The fluorescent toolbox for assessing protein location and function

Aggregation-induced emission-based aptasensors for the detection of various targets: Recent progress

The advancement of aptasensors utilizing aggregation-induced emission (AIE) has progressed remarkably in recent years, owing to various unique benefits provided by aggregation-induced emission luminogens (AIEgens) as a novel category of fluorescent substances and aptamers as exceptional recognition components. AIE refers to a photophysical phenomenon identified in certain luminogens that show minimal or absent emission in dilute solutions, yet display considerable emission when in aggregate or solid states. Fluorescent sensing is an effective technique for the detection of various targets; however, many traditional dyes frequently demonstrate an aggregation-caused quenching (ACQ) effect in solid form, which limits their applicability on a larger scale. In contrast, fluorescent probes that leverage AIE characteristics have garnered considerable interest, owing to their elevated fluorescence quantum yields and ease of fabrication. This review discusses the application of various AIEgens in the design of diverse sensitive and selective AIE-based aptasensors for monitoring various targets, with a particular focus on recent advances. The AIE-based aptasensors exploit the supreme affinity of the aptamers to their targets and the remarkable properties of AIEgen, including its photostability and high quantum yield, and the interaction between AIEgen and DNA. The objective is to acquaint researchers with the various categories of materials exhibiting AIE characteristics and their potential applications in the creation of different aptasensors, enabling them to introduce novel kinds of innovative AIEgens and AIE-integrated aptasensors.

Fluorescent tools for imaging class A G-protein coupled receptors

G protein-coupled receptors (GPCRs) are pivotal in biological processes and represent a significant class of drug targets, with 516 approved drugs acting on 121 GPCRs. Many GPCRs, particularly orphan receptors, remain underexplored, emphasizing the need for innovative investigative tools. Fluorescent ligands provide a powerful means to characterize GPCRs including their functional mechanisms and spatial organization, bridging fundamental research and drug discovery. This review presents recent advances (2018-2024) in fluorescent probe development for Class A GPCRs, analyzing over 120 newly developed probes covering 60 GPCRs. We examine their distribution across receptor subclasses, comparing pre-2018 data with contemporary findings and identifying previously uncharted GPCRs that now have fluorescent ligands. Notably, novel probes have been developed for 12 new receptor subtypes and 6 orphan receptors such as GPR6, GPR52, GPR84, MAS1, MRGPRX2, and MRGPRX4. Advances in GPCR structural biology, driven by cryo-EM and AlphaFold technologies, have significantly enhanced probe development, facilitating the design of selective fluorescent ligands across aminergic, peptidergic, lipid, nucleotide, alicarboxylic, melatonin, protein, and orphan GPCRs. These innovations support a broad range of applications, from single-molecule imaging and in vivo bioimaging to diagnostics and fluorescence-guided surgery. By integrating fluorescence-based approaches with structural and pharmacological insights, this field continues to refine polypharmacology profiling, optimize drug-receptor interactions, and accelerate GPCR-targeted drug discovery.

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.

Visualizing Kv7 channels in living cells using a novel fluorescent probe

Kv7 (KCNQ) channels are widely expressed on the membrane of excitable cells in central nervous system and play dominant roles in controlling membrane excitability. Abnormal of their surface abundance and activity can cause central nervous system disorders such as epilepsy and painful schizophrenia. Thus, it is important to find a simple and effective molecular tool for detecting the expression of Kv7 channels and further studying their roles in physiology. Fluorescent probe is an effective method for visualizing protein analysis in biological systems with high sensitivity and spatiotemporal resolution. To further understand the roles of Kv7 channels in physiological and pathological processes, we designed fluorescent probes for imaging Kv7 channels (FPKv-1 and FPKv-2) based on the fluorescent emission mechanism of intramolecular rotation restriction using fluorophore quinoline malononitrile as report group. This mechanism was identified by the measurement of absorption and fluorescence spectra in the different solutions. Electrophysiology and confocal imaging showed that FPKv-1 had a higher affinity and selectivity to Kv7 channels over other ion channels such as TRPA1, TRPV1 and TRPV3. We also identified FPKv-1 as a molecular imaging tool can be applied in high-throughput screening of Kv7 agonists.

Development of SNAP-Tag Based Nanobodies as Secondary Antibody Mimics for Indirect Immunofluorescence Assays

The immunofluorescence assay is widely used for cellular biology and diagnosis applications. Such an antigen-antibody detection system enables the assessment and visualization of the expression and localization of target proteins. In the classical indirect immunofluorescence assay, secondary antibodies are conjugated to fluorophores. However, conventional secondary antibodies have limited applications due to their large size (150 kDa). Moreover, as animal-derived products, secondary antibodies are associated with ethical concerns and batch-to-batch variability. In this study, we developed fluorescence-labeled recombinant nanobodies as secondary antibodies by utilizing previously established anti-mouse and anti-rabbit IgG secondary nanobodies in combination with the self-labeling SNAP-tag. Nanobodies, which are significantly smaller (15 kDa), are capable to detect primary antibodies produced in mice and rabbits. The SNAP-tag (20 kDa) enables site-specific binding of various O6-benzylguanine (BG)-modified fluorophores to the recombinant nanobodies. These recombinant nanobodies were produced using mammalian cell expression system, and their specific binding to mouse or rabbit antibodies was validated using flow cytometry and multi-color fluorescence microscopy. The low cost, easy of expression, purification and site-specific conjugation procedures for these anti-mouse and anti-rabbit IgG secondary nanobodies make them an attractive alternative to traditional secondary antibodies for indirect immunofluorescence assays.

Binding characterization of small protein-conjugated ssDNA aptamer to recombinant human ICAM-1

This study investigates the potential of a protein-DNA aptamer conjugate to enhance aptamer binding to recombinant human intercellular adhesion molecule 1 (rhICAM-1). Aptamers are single-stranded nucleic acids that bind target molecules through hydrogen bonding and hydrophobic interactions. Conjugating aptamers with antibodies or proteins has been shown to improve their binding affinity. Using Systematic Evolution of Ligands by Exponential Enrichment (SELEX), eight rounds of selection were performed with ICAM-1-coupled Dynabeads Protein A, identifying a DI05 as having the strongest binding affinity to rhICAM-1. An antibody inhibition assay showed a significant reduction in rhICAM-1 binding to immobilized aptamers (DI05, DI20, DI31, and DI33). Additionally, the binding affinity of eGFP-conjugated DI05 to rhICAM-1 was higher than that of unconjugated DI05. Docking simulations revealed close contact between DI05 and ICAM-1, with interactions primarily mediated by hydrogen bonds within three hairpin structures at ≤2.8 Å. These findings highlight the potential of aptamer-small protein conjugates as a promising strategy to enhance aptamer binding characteristics.

