselective Vilsmeier reaction between 6-AF and N-methylformanilide, the electrophilic addition reaction between 6-AF and propargyl bromide, and a highly controllable reduction process between 6-AF and NaBH4/I2. The combination of asymmetric nanopores with small molecules not only expands traditional fluorescent spirocyclic molecules to the realm of electrochemistry but also offers valuable insights for the achievement of novel fluorescence-electrochemical coupling detection methods. Besides, the introduction of spirocyclic small molecules to asymmetric nanopores serves as an inspiration source to explore new design concepts for nanofluidic devices.

DELTA: a method for brain-wide measurement of synaptic protein turnover reveals localized plasticity during learning

Synaptic plasticity alters neuronal connections in response to experience, which is thought to underlie learning and memory. However, the loci of learning-related synaptic plasticity, and the degree to which plasticity is localized or distributed, remain largely unknown. Here we describe a new method, DELTA, for mapping brain-wide changes in synaptic protein turnover with single-synapse resolution, based on Janelia Fluor dyes and HaloTag knock-in mice. During associative learning, the turnover of the ionotropic glutamate receptor subunit GluA2, an indicator of synaptic plasticity, was enhanced in several brain regions, most markedly hippocampal area CA1. More broadly distributed increases in the turnover of synaptic proteins were observed in response to environmental enrichment. In CA1, GluA2 stability was regulated in an input-specific manner, with more turnover in layers containing input from CA3 compared to entorhinal cortex. DELTA will facilitate exploration of the molecular and circuit basis of learning and memory and other forms of plasticity at scales ranging from single synapses to the entire brain.

Acid-Controlled Fabrication of Multicolor Carbon Dots with Switchable Organelle-Targeting Capability for Visualizing Organelle Interactions

Synchronous regulation of the photoluminescence and physicochemical characteristics of multicolor carbon dots (CDs) can fully realize their application potential in multicomponent imaging. Herein, by utilizing an acid-regulated synthetic strategy, green-emissive and orange-emissive CDs that target lipid droplets (LDs) and mitochondria (Mito) have been developed for fluorescence visualization of LD-Mito interactions. The finding of different molecular fluorophores reveals that the precursor undergoes different reaction pathways in neutral and acidic conditions, which alters the size of sp2-conjugated domain and surface properties for the successful regulation of photoluminescence properties and organelle-targeting ability. Moreover, the one-step fabrication of these two CDs was also realized by lowering the dosage of acid. Therefore, the multicolor imaging of LDs and Mito has been achieved with one-step staining, disclosing that their interaction frequency decreases during the lipotoxicity process. This work successfully demonstrates the high coupling potential between multicolor CDs and organelle-interaction visualization, which would provide guidance on the correlation between photoluminescence features and other properties of multicolor CDs for extending application space.

Fluorescent labeling strategies for molecular bioimaging

Super-resolution microscopy (SRM) has transformed biological imaging by circumventing the diffraction limit of light and enabling the visualization of cellular structures and processes at the molecular level. Central to the capabilities of SRM is fluorescent labeling, which ensures the precise attachment of fluorophores to biomolecules and has direct impact on the accuracy and resolution of imaging. Continuous innovation and optimization in fluorescent labeling are essential for the successful application of SRM in cutting-edge biological research. In this review, we discuss recent advances in fluorescent labeling strategies for molecular bioimaging, with a special focus on protein labeling. We compare different approaches, highlight technological breakthroughs, and address challenges such as linkage error and labeling density. By evaluating both established and emerging methods, we aim to guide researchers through all aspects that should be considered before opting for any labeling technique.

Xanthene-based NIR organic phototheranostics agents: design strategies and biomedical applications

Fluorescence imaging and phototherapy in the near-infrared window (NIR, 650-1700 nm) have attracted great attention for biomedical applications due to their minimal invasiveness, ultra-low photon scattering and high spatial-temporal precision. Among NIR emitting/absorbing organic dyes, xanthene derivatives with controllable molecular structures and optical properties, excellent fluorescence quantum yields, high molar absorption coefficients and remarkable chemical stability have been extensively studied and explored in the field of biological theranostics. The present study was aimed at providing a comprehensive summary of the progress in the development and design strategies of xanthene derivative fluorophores for advanced biological phototheranostics. This study elucidated several representative controllable strategies, including electronic programming strategies, extension of conjugated backbones, and strategic establishment of activatable fluorophores, which enhance the NIR fluorescence of xanthene backbones. Subsequently, the development of xanthene nanoplatforms based on NIR fluorescence for biological applications was detailed. Overall, this work outlines future efforts and directions for improving NIR xanthene derivatives to meet evolving clinical needs. It is anticipated that this contribution could provide a viable reference for the strategic design of organic NIR fluorophores, thereby enhancing their potential clinical practice in future.

