The fluorescent toolbox for assessing protein location and function

Aggregation-Induced Emission Active Donor-Acceptor Fluorophore as a Dual Sensor for Volatile Acids and Aromatic Amines

In the present work, a novel donor (D)-acceptor (A) fluorophore based on indeno-pyrrole derivative (PYROMe) has been utilized as a dual sensor for volatile acids and aromatic amines, where sensory responses were regulated by the aggregation-induced emission (AIE) property. The twisted structural framework of PYROMe, confirmed by crystal study, avoids closed cofacial encounter upon aggregation and aided with augmented rigidity via different noncovalent interactions that ultimately ensued restricted intramolecular rotation (RIR). Consequently, PYROMe exhibited AIE in THF/H₂O mixture along with bright solid-state emission. The accessibility of protonation at carbonyl site and feasible HOMO energy to accept electrons from aromatic amines during photoexcitation enabled PYROMe as a potential dual sensor. A thin film of PYROMe was utilized for the quantitative detection of volatile acids and aromatic amines, and the detection limit (DL) was found to be as low as 0.77 ppm and 6.04 ppb for trifluoroacetic acid (TFA) and aniline vapors, respectively. Beyond the established scopes of substituted indeno-pyrroles, the present study paves the way, for the first time, toward an AIE-driven dual-stimuli response in indeno-pyrrole based D-A fluorophores.

Luminophore and Magnetic Multicore Nanoassemblies for Dual-Mode MRI and Fluorescence Imaging

Nanoassemblies encompass a large variety of systems (organic, crystalline, amorphous and porous). The nanometric size enables these systems to interact with biological entities and cellular organelles of similar dimensions (proteins, cells, …). Over the past 20 years, the exploitation of their singular properties as contrast agents has led to the improvement of medical imaging. The use of nanoprobes also allows the combination of several active units within the same nanostructure, paving the way to multi-imaging. Thus, the nano-object provides various additional information which helps simplify the number of clinical procedures required. In this review, we are interested in the combination between fluorescent units and magnetic nanoparticles to perform dual-mode magnetic resonance imaging (MRI) and fluorescent imaging. The effect of magnetic interaction in multicore iron oxide nanoparticles on the MRI contrast agent properties is highlighted.

Facile autofluorescence suppression enabling tracking of single viruses in live cells

Live cell fluorescence imaging is the method of choice for studying dynamic processes, such as nuclear transport, vesicular trafficking, and virus entry and egress. However, endogenous cellular autofluorescence masks a useful fluorescence signal, limiting the ability to reliably visualize low-abundance fluorescent proteins. Here, we employed synchronously amplified fluorescence image recovery (SAFIRe), which optically alters ground versus photophysical dark state populations within fluorescent proteins to modulate and selectively detect their background-free emission. Using a photoswitchable rsFastLime fluorescent protein combined with a simple illumination and image-processing scheme, we demonstrate the utility of this approach for suppressing undesirable, unmodulatable fluorescence background. Significantly, we adapted this technique to different commercial wide-field and spinning-disk confocal microscopes, obtaining >10-fold improvements in signal to background. SAFIRe allowed visualization of rsFastLime targeted to mitochondria by efficiently suppressing endogenous autofluorescence or overexpressed cytosolic unmodulatable EGFP. Suppression of the overlapping EGFP signal provided a means to perform multiplexed imaging of rsFastLime and spectrally overlapping fluorophores. Importantly, we used SAFIRe to reliably visualize and track single rsFastLime-labeled HIV-1 particles in living cells exhibiting high and uneven autofluorescence signals. Time-lapse SAFIRe imaging can be performed for an extended period of time to visualize HIV-1 entry into cells. SAFIRe should be broadly applicable for imaging live cell dynamics with commercial microscopes, even in strongly autofluorescent cells or cells expressing spectrally overlapping fluorescent proteins.

Probing Structure and Reaction Dynamics of Proteins Using Time-Resolved Resonance Raman Spectroscopy

The mechanistic understanding of protein functions requires insight into the structural and reaction dynamics. To elucidate these processes, a variety of experimental approaches are employed. Among them, time-resolved (TR) resonance Raman (RR) is a particularly versatile tool to probe processes of proteins harboring cofactors with electronic transitions in the visible range, such as retinal or heme proteins. TR RR spectroscopy offers the advantage of simultaneously providing molecular structure and kinetic information. The various TR RR spectroscopic methods can cover a wide dynamic range down to the femtosecond time regime and have been employed in monitoring photoinduced reaction cascades, ligand binding and dissociation, electron transfer, enzymatic reactions, and protein un- and refolding. In this account, we review the achievements of TR RR spectroscopy of nearly 50 years of research in this field, which also illustrates how the role of TR RR spectroscopy in molecular life science has changed from the beginning until now. We outline the various methodological approaches and developments and point out current limitations and potential perspectives.

A benzoperylene self-assembly complex with turn-on excimer emission for wash-free cell membrane fluorescence imaging

A rational design of a benzoperylene probe BP-3 with positive charge allows for turn-on excimer emission, and wash-free cell membrane imaging. BP-3 possesses excellent chemical, thermal and photo stability. And the Stokes shift of the excimer emission is considerably large (90-100 nm), which very much avoids the background fluorescence interference.