Search for improved triplet-state quenchers for fluorescence imaging: a computational framework incorporating excited-state Baird-aromaticity

Fluorescence imaging is crucial for studying biology. Triplet state quenchers (TSQs), especially cyclooctatetraene (COT), can dramatically improve fluorophore performance, particularly when linked intramolecularly so as to enable "self-healing". Leveraging knowledge revealed through investigations of the self-healing mechanism enabled by COT, we computationally screened for cyclic 8π-electron species, and their annulated derivatives, with efficient triplet-triplet energy transfer potential, high photostability, and strong spin-orbit coupling (SOC) between the lowest triplet state to the singlet ground state. Here, we report theory-based analyses of a broad array of candidates that demonstrate various extents of triplet state Baird-aromaticity, indicating self-healing potential. We identify specific candidates with 7-membered ring structures predicted to exhibit favorable enhancements in fluorophore performance spanning the visible spectrum, with several possessing estimated intersystem crossing (ISC) rates up to 4 × 106 times faster than that of COT, the current benchmark for the self-healing strategy.

Dynamic proton coupled electron transfer quenching as a sensing modality in fluorescent probes

Fluorescent off-on probes based on a modular design where an analyte sensitive PET moiety is attached to a fluorophore are extremely successful. Here we report a new modular fluorescence probe design switched by dynamic quenching due to proton coupled electron transfer (PCET) mediated by collision with weak bases in solution. The fluorescence lifetime of this probe directly reports on the rate of deprotonation by the weak bases in the solution. We investigate the probe design, mechanism of response, and sensitivity to various abundant weak bases/metabolites including acetate, glutamate, phosphate, valine, and amines. We find that this modular PCET based probe design, in contrast to traditional PET probes, can work efficiently with a fluorescence lifetime readout providing a calibration free probe for weak bases. Upon further development we envision such dynamic PCET probes as sensitive tools for studies of cellular buffer systems and metabolite pools.

Light-Induced Electrode Scanning Microscopy

Patch clamps and microelectrode arrays have been widely used to detect the electrical properties of cells in biomedicine. Yet, both technologies can record signals only in an invasive manner or at fixed positions. Based on the resolution (LAPS) and optically induced dielectrophoretic, we present a novel light-induced electrode scanning microscopy. It works like a "radar", scans the whole area with living cells in culture, and detects the electrical signals of single cells on a photosensitive chip. In the system, a light pattern projected onto the chip is used to form the corresponding light-induced electrode, and the electrode scanning mode is implemented by moving the light pattern or the chip position for the measurement of the electrical characteristics of biological cells and cell localizations. It provides a new tool for the detection of cell electrical properties and is expected to become the next generation of electrophysiological detection technology.

Alterations in Gene Expression and Alternative Splicing Induced by Plasmid-Mediated Overexpression of GFP and P2RY12 Within the A549 Cell Line

Phenotypic modifications and their effects on cellular functions through the up-regulation of target gene expression have frequently been observed in genetic studies, but the unique roles of cell lines and their introduced plasmids in influencing these functions have not been fully revealed. In this research, we developed two distinct cell lines derived from the A549 cell line: one that stably overexpresses GFP and another that is a polyclonal stable line overexpressing both GFP and P2RY12. We then utilized transcriptome sequencing (RNA-seq) technology to screen out differentially expressed genes (DEGs) and genes with differential transcript usage (gDTUs) after GFP overexpression (GFP-OE) and P2RY12 overexpression (P2RY12-OE). We found that, compared with A549, there were more than 1700 differentially expressed genes (DEGs) in both GFP-OE and P2RY12-OE cells, while only 866 DEGs were identified in GFP-OE and P2RY12-OE cells. Notably, the differences in transcript usage were relatively minor, with only over 400 genes exhibiting changes across all three groups. The functional analysis of DEGs and gDTUs showed that they were both highly enriched in the pathways associated with cell proliferation and migration. In summary, we performed an extensive analysis of the transcriptome profile of gene expression and alternative splicing with GFP-OE and P2RY12-OE, enhancing our comprehension of how genes function within cells and the processes that control gene expression.

Harnessing the Power of Plasmonics for in Vitro and in Vivo Biosensing

Plasmonic nanostructures exhibit localized surface plasmon resonances due to collective oscillation of conducting electrons that can be tuned by modulating the nanostructure size, shape, material composition, and local dielectric environment. The strong field confinement and enhancement provided by plasmonic nanostructures have been exploited over the years to enhance the sensitivity for analyte detection down to the single-molecule level, rendering these devices as potentially outstanding biosensors. Here, we summarize methods to detect biological analytes in vitro and in living cells, with a focus on plasmon-enhanced fluorescence, Raman scattering, infrared absorption, circular dichroism, and refractive index sensing. Given the tremendous advances in the field, we concentrate on a few recent examples toward biosensing under highly challenging detection conditions, including clinically relevant biomarkers in body fluids and nascent applications in living cells and in vivo. These emerging platforms serve as inspiration for exploring future directions of nanoplasmonics that can be further harnessed to advance real-world biosensing applications.

A dual-response ratiometric near-infrared fluorescence probe based on cyanine platform for Cu2+ detection and its imaging in vitro and vivo

A near-infrared fluorescent probe (NUST-Cy-1) was disclosed here, which displays ratiometric and dual-channel response for Cu2+ (λex1 = 450 nm, λex2 = 750 nm) with large Stokes shifts (143 nm, 375 nm, 75 nm respectively). This probe demonstrates high sensitivity with low detection limit (1.4 μM) and selectivity for Cu2+ detection. Furthermore, fluorescent imaging of Cu2+ in vitro and vivo were successfully achieved.

Aggregation-Induced Emission Luminogens Realizing High-Contrast Bioimaging

A revolutionary transformation in biomedical imaging is unfolding with the advent of aggregation-induced emission luminogens (AIEgens). These cutting-edge molecules not only overcome the limitations of traditional fluorescent probes but also improve the boundaries of high-contrast imaging. Unlike conventional fluorophores suffering from aggregation-caused quenching, AIEgens exhibit enhanced luminescence when aggregated, enabling superior imaging performance. This review delves into the molecular mechanisms of aggregation-induced emission (AIE), demonstrating how strategic molecular design unlocks exceptional luminescence and superior imaging contrast, which is crucial for distinguishing healthy and diseased tissues. This review also highlights key applications of AIEgens, such as time-resolved imaging, second near-infrared window (NIR-II), and the advancement of AIEgens in sensitivity to physical and biochemical cue-responsive imaging. The development of AIE technology promises to transform healthcare from early disease detection to targeted therapies, potentially reshaping personalized medicine. This paradigm shift in biophotonics offers efficient tools to decode the complexities of biological systems at the molecular level, bringing us closer to a future where the invisible becomes visible and the incurable becomes treatable.

Multiplex basophil activation tests for allergy diagnosis: present and future applications

The basophil activation test (BAT) has become a major cellular in vitro test for evaluating the allergenic activity of specific IgEs. The impact of the BAT is due to the ability of blood basophil granulocytes to present IgE on the high-affinity FcεRI receptor and to mirror the mast cell response that elicits an acute allergic reaction. The BAT proved to be able to identify allergic patients at risk of reacting to a low dose of the allergen and/or developing life-threatening reactions and thus can significantly improve the current management of allergic patients. However, to improve the diagnostic utility for identifying the allergenic activity of different genuinely sensitizing allergens and lower the procedure and labour requirements, developing a multiplex BAT approach incorporating multiple allergen components would be highly anticipated. Recently, the novel multiplex BAT was described utilizing two major innovative steps. The first step was the fluorescent labeling of allergens. The second step was applying fluorescently labeled allergens in flow cytometry assessment to analyze the activation of basophil subpopulations gated according to the binding of different allergens or to evaluate the fluorescence intensity of multiple allergens on the surface of basophils. These novel cellular multiplex approaches will advance our understanding of IgE-mediated responses. Integration of multiplex BAT, in addition to multiplex IgE assays into practice, will personalize the measurement of allergenic IgE activity and can help estimate the likelihood of clinical relevance and risks for multiple allergens when testing individual allergic patients.