Analyzing the Cholesteryl Ester Fraction in Lipid Droplets with a Polarity-Ultrasensitive Fluorescence Lifetime Probe

Quantifying the lipid composition of cellular lipid droplets (LDs) in situ is challenging but crucial for understanding lipid metabolic diseases. Here, we propose a fluorescence lifetime imaging method based on a polarity-sensitive probe (LD660) for analyzing the lipid composition of the LDs. The probe emits strong fluorescence at 660 nm only in apolar LD environments, with dielectric constants of 2-4, and outperforms Nile red in LD imaging. Importantly, the fluorescence lifetime of LD660 increases with the incremental fraction of cholesteryl ester in neutral lipid mixtures. Using fluorescence lifetime microscopy with LD660, we imaged and quantified the cholesteryl ester fractions of LDs in cells and tissues. It is found that macrophages and surrounding hepatocytes in fatty liver diseases show significantly higher cholesteryl ester contents than other hepatocytes. This finding suggests that cholesteryl ester may serve as a potential indicator of the degree of hepatic steatosis.

Biocompatible Sulfonium-Based Covalent Probes For Endogenous Tubulin Fluorescence Nanoscopy In Live And Fixed Cells

Fluorescent probes enable the visualization of dynamic cellular processes with high precision, particularly when coupled with super-resolution imaging techniques that surpass the diffraction limit. Traditional methods include fluorescent protein fusion (e.g., GFP) or organic fluorophores linked to ligands targeting the protein of interest. However, these approaches often introduce functional disruptions or ligand-associated biological effects. Herein, we address these challenges by developing covalent fluorescent probes for endogenous tubulin, a critical cytoskeletal protein involved in processes such as cell movement, division, and biomolecule trafficking. Using well-known tubulin binder cabazitaxel and cell permeable fluorophore silicon-rhodamine as a basis, we introduce a novel biocompatible cleavable linker containing a sulfonium center. This allowed the construction of the optimized probe, 6-SiR-o-C 9 -CTX, demonstrating excellent cell permeability, fluorogenic properties, and the ability to covalently label tubulin across various human cell lines. Importantly, the targeting moiety could be washed out while preserving tubulin staining, ensuring minimal disruption of tubulin function. This labeling technique is compatible with STED nanoscopy in both live and fixed cells, offering a powerful high-resolution imaging tool.

Biocompatible sulfonium-based covalent probes for endogenous tubulin fluorescence nanoscopy in live and fixed cells

Fluorescent probes enable the visualization of dynamic cellular processes with high precision, particularly when coupled with super-resolution imaging techniques that surpass the diffraction limit. Traditional methods include fluorescent protein fusion (e.g., GFP) or organic fluorophores linked to ligands targeting the protein of interest. However, these approaches often introduce functional disruptions or ligand-associated biological effects. Herein, we address these challenges by developing covalent fluorescent probes for endogenous tubulin, a critical cytoskeletal protein involved in processes such as cell movement, division, and biomolecule trafficking. Using well-known tubulin binder cabazitaxel and cell permeable fluorophore silicon-rhodamine-as a basis, we introduce a novel biocompatible cleavable linker containing a sulfonium center. This allowed the construction of the optimized probe, 6-SiR-o-C 9 -CTX, demonstrating excellent cell permeability, fluorogenic properties, and the ability to covalently label tubulin across various human cell lines. Importantly, the targeting moiety could be washed out while preserving tubulin staining, ensuring minimal disruption of tubulin function. This labeling technique is compatible with STED nanoscopy in both live and fixed cells, offering a powerful high-resolution imaging tool.