Protein trap: a new Swiss army knife for geneticists?

The protein trap is a powerful tool for genetic and biochemical studies of gene function in the animal kingdom. Although the original protein trap was developed for flies, it can be easily adapted to other multicellular organisms, both known models and ones with an unsequenced genome. The protein trap has been successfully applied to the fruit fly, crustaceans Parhyale hawaiensis, zebrafish, and insect and animal cell cultures. This approach is based on the integration into genes of an artificial exon that carries DNA encoding a fluorescent marker, standardized immunoepitopes, an integrase docking site, and splice acceptor and donor sites. The protein trap for cell cultures additionally contains an antibiotic resistance gene, which facilitates the selection of trapped clones. Resulting chimeric tagged mRNAs can be interfered by dsRNA against GFP (iGFPi-in vivo GFP interference), or the chimeric proteins can be efficiently knocked down by deGradFP technology. Both RNA and protein knockdowns produce a strong loss of function phenotype in tagged cells. The fluorescent and protein affinity tags can be used for tagged protein localisation within the cell and for identifying their binding partners in their native complexes. Insertion into protein trap integrase docking sites allows the replacement of trap contents by any new constructs, including other markers, cell toxins, stop-codons, and binary expression systems such as GAL4/UAS, LexA/LexAop and QF/QUAS, that reliably reflect endogenous gene expression. A distinctive feature of the protein trap approach is that all manipulations with a gene or its product occur only in the endogenous locus, which cannot be achieved by any other method.

Competitive Binding Study Revealing the Influence of Fluorophore Labels on Biomolecular Interactions

Fluorescence methods are important tools in modern biology. Direct labeling of biomolecules with a fluorophore might, however, change interaction surfaces. Here, we introduce a competitive binding assay in combination with fluorescence correlation spectroscopy that reports binding affinities of both labeled and unlabeled biomolecules to their binding target. We investigated how fluorophore labels at different positions of a DNA oligonucleotide affect hybridization to a complementary oligonucleotide and found dissociation constants varying within 2 orders of magnitude. We next demonstrated that placing a fluorophore label at position Leu280 in the protein ligand internalin B does not alter the binding affinity to the MET receptor tyrosine kinase, compared to unlabeled internalin B. Our approach is simple to implement and can be applied to investigate the influence of fluorophore labels in a large variety of biomolecular interactions.

Implementing VIPER for Imaging Cellular Proteins by Fluorescence Microscopy

Genetically-encoded tags are useful tools for multicolor and multi-scale cellular imaging. Versatile Interacting Peptide (VIP) tags, such as VIPER, are new genetically-encoded tags that can be used in various imaging applications. VIP tags consist of a coiled-coil heterodimer, with one peptide serving as the genetic tag and the other ("probe peptide") delivering a reporter compatible with imaging. Heterodimer formation is rapid and specific, allowing proteins to be selectively labeled for live-cell and fixed-cell imaging. In this Bio-Protocol, we include a detailed guide for implementing the VIPER technology for imaging receptors on live cells and intracellular targets in fixed cells. This protocol is complemented by two other Bio-Protocols outlining the use of VIPER (Doh et al., 2019a and 2019b).

Large-scale femtosecond holography for near simultaneous optogenetic neural modulation

For better understanding of brain functions, optogenetic neural modulation has been widely employed in neural science research. For deep tissue in vivo applications, large-scale two-photon based near simultaneous 3D laser excitation is needed. Although 3D holographic laser excitation is nowadays common practice, the inherent short coherence length of the commonly used femtosecond pulses fundamentally restricts the achievable field-of-view. Here we report a technique for near simultaneous large-scale femtosecond holographic 3D excitation. Specifically, we achieved two-photon excitation over 1.3 mm field-of-view within 1.3 milliseconds, which is sufficiently fast even for spike timing recording. The method is scalable and compatible with the commonly used two-photon sources and imaging systems in neuroscience research.

Cell penetrating peptide functionalized perfluorocarbon nanoemulsions for targeted cell labeling and enhanced fluorine-19 MRI detection

PURPOSE

A bottleneck in developing cell therapies for cancer is assaying cell biodistribution, persistence, and survival in vivo. Ex vivo cell labeling using perfluorocarbon (PFC) nanoemulsions, paired with ¹⁹ F MRI detection, is a non-invasive approach for cell product detection in vivo. Lymphocytes are small and weakly phagocytic limiting PFC labeling levels and MRI sensitivity. To boost labeling, we designed PFC nanoemulsion imaging probes displaying a cell-penetrating peptide, namely the transactivating transcription sequence (TAT) of the human immunodeficiency virus. We report optimized synthesis schemes for preparing TAT co-surfactant to complement the common surfactants used in PFC nanoemulsion preparations.

METHODS

We performed ex vivo labeling of primary human chimeric antigen receptor (CAR) T cells with nanoemulsion. Intracellular labeling was validated using electron microscopy and confocal imaging. To detect signal enhancement in vivo, labeled CAR T cells were intra-tumorally injected into mice bearing flank glioma tumors.