N-Acyl-N-alkyl/aryl Sulfonamide Chemistry Assisted by Proximity for Modification and Covalent Inhibition of Endogenous Proteins in Living Systems

Selective chemical modification of endogenous proteins in living systems with synthetic small molecular probes is a central challenge in chemical biology. Such modification has a variety of applications important for biological and pharmaceutical research, including protein visualization, protein functionalization, proteome-wide profiling of enzyme activity, and irreversible inhibition of protein activity. Traditional chemistry for selective protein modification in cells largely relies on the high nucleophilicity of cysteine residues to ensure target-selectivity and site-specificity of modification. More recently, lysine residues, which are more abundant on protein surfaces, have attracted attention for the covalent modification of proteins. However, it has been difficult to efficiently modify the ε-amino groups of lysine side-chains, which are mostly (∼99.9%) protonated and thus exhibit low nucleophilicity at physiological pH. Our group revealed that N-acyl-N-alkyl sulfonamide (NASA) moieties can rapidly and efficiently acylate noncatalytic (i.e., less reactive) lysine residues in proteins by leveraging a reaction acceleration effect via proximity. The excellent reaction kinetics and selectivity for lysine of the NASA chemistry enable covalent modification of natural intracellular and cell-surface proteins, which is intractable using conventional chemistries. Moreover, recently developed N-acyl-N-aryl sulfonamide (ArNASA) scaffolds overcome some problems faced by the first-generation NASA compounds. In this Account, we summarize our recent works in the development of NASA/ArNASA chemistry and several applications reported by ourselves and other groups. First, we characterize the basic properties of NASA/ArNASA chemistry, including the labeling kinetics, amino acid preference, and biocompatibility, and compare this approach with other ligand-directed chemistries. This section also describes the principles of nucleophilic organocatalyst-mediated protein acylation, another important protein labeling strategy using the NASA reactive group, and its application to neurotransmitter receptor labeling in brain slices. Second, we highlight various recent examples of protein functionalization using NASA/ArNASA chemistry, such as visualization of membrane proteins including therapeutically important G-protein coupled receptors, gel-based ligand screening assays, photochemical control of protein activity, and targeted protein degradation. Third, we survey covalent inhibition of proteins by NASA/ArNASA-based lysine-targeting. The unprecedented reactivity of NASA/ArNASA toward lysine allows highly potent, irreversible inhibition of several drug targets for the treatment of cancer, including HSP90, HDM2-p53 protein-protein interaction, and a Bruton's tyrosine kinase mutant that has developed resistance to cysteine-targeted covalent-binding drugs. Finally, current limitations of, and future perspectives on, this research field are discussed. The new chemical labeling techniques offered by NASA/ArNASA chemistry and its derivatives create a valuable molecular toolbox for studying numerous biomolecules in living cells and even in vivo.

Upconversion nanoparticles-CuMnO2 nanoassemblies for NIR-excited imaging of reactive oxygen species in vivo

Here, we designed a ratiometric luminescent nanoprobe based on lanthanide-doped upconversion nanoparticles-CuMnO2 nanoassemblies for rapid and sensitive detection of reactive oxygen species (ROS) levels in living cells and mouse. CuMnO2 nanosheets exhibit a wide absorption range of 300-700 nm, overlapping with the visible-light emission of upconversion nanoparticles (UCNPs), resulting in a significant upconversion luminescence quenching. In an acidic environment, H2O2 can promote the redox reaction of CuMnO2, leading to its dissociation from the surface of UCNPs and the restoration of upconversion luminescence. The variation in luminescence intensity ratio (UCL475/UCL450) were monitored to detect ROS levels. The H2O2 nanoprobe exhibited a linear response in the range of 0.314-10 μM with a detection limit of 11.3 nM. The biological tests proved the excellent biocompatibility and low toxicity of obtained UCNPs-CuMnO2 nanoassemblies. This ratiometric luminescent nanoprobe was successfully applied for the detection of exogenous and endogenous ROS in live cells as well as in vivo ROS quantitation. The dual transition metal ions endow this probe efficient catalytic decomposition capabilities, and this sensing strategy broadens the application of UCNPs-based nanomaterials in the field of biological analysis and diagnosis.

Exploring the landscape of FRET-based molecular sensors: Design strategies and recent advances in emerging applications

Probing biological processes in living organisms that could provide one-of-a-kind insights into real-time alterations of significant physiological parameters is a formidable task that calls for specialized analytic devices. Classical biochemical methods have significantly aided our understanding of the mechanisms that regulate essential biological processes. These methods, however, are typically insufficient for investigating transient molecular events since they focus primarily on the end outcome. Fluorescence resonance energy transfer (FRET) microscopy is a potent tool used for exploring non-invasively real-time dynamic interactions between proteins and a variety of biochemical signaling events using sensors that have been meticulously constructed. Due to their versatility, FRET-based sensors have enabled the rapid and standardized assessment of a large array of biological variables, facilitating both high-throughput research and precise subcellular measurements with exceptional temporal and spatial resolution. This review commences with a brief introduction to FRET theory and a discussion of the fluorescent molecules that can serve as tags in different sensing modalities for studies in chemical biology, followed by an outlining of the imaging techniques currently utilized to quantify FRET highlighting their strengths and shortcomings. The article also discusses the various donor-acceptor combinations that can be utilized to construct FRET scaffolds. Specifically, the review provides insights into the latest real-time bioimaging applications of FRET-based sensors and discusses the common architectures of such devices. There has also been discussion of FRET systems with multiplexing capabilities and multi-step FRET protocols for use in dual/multi-analyte detections. Future research directions in this exciting field are also mentioned, along with the obstacles and opportunities that lie ahead.

Suppressing ROS Production of AIE Nanoprobes by Simple Matrices Optimization for CNS Cell Observation and Minimized Influence of Cytoskeleton Morphology

The visualization of the central nervous system (CNS) has proposed stringent criteria for fluorescent probes, as the inevitable production of reactive oxygen species (ROS) or heat generated from most photoluminescent probes upon excitation can disturb the normal status of relatively delicate CNS cells. In this work, a red-emitting fluorogen with aggregation-induced emission (AIE) characteristics, known as DTF, was chosen as the model fluorogen to investigate whether the side effects of ROS and heat could be suppressed through easy-to-operate processes. Specifically, DTF was encapsulated with different amphiphilic matrices to yield AIE nanoprobes, and their photoluminescent properties, ROS production, and photothermal conversion rates were examined. BSA@DTF NPs possessed 1.3-fold brightness compared to that of DSPE-PEG@DTF NPs and F127@DTF NPs but its ROS generation efficiency is markedly decreased to only 2.4% of that produced by F127@DTF NPs. Meanwhile, BSA@DTF NPs showed a negligible photothermal effect. These features make BSA@DTF NPs favorable for long-term live cell imaging, particularly for fluorescent imaging of CNS cells. BSA@DTF NPs were able to sustain the normal state of HT-22 neuronal cells with continuous illumination for at least 25 min, and they also preserved the cytoskeleton of microglia BV-2 cells as the untreated control group. This work represents a successful but easy-to-operate process to suppress the ROS generation of red-emissive AIEgen, and it highlights the importance of minimizing the ROS generation of the fluorescent probes, particularly in the application of long-term imaging of CNS cells.