Strategic Modulation of Polarity and Viscosity Sensitivity of Bimane Molecular Rotor-Based Fluorophores for Imaging α-Synuclein

Molecular rotor-based fluorophores (RBFs) that are target-selective and sensitive to both polarity and viscosity are valuable for diverse biological applications. Here, we have designed next-generation RBFs based on the underexplored bimane fluorophore through either changing in aryl substitution or varying π-linkages between the rotatable electron donors and acceptors to produce red-shifted fluorescence emissions with large Stokes shifts. RBFs exhibit a twisted intramolecular charge transfer mechanism that enables control of polarity and viscosity sensitivity, as well as target selectivity. These features enable their application in: (1) turn-on fluorescent detection of α-synuclein (αS) fibrils, a hallmark of Parkinson's disease (PD), including amplified fibrils from patient samples; (2) monitoring early misfolding and oligomer formation during αS aggregation; and (3) selective imaging of αS condensates formed by liquid-liquid phase separation (LLPS). In all three cases, we show that our probes have high levels of selectivity for αS versus other aggregating proteins. These properties enable one to study the interplay of αS and tau in amyloid aggregation and the mechanisms underlying neurodegenerative disorders.

High-Performance Chemigenetic Potassium Ion Indicator

Potassium ion (K+) is the most abundant metal ion in cells and plays an indispensable role in practically all biological systems. Although there have been reports of both synthetic and genetically encoded fluorescent K+ indicators, there remains a need for an indicator that is genetically targetable, has high specificity for K+ versus Na+, and has a high fluorescent response in the red to far-red wavelength range. Here, we introduce a series of chemigenetic K+ indicators, designated as the HaloKbp1 series, based on the bacterial K+-binding protein (Kbp) inserted into HaloTag7 self-labeled with environmentally sensitive rhodamine derivatives. This series of high-performance indicators features high brightness in the red to far-red region, large intensiometric fluorescence changes, and a range of Kd values. We demonstrate that they are suitable for the detection of physiologically relevant K+ concentration changes such as those that result from the Ca2+-dependent activation of the BK potassium channel.

TRF1 and TRF2 form distinct shelterin subcomplexes at telomeres

The shelterin complex protects chromosome ends from the DNA damage repair machinery and regulates telomerase access to telomeres. Shelterin is composed of six proteins (TRF1, TRF2, TIN2, TPP1, POT1 and RAP1) that can assemble into various subcomplexes in vitro. However, the stoichiometry of the shelterin complex and its dynamic association with telomeres in cells is poorly defined. To quantitatively analyze the shelterin function in living cells we generated a panel of cancer cell lines expressing HaloTagged shelterin proteins from their endogenous loci. We systematically determined the total cellular abundance and telomeric copy number of each shelterin subunit, demonstrating that the shelterin proteins are present at telomeres in equal numbers. In addition, we used single-molecule live-cell imaging to analyze the dynamics of shelterin protein association with telomeres. Our results demonstrate that TRF1-TIN2-TPP1-POT1 and TRF2-RAP1 form distinct subcomplexes that occupy non-overlapping binding sites on telomeric chromatin. TRF1-TIN2-TPP1-POT1 tightly associates with chromatin, while TRF2-RAP1 binding to telomeres is more dynamic, allowing it to recruit a variety of co-factors to chromatin to protect chromosome ends from DNA repair factors. In total, our work provides critical mechanistic insight into how the shelterin proteins carry out multiple essential functions in telomere maintenance and significantly advances our understanding of macromolecular structure of telomeric chromatin.

Singlets-Driven Photoredox Catalysts: Transforming Noncatalytic Red Fluorophores to Efficient Catalysts

Red-light absorbing photoredox catalysts offer potential advantages for large-scale reactions, expanding the range of usable substrates and facilitating bio-orthogonal applications. While many red-light absorbing/emitting fluorophores have been developed recently, functional red-light absorbing photoredox catalysts are scarce. Many photoredox catalysts rely on long-lived triplet excited states (triplets), which can efficiently engage in single electron transfer (SET) reactions with substrates. However, triplets of π-conjugated molecules are often significantly lower in energy than photogenerated singlet excited states (singlets). Combined with the inherent low energy of red light, this could limit the reductive/oxidative powers. Here, we introduce a series of sustainable heavy atom-free photoredox catalysts based on red-light absorbing dibenzo-fused BODIPY. The catalysts consist of two covalently linked units: a dibenzo-fused BODIPY fluorophore and an electron donor, arranged orthogonally. Excitation of the dibenzoBODIPY unit induces charge separation (CS) from the donor to the dibenzoBODIPY unit, forming a radical pair (RP) state. Unlike the regular BODIPY counterparts, these catalysts do not form triplets. Instead, SET occurs from the high-energy singlet-born RP states, preventing energy loss and effectively utilizing the low-energy red light. The proximity of donor molecules allows efficient charge separation despite the CS being uphill in energy. The molecules demonstrate efficient catalysis of Atom Transfer Radical Addition (ATRA) reaction, yielding products with high yields ranging from 70 to 90%, while the molecule without a donor group does not exhibit catalytic activity. The mechanistic studies by transient absorption and electron paramagnetic resonance (EPR) spectroscopy methods support the proposed mechanism. The study presents a new molecular design strategy for converting noncatalytic fluorophores to efficient photoredox catalysts operating in the red spectral region.