RESULTS

By incorporating TAT into the nanoemulsion, a labeling efficiency of ~10¹² fluorine atoms per CAR T cell was achieved that is a >8-fold increase compared to nanoemulsion without TAT while retaining high cell viability (~84%). Flow cytometry phenotypic assays show that CAR T cells are unaltered after labeling with TAT nanoemulsion, and in vitro tumor cell killing assays display intact cytotoxic function. The ¹⁹ F MRI signal detected from TAT-labeled CAR T cells was 8 times higher than cells labeled with PFC without TAT.

CONCLUSION

The peptide-PFC nanoemulsion synthesis scheme presented can significantly enhance cell labeling and imaging sensitivity and is generalizable for other targeted imaging probes.

A dimerization-based fluorogenic dye-aptamer module for RNA imaging in live cells

Live-cell imaging of RNA has remained a challenge because of the lack of naturally fluorescent RNAs. Recently developed RNA aptamers that can light-up small fluorogenic dyes could overcome this limitation, but they still suffer from poor brightness and photostability. Here, we propose a concept of cell-permeable fluorogenic dimer of sulforhodamine B dyes (Gemini-561) and corresponding dimerized aptamer (o-Coral) that can drastically enhance performance of the current RNA imaging method. The unprecedented brightness and photostability together with high affinity of this complex allowed, for the first time, direct fluorescence imaging in live mammalian cells of RNA polymerase-III transcription products as well as messenger RNAs labelled with a single copy of the aptamer, i.e. without tag multimerization. The developed fluorogenic module enables fast and sensitive detection of RNA inside live cells, while the proposed design concept opens the route to new generation of ultrabright RNA probes.

Mechanical regulation of nucleocytoplasmic translocation in mesenchymal stem cells: characterization and methods for investigation

Mesenchymal stem cells (MSCs) have immune-modulatory and tissue-regenerative properties that make them a suitable and promising tool for cell-based therapy application. Since the bio-chemo-mechanical environment influences MSC fate and behavior, the understanding of the mechanosensors involved in the transduction of mechanical inputs into chemical signals could be pivotal. In this context, the nuclear pore complex is a molecular machinery that is believed to have a key role in force transmission and in nucleocytoplasmic shuttling regulation. To fully understand the nuclear pore complex role and the nucleocytoplasmic transport dynamics, recent advancements in fluorescence microscopy provided the possibility to study passive and facilitated nuclear transports also in mechanically stimulated cell culture conditions. Here, we review the current available methods for the investigation of nucleocytoplasmic shuttling, including photo-perturbation-based approaches, fluorescence correlation spectroscopy, and single-particle tracking techniques. For each method, we analyze the advantages, disadvantages, and technical limitations. Finally, we summarize the recent knowledge on mechanical regulation of nucleocytoplasmic translocation in MSC, the relevant progresses made so far, and the future perspectives in the field.

Evaluation of Structure-Function Relationships of Aggregation-Induced Emission Luminogens for Simultaneous Dual Applications of Specific Discrimination and Efficient Photodynamic Killing of Gram-Positive Bacteria

Bacterial infectious diseases, especially those caused by Gram-positive bacteria, have been seriously threatening human health. Preparation of a multifunctional system bearing both rapid bacterial differentiation and effective antibacterial effects is highly in demand, but remains a severe challenge. Herein, we rationally designed and successfully developed a sequence of aggregation-induced emission luminogens (AIEgens) with orderly enhanced D-A strength. Evaluation of structure-function relationships reveals that AIEgens having intrinsic positive charge and proper ClogP value are able to stain Gram-positive bacteria. Meanwhile, one of the presented AIEgens (TTPy) can generate reactive oxygen species (ROS) in extraordinarily high efficiency under white light irradiation due to the smaller singlet-triplet energy gap. Thanks to the NIR emission, excellent specificity to Gram-positive bacteria, and effective ROS generation efficiency, TTPy has been proved to perform well in selective photodynamic killing of Gram-positive bacteria in vitro, such as S. aureus and S. epidermidis, even in S. aureus-infected rat wounds.

Site-Directed Fluorescence Approaches for Dynamic Structural Biology of Membrane Peptides and Proteins

Membrane proteins mediate a number of cellular functions and are associated with several diseases and also play a crucial role in pathogenicity. Due to their importance in cellular structure and function, they are important drug targets for ~60% of drugs available in the market. Despite the technological advancement and recent successful outcomes in determining the high-resolution structural snapshot of membrane proteins, the mechanistic details underlining the complex functionalities of membrane proteins is least understood. This is largely due to lack of structural dynamics information pertaining to different functional states of membrane proteins in a membrane environment. Fluorescence spectroscopy is a widely used technique in the analysis of functionally-relevant structure and dynamics of membrane protein. This review is focused on various site-directed fluorescence (SDFL) approaches and their applications to explore structural information, conformational changes, hydration dynamics, and lipid-protein interactions of important classes of membrane proteins that include the pore-forming peptides/proteins, ion channels/transporters and G-protein coupled receptors.