Exploring Carbon Dots: Green Nanomaterials for Unconventional Lasing

In recent years, the progress toward lighting miniaturization is focused on luminescent nanomaterials. Among them, fluorescent carbon dots (CDs) are receiving increasing attention thanks to their astonishing optical properties complemented by their intrinsic biocompatibility and low toxicity. The CDs can be easily dispersed in water, organic solvents or incorporated in polymeric matrices, preserving their emission properties. However, the relationship between their structural and optical properties is still not fully elucidated, motivating a consistent research effort for the comprehension of their features. Nevertheless, CDs demonstrate to be efficient gain materials for lasing, thanks to their high quantum yield (QY), emission tunability in the visible and near infrared (NIR) range, short lifetimes, and high absorption cross section, even if the synthetic reproducibility, the low reaction yield and the spectral width of the emission may limit their effective exploitation. This review summarizes the latest advancements in the investigation of the characteristic properties of CDs that make laser action possible, illustrating optical geometries for lasing and random lasing, both in solution and solid state, and the few currently demonstrated breakthroughs. While the journey toward their effective application is still long, the potential of CD-based laser sources is promising in various technological fields and futuristic perspectives will be discussed.

Novel Vibrational Proteins

Genetically encoded green fluorescent protein (GFP) and its brighter and redder variants have tremendously revolutionized modern molecular biology and life science by enabling direct visualization of gene regulated protein functions on microscopic and nanoscopic scales. However, the current fluorescent proteins (FPs) only emit a few colors with an emission width of about 30-50 nm. Here, we engineer novel vibrational proteins (VPs) that undergo much finer vibrational transitions and emit rather narrow vibrational spectra (0.1-0.3 nm, roughly 3-10 cm-1). In response to an amber stop codon (UAG), a terminal alkyne bearing an unnatural amino acid (UAA, pEtF) is directly incorporated in place of Tyr64 in the chromophore of pr-Kaede by genetic code expansion. Essentially, the UAA64 further conjugates into a large π system with the contiguous two editable amino acid residues (His63 and Gly65), resulting in a programmable Raman resonance shift of the embedded alkyne. In the proof-of-concept experiment, we constructed a series of novel pEtF-VP mutants and observed fine Raman shifts of the alkynyl group in different chromophores. The genetically encoded novel VPs, could potentially label tens of proteins in the future.

Fluorescent Reporters, Imaging, and Artificial Intelligence Toolkits to Monitor and Quantify Autophagy, Heterophagy, and Lysosomal Trafficking Fluxes

Lysosomal compartments control the clearance of cell-own material (autophagy) or of material that cells endocytose from the external environment (heterophagy) to warrant supply of nutrients, to eliminate macromolecules or parts of organelles present in excess, aged, or containing toxic material. Inherited or sporadic mutations in lysosomal proteins and enzymes may hamper their folding in the endoplasmic reticulum (ER) and their lysosomal transport via the Golgi compartment, resulting in lysosomal dysfunction and storage disorders. Defective cargo delivery to lysosomal compartments is harmful to cells and organs since it causes accumulation of toxic compounds and defective organellar homeostasis. Assessment of resident proteins and cargo fluxes to the lysosomal compartments is crucial for the mechanistic dissection of intracellular transport and catabolic events. It might be combined with high-throughput screenings to identify cellular, chemical, or pharmacological modulators of these events that may find therapeutic use for autophagy-related and lysosomal storage disorders. Here, discuss qualitative, quantitative and chronologic monitoring of autophagic, heterophagic and lysosomal protein trafficking in fixed and live cells, which relies on fluorescent single and tandem reporters used in combination with biochemical, flow cytometry, light and electron microscopy approaches implemented by artificial intelligence-based technology.

Expanding Our Horizons: AIE Materials in Bacterial Research

Bacteria share a longstanding and complex relationship with humans, playing a role in protecting gut health and sustaining the ecosystem to cause infectious diseases and antibiotic resistance. Luminogenic materials that share aggregation-induced emission (AIE) characteristics have emerged as a versatile toolbox for bacterial studies through fluorescence visualization. Numerous research efforts highlight the superiority of AIE materials in this field. Recent advances in AIE materials in bacterial studies are categorized into four areas: understanding bacterial interactions, antibacterial strategies, diverse applications, and synergistic applications with bacteria. Initial research focuses on visualizing the unseen bacteria and progresses into developing strategies involving electrostatic interactions, amphiphilic AIE luminogens (AIEgens), and various AIE materials to enhance bacterial affinity. Recent progress in antibacterial strategies includes using photodynamic and photothermal therapies, bacterial toxicity studies, and combined therapies. Diverse applications from environmental disinfection to disease treatment, utilizing AIE materials in antibacterial coatings, bacterial sensors, wound healing materials, etc., are also provided. Finally, synergistic applications combining AIE materials with bacteria to achieve enhanced outcomes are explored. This review summarizes the developmental trend of AIE materials in bacterial studies and is expected to provide future research directions in advancing bacterial methodologies.

Near infrared aggregation-induced emission fluorescent materials for lipid droplets testing and photodynamic therapy

Near-infrared (NIR) fluorescent probes with aggregation-induced emission (AIE) properties are of great significance in cell imaging and cancer therapy. However, the complexity of its synthesis, poor photostabilities, and expensive raw materials still pose some obstacles to their practical application. This study reported an AIE luminescent material with red emission and its application in in vitro imaging and photodynamic therapy (PDT) study. This material has the characteristics of simple synthesis, large Stokes shift, good photostabilities, and excellent lipid droplets-specific testing ability. Interestingly, this red-emitting material can effectively produce reactive oxygen species (ROS) under white light irradiation, further achieving PDT-mediated killing of cancer cells. In conclusion, this study demonstrates a simple approach to synthesize NIR AIE probes with both imaging and therapeutic effects, providing an ideal architecture for constructing long-wavelength emission AIE materials.