Single-molecule orientation-localization microscopy: Applications and approaches

Single-molecule orientation-localization microscopy (SMOLM) builds upon super-resolved localization microscopy by imaging orientations and rotational dynamics of individual molecules in addition to their positions. This added dimensionality provides unparalleled insights into nanoscale biophysical and biochemical processes, including the organization of actin networks, movement of molecular motors, conformations of DNA strands, growth and remodeling of amyloid aggregates, and composition changes within lipid membranes. In this review, we discuss recent innovations in SMOLM and cover three key aspects: (1) biophysical insights enabled by labeling strategies that endow fluorescent probes to bind to targets with orientation specificity; (2) advanced imaging techniques that leverage the physics of light-matter interactions and estimation theory to encode orientation information with high fidelity into microscope images; and (3) computational methods that ensure accurate and precise data analysis and interpretation, even in the presence of severe shot noise. Additionally, we compare labeling approaches, imaging hardware, and publicly available analysis software to aid the community in choosing the best SMOLM implementation for their specific biophysical application. Finally, we highlight future directions for SMOLM, such as the development of probes with improved photostability and specificity, the design of “smart” adaptive hardware, and the use of advanced computational approaches to handle large, complex datasets. This review underscores the significant current and potential impact of SMOLM in deepening our understanding of molecular dynamics, paving the way for future breakthroughs in the fields of biophysics, biochemistry, and materials science.

Steric and Distance Effect on Electron Transfer in Dibenzo-Fused BODIPY-Based Photoredox Catalysts

π-Extended BODIPY compounds are a compelling class of fluorophores known for their red or near-infrared (NIR) emission and high quantum yields, which are crucial for applications in materials science, solar cells, and biomedical imaging. Our recent study shows that we can use a dibenzo-fused BODIPY as a singlet-driven red photoredox catalyst by installing a simple electron donor group. Despite their potential in these applications, knowledge of electron transfer reactions involving dibenzo-fused BODIPY is still scarce. This paper presents the synthesis and systematic photophysical investigations of donor-acceptor (D-A) and donor-bridge-acceptor (D-bridge-A) series of dibenzo-fused BODIPY with N,N'-diethylaniline fragments serving as an electron donor. We examined the effects of methyl substituents and bridge length on the rates of photoinduced electron transfer (PeT). Through steady-state and time-resolved optical spectroscopy, electrochemistry, and density functional theory calculations, we elucidated how these simple structural modifications controlled the PeT rates and examined their impacts on catalytic activities in atom transfer radical addition (ATRA) reactions. Our results support previous studies on the (D-A) design of red heavy atom-free photocatalysts.

Recent Progress of Photoswitchable Fluorescent Diarylethenes for Bioimaging

Photochromic diarylethene has attracted broad research interest in optical applications owing to its excellent fatigue resistance and unique bistability. Photoswitchable fluorescent diarylethene become a powerful molecular tool for fluorescence imaging recently. Herein, the recent progress on photoswitchable fluorescent diarylethenes in bioimaging is reviewed. We summarize the structures and properties of diarylethene fluorescence probes and emphatically introduce their applications in bioimaging as well as super-resolution imaging. Additionally, we highlight the current challenges in practical applications and provide the prospects of the future development directions of photoswitchable fluorescent diarylethene in the field of bioimaging. This comprehensive review aims to stimulate further research into higher-performance photoswitchable fluorescent molecules and advance their progress in biological application.

Data-Driven Discovery of a New Fluorescent BASHY Dye for Bioimaging

Fluorescent molecules play a crucial role in biomedicine by facilitating the visualization and tracking of biological processes with sensitivity and specificity. However, tailoring their structure to meet the demands of live cell and in vivo imaging presents a significant challenge due to the intricate interplay of factors governing their structural and photophysical properties. In this study, we explored the potential of using multivariate linear free-energy relationships (mLFER) to optimize a multicomponent fluorescent platform. We prepared a small library of 20 fluorescent boronic-acid-derived salicylidenehydrazone (BASHY) complexes using a versatile reaction protocol and characterized their chemical stability in water-containing media. The obtained data served as input for the development of an mLFER model, enabling the prediction of a new BASHY dye and unraveling previously unknown mechanisms governing the stability of this unique platform of fluorescent dyes. The optimized dye was successfully employed in live cell experiments and in zebrafish larvae.