Formation of the inclusion complex of water soluble fluorescent calix[4]arene and naringenin: solubility, cytotoxic effect and molecular modeling studies

Naringenin is considered as an important flavonoid in phytochemistry because of its important effect on cancer chemoprevention. Unfortunately its poor solubility has restricted its therapeutic applications. In this study, an efficient water-soluble fluorescent calix[4]arene (compound 5) was synthesized as host macromolecule to increase solubility and cytotoxicity in cancer cells of water-insoluble naringenin as well as to clarify localization of naringenin into the cells. Complex formed by host-guest interaction between compound 5 and naringenin was analyzed with UV-visible, fluorescence, FTIR spectroscopic techniques and molecular modeling studies. Stern-Volmer analysis showed binding constant value of K_sv 3.5 × 10⁷ M^-1 suggesting strong interaction between host and guest. Binding capacity shows 77% of naringenin was loaded on compound 5. Anticarcinogenic effects of naringenin complex were evaluated on human colorectal carcinoma cells (DLD-1) and it was found that 5-naringenin complex inhibits proliferation of DLD-1 cells 3.4-fold more compared to free naringenin. Fluorescence imaging studies show 5-naringenin complex was accumulated into the cytoplasm instead of the nucleus. Increased solubility and cytotoxicity of naringenin with fluorescent calix[4]arene makes it one of the potential candidates as a therapeutic enhancer. For deep understanding of host-guest interaction mechanisms, complementary multiscale molecular modeling studies were also carried out.Communicated by Ramaswamy H. Sarma.

Using Tetracysteine-Tagged TDP-43 with a Biarsenical Dye To Monitor Real-Time Trafficking in a Cell Model of Amyotrophic Lateral Sclerosis

TAR DNA-binding protein 43 (TDP-43) has been identified as the major constituent of the proteinaceous inclusions that are characteristic of most forms of amyotrophic lateral sclerosis (ALS) and ubiquitin positive frontotemporal lobar degeneration (FTLD). Wild type TDP-43 inclusions are a pathological hallmark of >95% of patients with sporadic ALS and of the majority of familial ALS cases, and they are also found in a significant proportion of FTLD cases. ALS is the most common form of motor neuron disease, characterized by progressive weakness and muscular wasting, and typically leads to death within a few years of diagnosis. To determine how the translocation and misfolding of TDP-43 contribute to ALS pathogenicity, it is crucial to define the dynamic behavior of this protein within the cellular environment. It is therefore necessary to develop cell models that allow the location of the protein to be defined. We report the use of TDP-43 with a tetracysteine tag for visualization using fluorogenic biarsenical compounds and show that this model displays features of ALS observed in other cell models. We also demonstrate that this labeling procedure enables live-cell imaging of the translocation of the protein from the nucleus into the cytosol.

Aggregation-Induced Emission Luminogens for Activity-Based Sensing

Fluorescent sensing has emerged as a powerful tool for detecting various analytes and visualizing numerous biological processes by virtue of its superb sensitivity, rapidness, excellent temporal resolution, easy operation, and low cost. Of particular interest is activity-based sensing (ABS), a burgeoning sensing approach that is actualized on the basis of dynamic molecular reactivity rather than conventional lock-and-key molecular recognition. ABS has been recognized to possess some distinct advantages, such as high specificity, extraordinary sensitivity, and accurate signal outputs. A majority of ABS sensors are constructed by modifying conventional fluorogens, which are strongly emissive when molecularly dissolved in solvents but experience emission quenching upon aggregate formation or concentration increase. The aggregation-caused quenching (ACQ) phenomenon leads to a limited amount of labeling of the analyte with the sensor and low photobleaching resistance, which could impede practical applications of the ABS protocol. As an anti-ACQ phenomenon, aggregation-induced emission (AIE) provides a straightforward solution to the ACQ problem. Thanks to their intrinsic advantages, including high photobleaching threshold, high signal-to-noise ratio, fluorescence turn-on nature, and large Stokes shift, AIE-active luminogens (AIEgens) represent a class of extraordinary fluorogen alternatives for the ABS protocol. The use of AIEgen-involved ABS can integrate the advantages of AIEgens and ABS, and additionally, the AIE process offers some unique properties to the ABS approach. For instance, in some cases of water-soluble AIEgen-involved ABS, chemical reaction not only leads to a chang in the emission color of the AIEgens but also causes solubility variations, which could result in specific "light-up" signaling. In this Account, the basic concepts and mechanistic insights of the ABS approach involving the AIE principle are briefly summarized, and then we highlight the new breakthroughs, seminal studies, and trends in the area that have been most recently reported by our group. This emerging sensing protocol has been successfully utilized for detecting an array of targets including ions, small molecules, biomacromolecules, and microenvironments, all of which closely relate to human health, medical, and public concerns. These detections are smoothly achieved on the basis of various reactions (e.g., hydrolysis, boronate cleavage, dephosphorylation, addition, cyclization, and rearrangement reactions) through different sensing principles. In these studies, the AIEgen-involved ABS strategy generally shows good biocompatibility, high selectivity, excellent reliability and high signal contrast, strongly indicating its great potential for high-tech innovations in the sensing field, among which bioprobing is of particular interest. With this Account, we hope to spark new ideas and inspire new endeavors in this emerging research area, further promoting state-of-the-art developments in the field of sensing.