Shining New Light on Biological Systems: Luminescent Transition Metal Complexes for Bioimaging and Biosensing Applications

Luminescence imaging is a powerful and versatile technique for investigating cell physiology and pathology in living systems, making significant contributions to life science research and clinical diagnosis. In recent years, luminescent transition metal complexes have gained significant attention for diagnostic and therapeutic applications due to their unique photophysical and photochemical properties. In this Review, we provide a comprehensive overview of the recent development of luminescent transition metal complexes for bioimaging and biosensing applications, with a focus on transition metal centers with a d6, d8, and d10 electronic configuration. We elucidate the structure-property relationships of luminescent transition metal complexes, exploring how their structural characteristics can be manipulated to control their biological behavior such as cellular uptake, localization, biocompatibility, pharmacokinetics, and biodistribution. Furthermore, we introduce the various design strategies that leverage the interesting photophysical properties of luminescent transition metal complexes for a wide variety of biological applications, including autofluorescence-free imaging, multimodal imaging, organelle imaging, biological sensing, microenvironment monitoring, bioorthogonal labeling, bacterial imaging, and cell viability assessment. Finally, we provide insights into the challenges and perspectives of luminescent transition metal complexes for bioimaging and biosensing applications, as well as their use in disease diagnosis and treatment evaluation.

Hexagonal Plasmonic Arrays for High-Throughput Multicolor Single-Molecule Studies

Nanophotonic biosensors offer exceptional sensitivity in the presence of strong background signals by enhancing and confining light in subwavelength volumes. In the field of nanophotonic biosensors, antenna-in-box (AiB) designs consisting of a nanoantenna within a nanoaperture have demonstrated remarkable single-molecule fluorescence detection sensitivities under physiologically relevant conditions. However, their full potential has not yet been exploited as current designs prohibit insightful correlative multicolor single-molecule studies and are limited in terms of throughput. Here, we overcome these constraints by introducing aluminum-based hexagonal close-packed AiB (HCP-AiB) arrays. Our approach enables the parallel readout of over 1000 HCP-AiBs with multicolor single-molecule sensitivity up to micromolar concentrations using an alternating three-color excitation scheme and epi-fluorescence detection. Notably, the high-density HCP-AiB arrays not only enable high-throughput studies at micromolar concentrations but also offer high single-molecule detection probabilities in the nanomolar range. We demonstrate that robust and alignment-free correlative multicolor studies are possible using optical fiducial markers even when imaging in the low millisecond range. These advancements pave the way for the use of HCP-AiB arrays as biosensor architectures for high-throughput multicolor studies on single-molecule dynamics.

Advances in Medicine: Photodynamic Therapy

Over the past decades, medicine has made enormous progress, revolutionized by modern technologies and innovative therapeutic approaches. One of the most exciting branches of these developments is photodynamic therapy (PDT). Using a combination of light of a specific wavelength and specially designed photosensitizing substances, PDT offers new perspectives in the fight against cancer, bacterial infections, and other diseases that are resistant to traditional treatment methods. In today's world, where there is a growing problem of drug resistance, the search for alternative therapies is becoming more and more urgent. Imagine that we could destroy cancer cells or bacteria using light, without the need to use strong chemicals or antibiotics. This is what PDT promises. By activating photosensitizers using appropriately adjusted light, this therapy can induce the death of cancer or bacterial cells while minimizing damage to surrounding healthy tissues. In this work, we will explore this fascinating method, discovering its mechanisms of action, clinical applications, and development prospects. We will also analyze the latest research and patient testimonies to understand the potential of PDT for the future of medicine.

Characterization and structural basis for the brightness of mCLIFY: a novel monomeric and circularly permuted bright yellow fluorescent protein

We present mCLIFY: a monomeric, bright, yellow, and long-lived fluorescent protein (FP) created by circular permutation of YPet, the brightest yellow FP from Aequorea Victoria for use in cellular and in vitro single molecule studies. mCLIFY retains the enhanced photophysical properties of YPET as a monomer at concentrations ≤ 40 μM. In contrast, we determined that YPet has a dimerization dissociation constant (K D 1-2) of 3.4 μM. Dimerization of YPet can cause homo-FRET, which underlies quantitative errors due to dimerization and homo-FRET. We determined the atomic structure of mCLIFY at 1.57 Å resolution and used its similarity with Venus for guided chromophore-targeted substitution studies to provide insights into its enhanced photophysical properties. The mutation V58L within the chromophore pocket improved quantum yield and extinction coefficient, making mCLIFY ~30% brighter than Venus. The extensive characterization of the photophysical and structural properties of YPet and mCLIFY presented here allowed us to reveal the basis of their long lifetimes and enhanced brightness and the basis of YPet's dimerization.

Ultrafast Hot Exciton Nonadiabatic Excited-State Dynamics in Green Fluorescent Protein Chromophore Analogue

The ultrafast high-energy nonadiabatic excited-state dynamics of the benzylidenedimethylimidazolinone chromophore dimer has been investigated using an electronic structure method coupled with on-the-fly quantitative wave function analysis to gain insight into the photophysics of hot excitons in biological systems. The dynamical simulation provides a rationalization of the behavior of the exciton in a dimer after the photoabsorption of light to higher-energy states. The results suggest that hot exciton localization within the manifold of excited states is caused by the hindrance of torsional rotation due to imidazolinone (I) or phenolate (P) bonds i.e., ΦI- or ΦP-dihedral rotation, in the monomeric units of a dimer. This hindrance arises due to weak π-π stacking interaction in the dimer, resulting in an energetically uphill excited-state barrier for ΦI- and ΦP-twisted rotation, impeding the isomerization process in the chromophore. Thus, this study highlights the potential impact of the weak π-π interaction in regulating the photodynamics of the green fluorescent protein chromophore derivatives.

NSPs: chromogenic linkers for fast, selective, and irreversible cysteine modification

The addition of a sulfhydryl group to water-soluble N-alkyl(o-nitrostyryl)pyridinium ions (NSPs) followed by fast and irreversible cyclization and aromatization results in a stable S-C sp2-bond. The reaction sequence, termed Click & Lock, engages accessible cysteine residues under the formation of N-hydroxy indole pyridinium ions. The accompanying red shift of >70 nm to around 385 nm enables convenient monitoring of the labeling yield by UV-vis spectroscopy at extinction coefficients of ≥2 × 104 M-1 cm-1. The versatility of the linker is demonstrated in the stapling of peptides and the derivatization of proteins, including the modification of reduced trastuzumab with Val-Cit-PAB-MMAE. The high stability of the linker in human plasma, fast reaction rates (k app up to 4.4 M-1 s-1 at 20 °C), high selectivity for cysteine, favorable solubility of the electrophilic moiety and the bathochromic properties of the Click & Lock reaction provide an appealing alternative to existing methods for cysteine conjugation.

Fluorescent styrenes for mitochondrial imaging and viscosity sensing

Fluorophores bearing cationic pendants, such as the pyridinium group, tend to preferentially accumulate in mitochondria, whereas those with pentafluorophenyl groups display a distinct affinity for the endoplasmic reticulum. In this study, we designed fluorophores incorporating pyridinium and pentafluorophenyl pendants and examined their impact on sub-cellular localization. Remarkably, the fluorophores exhibited a notable propensity for the mitochondrial membrane. Furthermore, these fluorophores revealed dual functionality by facilitating the detection of viscosity changes within the sub-cellular environment and serving as heavy-atom-free photosensitizers. With easy chemical tunability, wash-free imaging, and a favorable signal-to-noise ratio, these fluorophores are valuable tools for imaging mitochondria and investigating their cellular processes.