Induced degradation of SNAP-fusion proteins

Self-labeling protein tags are an efficient means to visualize, manipulate, and isolate engineered fusion proteins with suitable chemical probes. The SNAP-tag, which covalently conjugates to benzyl-guanine and -chloropyrimidine derivatives is used extensively in fluorescence microscopy, given the availability of suitable SNAP-ligand-based probes. Here, we extend the applicability of the SNAP-tag to targeted protein degradation. We developed a set of SNAP PROteolysis TArgeting Chimeras (SNAP-PROTACs), which recruit the VHL or CRBN-ubiquitin E3 ligases to induce the degradation of SNAP-fusion proteins. Endogenous tagging enabled the visualization and the selective depletion of a SNAP-clathrin light chain fusion protein using SNAP-PROTACs. The addition of PROTACs to the SNAP-tag reagent toolbox facilitates the comprehensive analysis of protein function with a single gene tagging event.

Superior Tumor Cell Uptake by Mono- and Tri-Nuclear Rhodamine-Gadolinium(III) Agents

The synthesis and characterization of a novel trinuclear rhodamine-Gd(III) complex, along with two analogous mononuclear rhodamine-Gd(III) complexes, are reported. All complexes displayed good selectivity in a human glioma cell line (T98G) when compared to a glial cell line (SVG p12), with low cytotoxicities. Superior tumor cell uptake for these Gd(III) complexes was observed at lower incubation concentrations compared to previously-reported delocalized lipophilic cations such as a rhodamine-lanthanoid(III) probe and Gd(III)-arylphosphonium complexes, with ca. 150 % and 250 % increases in Gd uptake, respectively.

Applications of Lightsheet Fluorescence Microscopy by High Numerical Aperture Detection Lens

This Review explores the evolution, improvements, and recent applications of Light Sheet Fluorescence Microscopy (LSFM) in biological research using a high numerical aperture detection objective (lens) for imaging subcellular structures. The Review begins with an overview of the development of LSFM, tracing its evolution from its inception to its current state and emphasizing key milestones and technological advancements over the years. Subsequently, we will discuss various improvements of LSFM techniques, covering advancements in hardware such as illumination strategies, optical designs, and sample preparation methods that have enhanced imaging capabilities and resolution. The advancements in data acquisition and processing are also included, which provides a brief overview of the recent development of artificial intelligence. Fluorescence probes that were commonly used in LSFM will be highlighted, together with some insights regarding the selection of potential probe candidates for future LSFM development. Furthermore, we also discuss recent advances in the application of LSFM with a focus on high numerical aperture detection objectives for various biological studies. For sample preparation techniques, there are discussions regarding fluorescence probe selection, tissue clearing protocols, and some insights into expansion microscopy. Integrated setups such as adaptive optics, single objective modification, and microfluidics will also be some of the key discussion points in this Review. We hope that this comprehensive Review will provide a holistic perspective on the historical development, technical enhancements, and cutting-edge applications of LSFM, showcasing its pivotal role and future potential in advancing biological research.

Supramolecular Complex of Cucurbit[7]uril with Diketopyrrolopyrole Dye: Fluorescence Boost, Biolabeling and Optical Microscopy

New photostable and bright supramolecular complexes based on cucurbit[7]uril (CB7) host and diketopyrrolopyrole (DPP) guest dyes having two positively charged 4-(trimethylammonio)phenyl groups were prepared and characterized. The dye core displays large Stokes shift (in H2O, abs./emission max. 480/550 nm; ϵ~19 000, τfl>4 ns), strong binding with the host (~560 nM Kd) and a linker affording fluorescence detection of bioconjugates with antibody and nanobody. Combination of protein-functionalized DPP dye with CB7 improves photostability and affords up to 12-fold emission gain. Two-color confocal and stimulated emission depletion (STED) microscopy with 595 nm or 655 nm STED depletion lasers shows that the presence of CB7 not only leads to improved brightness and image quality, but also results in DPP becoming cell-permeable.