Ultrabright and Stable Luminescent Labels for Correlative Cathodoluminescence Electron Microscopy Bioimaging

The mechanistic understanding of structure-function relationships in biological systems heavily relies on imaging. While fluorescence microscopy allows the study of specific proteins following their labeling with fluorophores, electron microscopy enables holistic ultrastructural analysis based on differences in electron density. To identify specific proteins in electron microscopy, immunogold labeling has become the method of choice. However, the distinction of immunogold-based protein labels from naturally occurring electron dense granules and the identification of several different proteins in the same sample remain challenging. Correlative cathodoluminescence electron microscopy (CCLEM) bioimaging has recently been suggested to provide an attractive alternative based on labels emitting characteristic light. While luminescence excitation by an electron beam enables subdiffraction imaging, structural damage to the sample by high-energy electrons has been identified as a potential obstacle. Here, we investigate the feasibility of various commonly used luminescent labels for CCLEM bioimaging. We demonstrate that organic fluorophores and semiconductor quantum dots suffer from a considerable loss of emission intensity, even when using moderate beam voltages (2 kV) and currents (0.4 nA). Rare-earth element-doped nanocrystals, in particular Y₂O₃:Tb³⁺ and YVO₄:Bi³⁺,Eu³⁺ nanoparticles with green and orange-red emission, respectively, feature remarkably high brightness and stability in the CCLEM bioimaging setting. We further illustrate how these nanocrystals can be readily differentiated from morphologically similar naturally occurring dense granules based on optical emission, making them attractive nanoparticle core materials for molecular labeling and (multi)color CCLEM.

Screening protocol for the identification of modulators by immunofluorescent cell-based assay

High-throughput assays are a common strategy for the identification of compounds able to modulate a certain cellular activity. Here, we show an automatized analysis platform for the quantification of nuclear foci as inhibitory effect of compounds on a target protein labeled by fluorescent antibodies. Our experience led us to a fast analysis platform that combines cell-based assays, high-content screening, and confocal microscopy, with an automatic and user-friendly statistical analysis of plate-based assays including positive and negative controls, able to identify inhibitory effect of compounds tested together with the Z-prime and Window of individual plate-based assays to assess the reliability of the results. The platform integrates a web-based tool implemented in Pipeline Pilot and R, and allows computing the inhibition values of different parameters obtained from the high-content screening and confocal microscopy analysis. This facilitates the exploration of the results using the different parameters, providing information at different levels as the number of foci observed, the sum of intensity of foci, area of foci, etc, the detection and filtering of outliers over the assay plate, and finally providing a set of statistics of the parameters studied together with a set of plots that we believe significantly helps to the interpretation of the assay results.

Monte Carlo Simulation of Brownian Motion using a Piezo-Actuated Microscope Stage

Single particle tracking is a powerful tool for studying and understanding the motions of biological macromolecules integral to cellular processes. In the past three decades there has been continuous and rapid development of these techniques in both optical microscope design and in algorithms to estimate the statistics and positions of the molecule's trajectory. Although there has been great progress, comparison between different microscope configurations and estimation algorithms has been difficult beyond simulated data. In this paper we explore using a piezo actuated microscope stage to reproduce Brownian motion. Our goal is to use this as a tool to test performance of single particle tracking optical microscopes and estimation algorithms. In this study, Monte Carlo simulations were used to assess the ability of piezo actuated microscope stages for reproducing Brownian motion. Surprisingly, the dynamics of the stage together with configuration of the system allow for preservation of the Brownian motion statistics. Further, feed forward model inverse control allows for low error tracking of Brownian motion trajectories over a wide range of diffusion constants, varying stage response times, and trajectory discrete time steps. These results show great promise in using a piezo actuated microscope stage for testing single particle tracking experimental setups.

Self-assembled multilayer surfaces of highly fluorescent spirobifluorene-based dye for label-free protein recognition

The preparation of smart surfaces for protein detection is a challenging field of research. With the aim to achieve label-free detection in the solid state, we report on the organic surface functionalization for protein recognition without the need of previous chemical modification of the fluorophore. Layer-by-layer deposition of polyelectrolyte poly(vinyl benzyl tetramethylammonium) chloride (p(VBTMA)Cl) and a tetrasulfonate water-soluble low molecular weight fluorophore (1) based on spirobifluorene leads to modified glass and quartz substrates with outstanding photophysical properties in response to bovine serum albumin (BSA). The absorbance, photoluminescence as well as the fluorescence lifetimes were recorded for all surfaces. The surface structure and height of the different number of bilayers polymer/fluorophore were characterized by atomic force microscopy and ellipsometry. The results show linear trends in the absorption, fluorescence and height of the multilayer with increasing number of functionalization steps. Upon incubation with BSA the multilayer shows an increase in fluorescence up to 3-fold, which is also detectable with the naked eye. In conclusion, we report an easy, fast and biocompatible approach for the construction of protein sensors by self-assembly.

Role of Hydrogen Bonding in Green Fluorescent Protein-like Chromophore Emission

The fluorescence emission from green fluorescent protein (GFP) is known to be heavily influenced by hydrogen bonding between the core fluorophore and the surrounding side chains or water molecules. Yet how to utilize this feature for modulating the fluorescence of GFP chromophore or GFP-like fluorophore still remains elusive. Here we present theoretical calculations to predict how hydrogen bonding could influence the excited states of the GFP-like fluorophores. These studies provide both a new perspective for understanding the photophysical properties of GFP as well as a solid basis for the rational design of GFP-based fluorophores.