Fluorescence resonance energy transfer in atomically precise metal nanoclusters by cocrystallization-induced spatial confinement

Understanding the fluorescence resonance energy transfer (FRET) of metal nanoparticles at the atomic level has long been a challenge due to the lack of accurate systems with definite distance and orientation of molecules. Here we present the realization of achieving FRET between two atomically precise copper nanoclusters through cocrystallization-induced spatial confinement. In this study, we demonstrate the establishment of FRET in a cocrystallized Cu8(p-MBT)8(PPh3)4@Cu10(p-MBT)10(PPh3)4 system by exploiting the overlapping spectra between the excitation of the Cu10(p-MBT)10(PPh3)4 cluster and the emission of the Cu8(p-MBT)8(PPh3)4 cluster, combined with accurate control over the confined space between the two nanoclusters. Density functional theory is employed to provide deeper insights into the role of the distance and dipole orientations of molecules to illustrate the FRET procedure between two cluster molecules at the electronic structure level.

Super-resolution microscopies, technological breakthrough to decipher mitochondrial structure and dynamic

Mitochondria are complex organelles with an outer membrane enveloping a second inner membrane that creates a vast matrix space partitioned by pockets or cristae that join the peripheral inner membrane with several thin junctions. Several micrometres long, mitochondria are generally close to 300 nm in diameter, with membrane layers separated by a few tens of nanometres. Ultrastructural data from electron microscopy revealed the structure of these mitochondria, while conventional optical microscopy revealed their extraordinary dynamics through fusion, fission, and migration processes but its limited resolution power restricted the possibility to go further. By overcoming the limits of light diffraction, Super-Resolution Microscopy (SRM) now offers the potential to establish the links between the ultrastructure and remodelling of mitochondrial membranes, leading to major advances in our understanding of mitochondria's structure-function. Here we review the contributions of SRM imaging to our understanding of the relationship between mitochondrial structure and function. What are the hopes for these new imaging approaches which are particularly important for mitochondrial pathologies?

Amyloids, amorphous aggregates and assemblies of peptides - Assessing aggregation

Amyloid and amorphous aggregates represent the two major categories of aggregates associated with diseases, and although exhibiting distinct features, researchers often treat them as equivalent, which demonstrates the need for more thorough characterization. Here, we compare amyloid and amorphous aggregates based on their biochemical properties, kinetics, and morphological features. To further decipher this issue, we propose the use of peptide self-assemblies as minimalistic models for understanding the aggregation process. Peptide building blocks are significantly smaller than proteins that participate in aggregation, however, they make a plausible means to bridge the gap in discerning the aggregation process at the more complex, protein level. Additionally, we explore the potential use of peptide-inspired models to research the liquid-liquid phase separation as a feasible mechanism preceding amyloid formation. Connecting these concepts can help clarify our understanding of aggregation-related disorders and potentially provide novel drug targets to impede and reverse these serious illnesses.

Awareness for artifacts in fluorescence microscopy of β-TCP

Fluorescence analysis of β-TCP ceramics is often used to describe cells found on said ceramics. However, we found, to our knowledge, so far undescribed artifacts which might sometimes be hard to differentiate from cells due to shape and fluorescence behavior. We tried prolonged ultrasound washing as well as Technovit 9100 fixation to reduce these artifacts. While untreated dowels showed no reduction in artifacts no matter the further treatment, Technovit fixation reduced the artifacts with even further reduction achieved by mechanical cleaning. As a consequence, scientists working with these dowels and likely even other types should try to avoid creating false positive results by considering the existence of these artifacts, checking additional filters for unusual fluorescence and by reducing them by using Technovit fixation when possible.

Recent advances in Si-rhodamine-based fluorescent probes for live-cell imaging

Fluorescence imaging is a powerful technique for visualizing biological events in living samples with high temporal and spatial resolution. Fluorescent probes emitting far-red to near infrared (NIR) fluorescence are particularly advantageous for in vivo imaging due to their high tissue permeability and low autofluorescence, as well as their suitability for multicolor imaging. Among the far-red to NIR fluorophores, Si-rhodamine is one of the most practical fluorophores for the development of tailor-made NIR fluorescent probes because of the relative ease of synthesis of various derivatives, the unique intramolecular spirocyclization behavior, and the relatively high water solubility and high photostability of the probes. This review summarizes these features of Si-rhodamines and presents recent advances in the synthesis and applications of far-red to NIR fluorescent probes based on Si-rhodamines, focusing on live-cell imaging applications such as fluorogenic probes, super-resolution imaging and dye-protein hybrid-based indicators.

Multiple-Emitting Luminescent Metal-Organic Framework as an Array-on-a-MOF for Rapid Screening and Discrimination of Nitroaromatics

Fluorescence array technologies have attracted great interest in the sensing field because of their high sensitivity, low cost, and capability of multitarget detection. However, traditional array sensing relies on multiple independent sensors and thus often requires time-consuming and laborious measurement processes. Herein, we introduce a novel fluorescence array strategy of the array-on-a-metal-organic framework (MOF), which integrates multiple array elements into a single MOF matrix to achieve facile sensing and discrimination of multiple target analytes. As a proof-of-concept system, we constructed a luminescent MOF containing three different emitting channels, including a lanthanide ion (europium/Eu3+, red emission), a fluorescent dye (7-hydroxycoumarin-4-acetic acid/HCAA, blue emission), and the MOF itself (UiO-66-type MOF, blue-violet emission). Five structurally similar nitroaromatic compounds (NACs) were chosen as the targets. All three channels of the array-on-a-MOF displayed rapid and stable fluorescence quenching responses to NACs (response equilibrium achieved within 30 s). Different responses were generated for each channel against each NAC due to the various quenching mechanisms, including photoinduced electron transfer, energy competition, and the inner filter effect. Using linear discriminant analysis, the array-on-a-MOF successfully distinguished the five NACs and their mixtures at varying concentrations and demonstrated good sensitivity to quantify individual NACs (detect limit below the advisory concentration in drinking water). Moreover, the array also showed feasibility in the sensing and discrimination of multiple NACs in real water samples. The proposed "array-on-a-MOF" strategy simplifies multitarget discrimination procedures and holds great promise for various sensing applications.