Chemigenetic Far-Red Labels and Ca2+ Indicators Optimized for Photoacoustic Imaging

Photoacoustic imaging is an emerging modality with significant promise for biomedical applications such as neuroimaging, owing to its capability to capture large fields of view deep inside complex scattering tissue. However, widespread adoption of this technique has been hindered by a lack of suitable molecular reporters for this modality. In this work, we introduce chemigenetic labels and calcium sensors specifically tailored for photoacoustic imaging, using a combination of synthetic dyes and HaloTag-based self-labeling proteins. We rationally design and engineer far-red "acoustogenic" dyes, showing high photoacoustic turn-ons upon binding to HaloTag, and develop a suite of tunable calcium indicators based on these scaffolds. These first-generation photoacoustic reporters show excellent performance in tissue-mimicking phantoms, with the best variants outperforming existing sensors in terms of signal intensity, sensitivity, and photostability. We demonstrate the application of these ligands for labeling HaloTag-expressing neurons in mouse brain tissue, producing strong, specifically targeted photoacoustic signal, and provide a first example of in vivo labeling with these chemigenetic photoacoustic probes. Together, this work establishes a new approach for the design of photoacoustic reporters, paving the way toward deep tissue functional imaging.

Cu-Catalyzed Amination of Base-Sensitive Aryl Bromides and the Chemoselective N- and O-Arylation of Amino Alcohols

We report a general and functional-group-tolerant method for the Cu-catalyzed amination of base-sensitive aryl bromides including substrates possessing acidic functional groups and small five-membered heteroarenes. The results presented herein substantially expand the scope of Cu-catalyzed C-N coupling reactions. The combination of L8, an anionic N1,N2-diarylbenzene-1,2-diamine ligand, along with the mild base NaOTMS leads to the formation of a stable yet reactive catalyst that resists deactivation from coordination to heterocycles or charged intermediates. This system enables the use of low catalyst and ligand loadings. Exploiting the differences in nucleophile deprotonation in C-O and C-N coupling reactions catalyzed by Cu·L8 we developed a method to chemoselectively N- and O-arylate a variety of amino alcohol substrates. Employing NaOt-Bu as the base resulted exclusively in C-O coupling when the amino alcohols featured primary alcohols and more hindered amines or aniline groups. Utilizing NaOTMS enabled the ability to override the steric-based selectivity of these reactions completely and exclusively promoted C-N coupling regardless of the structure of the amino alcohol. The ability to invert the observed chemoselectivity is distinct from previously described methods that require protecting group manipulations or rely entirely on steric effects to control reactivity. These results substantially improve the scope of Cu-catalyzed C-N coupling reactions using N1,N2-diarylbenzene-1,2-diamine ligands and introduce a new chemoselective method to arylate amino alcohols.

Xanthene-Based Dyes for Photoacoustic Imaging and their Use as Analyte-Responsive Probes

Developing imaging tools that can report on the presence of disease-relevant analytes in multicellular organisms can provide insight into fundamental disease mechanisms as well as provide diagnostic tools for the clinic. Photoacoustic imaging (PAI) is a light-in, sound-out imaging technique that allows for high resolution, deep-tissue imaging with applications in pre-clinical and point-of-care settings. The continued development of near-infrared (NIR) absorbing small-molecule dyes promises to improve the capabilities of this emerging imaging modality. For example, new dye scaffolds bearing chemoselective functionalities are enabling the detection and quantification of disease-relevant analytes through activity-based sensing (ABS) approaches. Recently described strategies to engineer NIR absorbing xanthenes have enabled development of analyte-responsive PAI probes using this classic dye scaffold. Herein, we present current strategies for red-shifting the spectral properties of xanthenes via bridging heteroatom or auxochrome modifications. Additionally, we explore how these strategies, coupled with chemoselective spiroring-opening approaches, have been employed to create ABS probes for in vivo detection of hypochlorous acid, nitric oxide, copper (II), human NAD(P)H: quinone oxidoreductase isozyme 1, and carbon monoxide. Given the versatility of the xanthene scaffold, we anticipate continued growth and development of analyte-responsive PAI imaging probes based on this dye class.