Recognition of Proteins by Metal Chelation-Based Fluorescent Probes in Cells

Fluorescent probes such as thiol-reactive and Ni2+-nitrilotriacetate (NTA) based probes provide a powerful toolbox for real-time visualization of a protein and a proteome in living cells. Herein, we first went through basic principles and applications of thiol-reactive based probes in protein imaging and recognition. We then summarize a family of metal-NTA based fluorescence probes in the visualization of His6-tagged protein and identification of metalloproteins at proteome-wide scale. The pros and cons of the probes, as well as ways to optimize them, are discussed.

Biomacromolecule-Functionalized AIEgens for Advanced Biomedical Studies

The advances in bioinformatics and biomedicine have promoted the development of biomedical imaging and theranostic systems to respectively extend the endogenous biomarker imaging with high contrast and enhance the therapeutic effect with high efficiency. The emergence of biomacromolecule-functionalized aggregation-induced emitters (AIEgens), utilizing AIEgens, and biomacromolecules (nucleic acids, peptides, glycans, and lipids), displays specific targeting ability to cancer cell, improved biocompatibility, reduced toxicity, enhanced therapeutic effect, and so forth. This review summarizes the rational design of biomacromolecule-functionalized AIEgens and their biomedical applications in recent ten years, including high-resolution optical imaging of cell, tissue, and small animal model with low background; the biomarker detection for early diagnosis and prognosis; the delivery and monitoring of prodrugs; image-guide photodynamic therapy and its combination with chemotherapy. Through illustrating their functional mechanisms and application, it is hoped that this review would open up a completely new train of research thought for attracted researchers in various fields.

Background-free two-photon fluorescence readout via a three-photon charge-state modulation of nitrogen-vacancy centers in diamond

We demonstrate that a background-free readout of two-photon fluorescence from nitrogen-vacancy (NV) centers in a strongly fluorescing environment can be accomplished by all-optical means via a multiphoton charge-state modulation of NV centers in a mixture of negatively charged and neutral NV centers. A 100 fs, 1060 nm output of an ytterbium fiber laser is ideally suited for this modality of multiphoton microscopy, providing, as our experiments show, an efficient two-photon excitation of both NV^- and NV⁰ charge states, but keeping the nonlinearity of n-photon ionization needed for NV^-/NV⁰ charge-state modulation to a minimum, n=3.

A real-time, click chemistry imaging approach reveals stimulus-specific subcellular locations of phospholipase D activity

The fidelity of signal transduction requires spatiotemporal control of the production of signaling agents. Phosphatidic acid (PA) is a pleiotropic lipid second messenger whose modes of action differ based on upstream stimulus, biosynthetic source, and site of production. How cells regulate the local production of PA to effect diverse signaling outcomes remains elusive. Unlike other second messengers, sites of PA biosynthesis cannot be accurately visualized with subcellular precision. Here, we describe a rapid, chemoenzymatic approach for imaging physiological PA production by phospholipase D (PLD) enzymes. Our method capitalizes on the remarkable discovery that bulky, hydrophilic trans-cyclooctene-containing primary alcohols can supplant water as the nucleophile in the PLD active site in a transphosphatidylation reaction of PLD's lipid substrate, phosphatidylcholine. The resultant trans-cyclooctene-containing lipids are tagged with a fluorogenic tetrazine reagent via a no-rinse, inverse electron-demand Diels-Alder (IEDDA) reaction, enabling their immediate visualization by confocal microscopy in real time. Strikingly, the fluorescent reporter lipids initially produced at the plasma membrane (PM) induced by phorbol ester stimulation of PLD were rapidly internalized via apparent nonvesicular pathways rather than endocytosis, suggesting applications of this activity-based imaging toolset for probing mechanisms of intracellular phospholipid transport. By instead focusing on the initial 10 s of the IEDDA reaction, we precisely pinpointed the subcellular locations of endogenous PLD activity as elicited by physiological agonists of G protein-coupled receptor and receptor tyrosine kinase signaling. These tools hold promise to shed light on both lipid trafficking pathways and physiological and pathological effects of localized PLD signaling.

Aggregation-induced emission fluorescent probe for monitoring endogenous alkaline phosphatase in living cells

Alkaline phosphatase (ALP) is a non-specific phosphate monoesterase and often regarded as an important biomarker of hypothyroidism and hepatobiliary diseases in medical diagnosis. In-situ detection of endogenous ALP and exploration of the distribution of ALP in cells are of great importance for the diagnosis of diseases associated with ALP. In this work, we designed and synthesized an aggregation-induced emission (AIE) fluorescent probe, (E)-2-(((9H-fluoren-9-ylidene) hydrazono)methyl)phenyl dihydrogen phosphate (FAS-P), that can respond to ALP with a remarkable large Stokes shift (>200 nm) based on excited state intramolecular proton transfer (ESIPT) mechanism. The probe FAS-P has high selectivity and sensitivity to the detection of ALP. And there is a linear relationship between the fluorescence intensity of FAS-P and ALP activity in the range of 1-100 U L^-1, the limit of detection (LOD) is as low as 0.6 U L^-1. More importantly, we successfully applied FAS-P to detect ALP in living cells and the monitoring of ALP in real time.