EuIII and TbIII upconversion intermediated by interparticle energy transfer in functionalized NaLnF4 nanoparticles

Lanthanide (LnIII)-doped sodium gadolinium tetrafluoride (NaGdF4) nanoparticles have been excelled as attractive upconversion systems for anti-counterfeiting or energy conversion for instance, with a special interest in the visible upconversion of EuIII and TbIII. The core@shell architecture has enabled the bright upconversion of EuIII and TbIII in this matrix by interfacial energy transfer sensibilized by the TmIII/YbIII pair. Another approach to enable EuIII and TbIII upconversion could be the interparticle energy transfer (IPET) between LnIII-doped sensitizer and acceptor nanoparticles. Yet, the low molar absorptivity of the LnIII through 4f ↔ 4f electronic transitions and the large distance between the nanoparticles are shortcomings that should decrease the energy transfer efficiency. On the other hand, it is feasible to predict that the association of organic ligands displaying large molar absorptivity on the acceptor nanoparticle surface could help to overcome the absorption limitation. Inspired by this exciting possibility, herein, we present the EuIII/TbIII upconversion intermediated by IPET between the donor TmIII, YbIII-doped NaGdF4 nanoparticle and the acceptor LnIII-doped NaGdF4 (Ln = Eu and/or Tb) nanoparticles functionalized with a series organic ligands on the surface (tta- = thenoyltrifluoroacetonate, acac- = acetylacetonate, or 3,5-bbza- = 3,5-dibromebenzoate). Either in solid state or in suspension, upon excitation at 980 nm, visible EuIII/TbIII upconversion could be observed. This emission comes from the absorption of the TmIII, YbIII pair in the donor nanoparticle, followed by IPET from the TmIII excited levels to the ligand singlet/triplet states on the acceptor nanoparticle surface, ligand-to-EuIII/TbIII energy transfer, and upconversion emission. Spectroscopic evidences from the analysis of the donor level lifetimes indicate the contribution of non-radiative energy transfer for the IPET mechanism; the radiative mechanism also contributes for the IPET. Moreover, the design herein introduced enables the development of luminescence temperature probes with relative thermal sensitivity as high as 1.67% K-1 at 373 K. Therefore, this new upconversion pathway opens an avenue of possibilities in an uncharted territory to tune the visible upconversion of LnIII ions.

Solution-Phase Late-Stage Chemoselective Photocatalytic Removal of Sulfonyl and Phenacyl Groups in Peptides

Herein, BPC catalyzed visible-light-triggered target-specific late-stage solution phase desulfonylation from tryptophan in oligopeptides is portrayed by overcoming the isolation issue up to octamers. This robust and mild method is highly predictable and chemoselective, tolerating myriad of functional groups in aza-heteroaromatics and peptides. Interestingly, reductive desulfonylation is also amenable to biologically significant reactive histidine and tyrosine side chains, signifying the versatility of the strategy. Additional efficacy of BPC is demonstrated by solution phase phenacyl deprotection from C-terminal in peptides. Furthermore, excellent catalyst loading of 0.5 mol% and recyclability demonstrate the practical utility and applicability of this strategy.

Identification of an N-terminal tag (580N) that improves the biosynthesis of fluorescent proteins in Francisella tularensis and other Gram-negative bacteria

Utilization of fluorescent proteins is widespread for the study of microbial pathogenesis and host-pathogen interactions. Here, we discovered that linkage of the 36 N-terminal amino acids of FTL_0580 (a hypothetical protein of Francisella tularensis) to fluorescent proteins increases the fluorescence emission of bacteria that express these recombinant fusions. This N-terminal peptide will be referred to as 580N. Western blotting revealed that the linkage of 580N to Emerald Green Fluorescent Protein (EmGFP) in F. tularensis markedly improved detection of this protein. We therefore hypothesized that transcripts containing 580N may be translated more efficiently than those lacking the coding sequence for this leader peptide. In support, expression of emGFPFt that had been codon-optimized for F. tularensis, yielded significantly enhanced fluorescence than its non-optimized counterpart. Furthermore, fusing emGFP with coding sequence for a small N-terminal peptide (Serine-Lysine-Isoleucine-Lysine), which had previously been shown to inhibit ribosomal stalling, produced robust fluorescence when expressed in F. tularensis. These findings support the interpretation that 580N enhances the translation efficiency of fluorescent proteins in F. tularensis. Interestingly, expression of non-optimized 580N-emGFP produced greater fluorescence intensity than any other construct. Structural predictions suggested that RNA secondary structure also may be influencing translation efficiency. When expressed in Escherichia coli and Klebsiella pneumoniae bacteria, 580N-emGFP produced increased green fluorescence compared to untagged emGFP (neither allele was codon optimized for these bacteria). In conclusion, fusing the coding sequence for the 580N leader peptide to recombinant genes might serve as an economical alternative to codon optimization for enhancing protein expression in bacteria.

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.

Chirality-Regulated Clusteroluminescence in Polypeptides

The low emission efficiency of clusteroluminogens restricts their practical applications in the fields of sensors and biological imaging. In this work, the clusteroluminescence of ordered/disordered polypeptides was observed, and the photoluminescence (PL) intensity of polypeptides can be modulated by the chirality of amino acid residues. Polyglutamates with different chiral compositions were synthesized, and the racemic polypeptides exhibited a significantly higher PL intensity than the enantiopure ones. This emission originates from the n-π* transition between C═O groups of polypeptides and is enhanced by clusterization of polypeptides. CD and Fourier transform infrared spectra demonstrated that the enantiopure and racemic polypeptides form α-helix and random coil structures, respectively. The disordered polypeptides can form more chain entanglements and interchain interactions because of their high flexibility, leading to more clusterizations and stronger PL intensity. The rigidity of ordered helical structures restrains the chain entanglements, and the formation of intrachain hydrogen bonds between amide groups of the backbone impairs the interchain interaction between polypeptides, resulting in lower PL intensity. The PL intensity of the polypeptides can also be manipulated by the addition of urea or trifluoroacetic acid. Our study not only elucidates the chirality/order-based structure-property relationship of clusteroluminescence in peptide-based polymers but also offers implications for the rational design of fluorescent peptides/proteins.

Illuminating the Path to Enhanced Bioimaging by Phosphole-based Fluorophores

As the research of biological systems becomes increasingly complex, there is a growing demand for fluorophores with a diverse range of wavelengths. In this study, we introduce phosphole-based fluorophores that surpass existing options like dansyl chloride. The reactive S-Cl bond in chlorosulfonylimino-5-phenylphosphole derivatives allows rapid and direct coupling to peptides making the fluorophores easily introducible to peptides. This coupling process occurs under mild conditions, demonstrated for [F7 ,P34 ]-NPY and its shorter analogues. Peptides linked with our fluorophores exhibit similar receptor activation to the control peptide, while maintaining high stability and low toxicity, making them ideal biolabeling reagents. In fluorescence microscopy experiments, they can be easily visualized even at low concentrations, without suffering from the typical issue of bleaching. These phosphole-based fluorophores represent a significant leap forward in the field. Their versatility, ease of modification, superior performance, and applicability in biological labeling make them a promising choice for researchers seeking advanced tools to unravel the details of complex biological systems.

A general fluorescence off/on strategy for fluorogenic probes: Steric repulsion-induced twisted intramolecular charge transfer (sr-TICT)

Various control strategies are available for building fluorogenic probes to visualize biological events in terms of a fluorescence change. Here, we performed the time-dependent density functional theory (TD-DFT) computational analysis of the twisted intramolecular charge transfer (TICT) process in rhodamine dyes. On the basis of the results, we designed and synthesized a series of rhodamine dyes and established a fluorescence quenching strategy that we call steric repulsion-induced TICT (sr-TICT), in which the fluorescence quenching process is greatly accelerated by simple intramolecular twisting. As proof of concept of this design strategy, we used it to develop a fluorogenic probe, 2-Me PeER (pentyloxyethylrhodamine), for the N-dealkylation activity of CYP3A4. We applied 2-Me PeER for CYP3A4 activity-based fluorescence-activated cell sorting (FACS), providing access to homogeneous, highly functional human-induced pluripotent stem cell (hiPSC)-derived hepatocytes and intestinal epithelial cells. Our results suggest that sr-TICT represents a general fluorescence control method for fluorogenic probes.