Design of Bright Chemogenetic Reporters Based on the Combined Engineering of Fluorogenic Molecular Rotors and of the HaloTag Protein

The combination of fluorogenic probes (fluorogens) and self-labeling protein tags represent a promising tool for imaging biological processes with high specificity but it requires the adequation between the fluorogen and its target to ensure a good activation of its fluorescence. In this work, we report a strategy to develop molecular rotors that specifically target HaloTag with a strong enhancement of their fluorescence. The divergent design facilitates the diversification of the structures to tune the photophysical and cellular properties. Four bright fluorogens with emissions ranging from green to red were identified and applied in wash-free live cell imaging experiments with good contrast and selectivity. A HaloTag mutant adapted from previous literature reports was also tested and shown to further improve the brightness and reaction rate of the most promising fluorogen of the series both in vitro and in cells. This work opens new possibilities to develop bright chemogenetic reporters with diverse photophysical and biological properties by exploring a potentially large chemical space of simple dipolar fluorophores in combination with protein engineering.

Radical reactions enabled by polyfluoroaryl fragments: photocatalysis and beyond

Polyfluoroarenes have been known for a long time, but they are most often used as fluorinated building blocks for the synthesis of aromatic compounds. At the same time, due to peculiar fluorine effect, they have unique properties that provide applications in various fields ranging from synthesis to materials science. This review summarizes advances in the radical chemistry of polyfluoroarenes, which have become possible mainly with the advent of photocatalysis. Transformations of the fluorinated ring via the C-F bond activation, as well as use of fluoroaryl fragments as activating groups and hydrogen atom transfer agents are discussed. The ability of fluoroarenes to serve as catalysts is also considred.

2X-Rhodamine: A Bright and Fluorogenic Scaffold for Developing Near-Infrared Chemigenetic Indicators

Chemigenetic fusion of synthetic dyes with genetically encoded protein tags presents a promising avenue for in vivo imaging. However, its full potential has been hindered by the lack of bright and fluorogenic dyes operating in the "tissue transparency" near-infrared window (NIR, 700-1700 nm). Here, we report 2X-rhodamine (2XR), a novel bright scaffold that allows for the development of live-cell-compatible, NIR-excited variants with strong fluorogenicity beyond 1000 nm. 2XR utilizes a rigidified π-skeleton featuring dual atomic bridges and functions via a spiro-based fluorogenic mechanism. This design affords longer wavelengths, higher quantum yield (ΦF = 0.11), and enhanced fluorogenicity in water when compared to the phosphine oxide-cored, or sulfone-cored rhodamine, the NIR fluorogenic benchmarks currently used. We showcase their bright performance in video-rate dynamic imaging and targeted deep-tissue molecular imaging in vivo. Notably, we develop a 2XR variant, 2XR715-HTL, an NIR fluorogenic ligand for the HaloTag protein, enabling NIR genetically encoded calcium sensing and the first demonstration of in vivo chemigenetic labeling beyond 1000 nm. Our work expands the library of NIR fluorogenic tools, paving the way for in vivo imaging and sensing with the chemigenetic approach.

Fluorogenic Rhodamine Probes with Pyrrole Substitution Enables STED and Lifetime Imaging of Lysosomes in Live Cells

Fluorogenic dyes with high brightness, large turn-on ratios, excellent photostability, favorable specificity, low cytotoxicity, and high membrane permeability are essential for high-resolution fluorescence imaging in live cells. In this study, we endowed these desirable properties to a rhodamine derivative by simply replacing the N, N-diethyl group with a pyrrole substituent. The resulting dye, Rh-NH, exhibited doubled Stokes shifts (54 nm) and a red-shift of more than 50 nm in fluorescence spectra compared to Rhodamine B. Rh-NH preferentially exists in a non-emissive but highly permeable spirolactone form. Upon binding to lysosomes, the collective effects of low pH, low polarity, and high viscosity endow Rh-NH with significant fluorescence turn-on, making it a suitable candidate for wash-free, high-contrast lysosome tracking. Consequently, Rh-NH enabled us to successfully explore stimulated emission depletion (STED) super-resolution imaging of lysosome dynamics, as well as fluorescence lifetime imaging of lysosomes in live cells.

A series of spontaneously blinking dyes for super-resolution microscopy

Spontaneously blinking fluorophores permit the detection and localization of individual molecules without reducing buffers or caging groups, thus simplifying single-molecule localization microscopy (SMLM). The intrinsic blinking properties of such dyes are dictated by molecular structure and modulated by environment, which can limit utility. We report a series of tuned spontaneously blinking dyes with duty cycles that span two orders of magnitude, allowing facile SMLM in cells and dense biomolecular structures.