Photoactivatable Fluorogenic Labeling via Turn-On "Click-Like" Nitroso-Diene Bioorthogonal Reaction

Fluorogenic labeling enables imaging cellular molecules of interest with minimal background. This process is accompanied with the notable increase of the quantum yield of fluorophore, thus minimizing the background signals from unactivated profluorophores. Herein, the development of a highly efficient and bioorthogonal nitroso-based Diels-Alder fluorogenic reaction is presented and its usefulness is validated as effective and controllable in fluorescent probes and live-cell labeling strategies for dynamic cellular imaging. It is demonstrated that nitroso-based cycloaddition is an efficient fluorogenic labeling tool through experiments of further UV-activatable fluorescent labeling on proteins and live cells. The ability of tuning the fluorescence of labeled proteins by UV-irradiation enables selective activation of proteins of interest in a particular cell compartment at a given time point, while leaving the remaining labeled molecules untouched.

High-resolution nonlinear fluorescence microscopy using repetitive stimulated transition based on the saturation of stimulated emission implemented with two-color continuous-wave lasers

High-resolution nonlinear fluorescence (NF) microscopy that utilizes repetitive stimulated transition due to the saturation of stimulated emission caused by two-color continuous-wave lasers was developed. The resulting NF signal, detected via the lock-in technique, is produced by the multiplicative combination of incident beams, which results in an improvement of the optical resolution. The proposed method is demonstrated to have a three-dimensional optical resolution superior to that of conventional NF microscopy. The results of biological imaging reveal the feasibility and superiority of the proposed method.

Crystal structure and spectral studies of green fluorescent protein (GFP) chromophore analogue ethyl 2-[(4Z)-(6-hydroxy naphthalen-2-yl) methylene)-2-methyl-5-oxo-4,5-di hydro-1H-imidazol-1-yl] acetate

Synthetically modified green fluorescent protein chromophore derivative was prepared, its crystal structure and spectral properties were studied. Crystal data for C19H18N2O4: triclinic, space group P-1 (no. 2), a = 8.2506(17) Å, b = 11.934(2) Å, c = 17.461(4) Å, α = 102.89(3)°,   β = 94.62(3)°, γ = 96.68(3)°, V = 1654.5(6) Å3, Z = 4, T = 173(2) K, μ(MoKα) = 0.096 mm-1, Dcalc = 1.358 g/cm3, 7227 reflections measured (4.722° ≤ 2Θ ≤ 53.996°), 7227 unique (Rint = 0.0453, Rsigma = 0.0662) which were used in all calculations. The final R1 was 0.0561 (I > 2σ(I)) and wR2 was 0.1658 (all data). The single crystal structure showed, the benzylidine moiety adopts Z-conformation in solid state and the molecules were associated by various O−H···O and C−H···O non-covalent interactions. The UV absorption-emission spectral analysis indicated that a significant red shift of emission observed at alkaline pH indicating its utility for live cell imaging applications.

Chemistry of Photosensitive Fluorophores for Single-Molecule Localization Microscopy

Development of single-molecule localization microscopy (SMLM) has sparked a revolution in biological imaging, allowing "super-resolution" fluorescence microscopy below the diffraction limit of light. The past decade has seen an explosion in not only optical hardware for SMLM but also the development or repurposing of fluorescent proteins and small-molecule fluorescent probes for this technique. In this review, written by chemists for chemists, we detail the history of single-molecule localization microscopy and collate the collection of probes with demonstrated utility in SMLM. We hope it will serve as a primer for probe choice in localization microscopy as well as an inspiration for the development of new fluorophores that enable imaging of biological samples with exquisite detail.

Label-free Imaging and Bending Analysis of Microtubules by ROCS Microscopy and Optical Trapping

Mechanical manipulation of single cytoskeleton filaments and their monitoring over long times is difficult because of fluorescence bleaching or phototoxic protein degradation. The integration of label-free microscopy techniques, capable of imaging freely diffusing, weak scatterers such as microtubules (MTs) in real-time, and independent of their orientation, with optical trapping and tracking systems, would allow many new applications. Here, we show that rotating-coherent-scattering microscopy (ROCS) in dark-field mode can also provide strong contrast for structures far from the coverslip such as arrangements of isolated MTs and networks. We could acquire thousands of images over up to 30 min without loss in image contrast or visible photodamage. We further demonstrate the combination of ROCS imaging with fast and nanometer-precise 3D interferometric back-focal-plane tracking of multiple beads in time-shared optical traps using acoustooptic deflectors to specifically construct and microrheologically probe small microtubule networks with well-defined geometries. Thereby, we explore the frequency-dependent elastic response of single microtubule filaments between 0.5 Hz and 5 kHz, which allows for investigating their viscoelastic response up to the fourth-order bending mode. Our spectral analysis reveals constant filament stiffness at low frequencies and frequency-dependent stiffening following a power law ∼ω^p with a length-dependent exponent p(L). We find further evidence for the dependence of the MT persistence length on the contour length L, which is still controversially debated. We could also demonstrate slower stiffening at high frequencies for longer filaments, which we believe is determined by the molecular architecture of the MT. Our results shed new light on the nanomechanics of this essential, multifunctional cytoskeletal element and pose new questions about the adaptability of the cytoskeleton.