Chemical control of excited-state reactivity of the anionic green fluorescent protein chromophore

Controlling excited-state reactivity is a long-standing challenge in photochemistry, as a desired pathway may be inaccessible or compete with other unwanted channels. An important example is internal conversion of the anionic green fluorescent protein (GFP) chromophore where non-selective progress along two competing torsional modes (P: phenolate and I: imidazolinone) impairs and enables Z-to-E photoisomerization, respectively. Developing strategies to promote photoisomerization could drive new areas of applications of GFP-like proteins. Motivated by the charge-transfer dichotomy of the torsional modes, we explore chemical substitution on the P-ring of the chromophore as a way to control excited-state pathways and improve photoisomerization. As demonstrated by methoxylation, selective P-twisting appears difficult to achieve because the electron-donating potential effects of the substituents are counteracted by inertial effects that directly retard the motion. Conversely, these effects act in concert to promote I-twisting when introducing electron-withdrawing groups. Specifically, 2,3,5-trifluorination leads to both pathway selectivity and a more direct approach to the I-twisted intersection which, in turn, doubles the photoisomerization quantum yield. Our results suggest P-ring engineering as an effective approach to boost photoisomerization of the anionic GFP chromophore.

Excited state hydrogen or proton transfer pathways in microsolvated n-cyanoindole fluorescent probes

The sensitivity of the fluorescence properties of n-cyanoindole (n-CNI) fluorescent probes to the microenvironment makes them potential reporters of protein conformation and hydration. The fluorescence intensity of 5-CNI, 6-CNI, and 7-CNI is quenched when exposed to water solvent whereas substitution on position 4 of indoles dramatically increases it. A potential mechanism for this sensitivity to water may be similar to that found in indole. The fluorescence of indole is found to be quenched when interacting with water and ammonia solvent molecules via radiationless decay through an S1 (πσ*)/S0 conical intersection caused by excited state proton or hydrogen transfer to the solvent molecules. In this study we examine this fluorescence quenching mechanism along the N-H bond stretch of n-CNI probes using water cluster models and quantum mechanical calculations of the excited states. We find that n-CNI-(H2O)1-2 clusters form cyclic or non-cyclic structures via hydrogen bonds which lead to different photochemical reaction paths that can potentially quench the fluorescence by undergoing internal conversion from S1 to S0. However, the existence of a high energy barrier along the potential energy surface of the S1 state in most cases prevents this from occurring. We show that substitution on position 4 leads to the highest energy barrier that prevents the fluorophore from accessing these non-radiative channels, in agreement with its high intensity. We also find that the energy barrier in the S1 state of non-cyclic 5-CNI-(H2O)1-2 excited complexes decreases as the number of water molecules increases, which suggests great sensitivity of the fluorescence quenching on the aqueous environment.

Illuminating T cell-dendritic cell interactions in vivo by FlAsHing antigens

Delineating the complex network of interactions between antigen-specific T cells and antigen presenting cells (APCs) is crucial for effective precision therapies against cancer, chronic infections, and autoimmunity. However, the existing arsenal for examining antigen-specific T cell interactions is restricted to a select few antigen-T cell receptor pairs, with limited in situ utility. This lack of versatility is largely due to the disruptive effects of reagents on the immune synapse, which hinder real-time monitoring of antigen-specific interactions. To address this limitation, we have developed a novel and versatile immune monitoring strategy by adding a short cysteine-rich tag to antigenic peptides that emits fluorescence upon binding to thiol-reactive biarsenical hairpin compounds. Our findings demonstrate the specificity and durability of the novel antigen-targeting probes during dynamic immune monitoring in vitro and in vivo. This strategy opens new avenues for biological validation of T-cell receptors with newly identified epitopes by revealing the behavior of previously unrecognized antigen-receptor pairs, expanding our understanding of T cell responses.

Implementation of Fluorescent-Protein-Based Quantification Analysis in L-Form Bacteria

Cell-wall-less (L-form) bacteria exhibit morphological complexity and heterogeneity, complicating quantitative analysis of them under internal and external stimuli. Stable and efficient labeling is needed for the fluorescence-based quantitative cell analysis of L-forms during growth and proliferation. Here, we evaluated the expression of multiple fluorescent proteins (FPs) under different promoters in the Bacillus subtilis L-form strain LR2 using confocal microscopy and imaging flow cytometry. Among others, Pylb-derived NBP3510 showed a superior performance for inducing several FPs including EGFP and mKO2 in both the wild-type and L-form strains. Moreover, NBP3510 was also active in Escherichia coli and its L-form strain NC-7. Employing these established FP-labeled strains, we demonstrated distinct morphologies in the L-form bacteria in a quantitative manner. Given cell-wall-deficient bacteria are considered protocell and synthetic cell models, the generated cell lines in our work could be valuable for L-form-based research.

Real-Time Spatiotemporal Measurement of Extracellular Signaling Molecules Using an Aptamer Switch-Conjugated Hydrogel Matrix

Cells rely on secreted signaling molecules to coordinate essential biological functions including development, metabolism, and immunity. Unfortunately, such signaling processes remain difficult to measure with sufficient chemical specificity and temporal resolution. To address this need, an aptamer-conjugated hydrogel matrix that enables continuous fluorescent measurement of specific secreted analytes - in two dimensions, in real-time is developed. As a proof of concept, real-time imaging of inter-cellular cyclic adenosine 3',5'-monophosphate (cAMP) signals in Dictyostelium discoideum amoeba cells is performed. A set of aptamer switches that generate a rapid and reversible change in fluorescence in response to cAMP signals is engineered. By combining multiple switches with different dynamic ranges, measure cAMP concentrations spanning three orders of magnitude in a single experiment can be measured. These sensors are embedded within a biocompatible hydrogel on which cells are cultured and their cAMP secretions can be imaged using fluorescent microscopy. Using this aptamer-hydrogel material system, the first direct measurements of oscillatory cAMP signaling that correlate closely with previous indirect measurements are achieved. Using different aptamer switches, this approach can be generalized for measuring other secreted molecules to directly visualize diverse extracellular signaling processes and the biological effects that they trigger in recipient cells.

A Brief Introduction to Single-Molecule Fluorescence Methods

One of the most popular single-molecule approaches in biological science is single-molecule fluorescence microscopy, which will be the subject of the following section of this volume. Fluorescence methods provide the sensitivity required to study biology on the single-molecule level, but they also allow access to useful measurable parameters on time and length scales relevant for the biomolecular world. Before several detailed experimental approaches will be addressed, we will first give a general overview of single-molecule fluorescence microscopy. We start with discussing the phenomenon of fluorescence in general and the history of single-molecule fluorescence microscopy. Next, we will review fluorescent probes in more detail and the equipment required to visualize them on the single-molecule level. We will end with a description of parameters measurable with such approaches, ranging from protein counting and tracking, single-molecule localization super-resolution microscopy, to distance measurements with Förster resonance energy transfer and orientation measurements with fluorescence polarization.