WellInverter: a web application for the analysis of fluorescent reporter gene data

Background

Fluorescent reporter genes have become widely used for monitoring gene expression in living cells. When a microbial strain carrying a reporter gene is grown in a microplate reader, the fluorescence and the absorbance (optical density) of the culture can be automatically measured every few minutes in a highly parallelized way. The extraction of useful information from the resulting large amounts of data is not easy to achieve, because the fluorescence and absorbance measurements are only indirectly related to promoter activities and protein concentrations, requiring mathematical models of the expression of reporter genes for their interpretation. Although the principles of the analysis of reporter gene data are well-established today, there is a lack of general-purpose bioinformatics tools based on generic measurement models and sound inference procedures. This has motivated the development of WellInverter, a web application based on well-known methods for regularized linear inversion.

Results

We present a new version of WellInverter that considerably improves the performance and usability of the original application. In particular, we have put in place a parallel computing architecture with a load balancer to distribute analysis queries over several back-end servers, we have completely redesigned the graphical user interface to better support the different analysis steps, and we have developed a plug-in system for the parsing of data files produced by microplate readers from different manufacturers. We illustrate the functioning of WellInverter by analyzing data of the expression of a fluorescent reporter gene controlled by a phage promoter in growing Escherichia coli populations. We show that the expression pattern in different growth media, supporting different growth rates, corresponds to the pattern expected for a constitutive gene.

Conclusions

The new version of WellInverter is a robust, easy-to-use and scalable web application, which has been deployed on two publicly accessible web servers and which can also be installed locally. A demo version of the application with two sample datasets is available on-line.

Electronic supplementary material

The online version of this article (10.1186/s12859-019-2920-4) contains supplementary material, which is available to authorized users.

Development of an effective protein-labeling system based on smart fluorogenic probes

Proteins are an important component of living systems and play a crucial role in various physiological functions. Fluorescence imaging of proteins is a powerful tool for monitoring protein dynamics. Fluorescent protein (FP)-based labeling methods are frequently used to monitor the movement and interaction of cellular proteins. However, alternative methods have also been developed that allow the use of synthetic fluorescent probes to target a protein of interest (POI). Synthetic fluorescent probes have various advantages over FP-based labeling methods. They are smaller in size than the fluorescent proteins, offer a wide variety of colors and have improved photochemical properties. There are various chemical recognition-based labeling techniques that can be used for labeling a POI with a synthetic probe. In this review, we focus on the development of protein-labeling systems, particularly the SNAP-tag, BL-tag, and PYP-tag systems, and understanding the fluorescence behavior of the fluorescently labeled target protein in these systems. We also discuss the smart fluorogenic probes for these protein-labeling systems and their applications. The fluorogenic protein labeling will be a useful tool to investigate complex biological phenomena in future work on cell biology.

Multi-Object Portion Tracking in 4D Fluorescence Microscopy Imagery with Deep Feature Maps

3D fluorescence microscopy of living organisms has increasingly become an essential and powerful tool in biomedical research and diagnosis. An exploding amount of imaging data has been collected, whereas efficient and effective computational tools to extract information from them are still lagging behind. This is largely due to the challenges in analyzing biological data. Interesting biological structures are not only small, but are often morphologically irregular and highly dynamic. Although tracking cells in live organisms has been studied for years, existing tracking methods for cells are not effective in tracking subcellular structures, such as protein complexes, which feature in continuous morphological changes including split and merge, in addition to fast migration and complex motion. In this paper, we first define the problem of multi-object portion tracking to model the protein object tracking process. A multi-object tracking method with portion matching is proposed based on 3D segmentation results. The proposed method distills deep feature maps from deep networks, then recognizes and matches objects' portions using an extended search. Experimental results confirm that the proposed method achieves 2.96% higher on consistent tracking accuracy and 35.48% higher on event identification accuracy than the state-of-art methods.

Green Fluorescent Probe for Imaging His6-Tagged Proteins Inside Living Cells

Small molecule-based fluorescent probes offer great opportunities for specifically tracking proteins in living systems with minimal perturbation on the protein function and localization. Herein, we report a small green fluorescent probe (Ni²⁺- NTA-AF) consisting of a Ni²⁺-NTA moiety, a fluorescein, and an arylazide group, that binds specifically to His₆-tagged proteins with fluorescence enhancement in vitro upon photoactivation of the arylazide group. Importantly, the probe can cross the cell membranes and stoichiometrically label His₆-tagged proteins rapidly (∼15 min) in living prokaryotic and eukaryotic cells exemplified by a DNA repair protein Xeroderma pigmentosum group A (XPA). Using the probe, we successfully visualized Sirtuin 5, which is localized to the mitochondria. This probe exhibits high quantum yields and improved solubility, offering a new opportunity for imaging intracellular His₆-tagged proteins inside living cells with better contrast.