Protein sensing in living cells by molecular rotor-based fluorescence-switchable chemical probes

Fluorescent, phosphorescent, magnetic resonance contrast and radioactive tracer labelling of extracellular vesicles

This review focusses on the significance of fluorescent, phosphorescent labelling and tracking of extracellular vesicles (EVs) for unravelling their biology, pathophysiology, and potential diagnostic and therapeutic uses. Various labeling strategies, such as lipid membrane, surface protein, luminal, nucleic acid, radionuclide, quantum dot labels, and metal complex-based stains, are evaluated for visualizing and characterizing EVs. Direct labelling with fluorescent lipophilic dyes is simple but generally lacks specificity, while surface protein labelling offers selectivity but may affect EV-cell interactions. Luminal and nucleic acid labelling strategies have their own advantages and challenges. Each labelling approach has strengths and weaknesses, which require a suitable probe and technique based on research goals, but new tetranuclear polypyridylruthenium(II) complexes as phosphorescent probes have strong phosphorescence, selective staining, and stability. Future research should prioritize the design of novel fluorescent probes and labelling platforms that can significantly enhance the efficiency, accuracy, and specificity of EV labeling, while preserving their composition and functionality. It is crucial to reduce false positive signals and explore the potential of multimodal imaging techniques to gain comprehensive insights into EVs.

Fluorogenic cell surface glycan labelling with fluorescence molecular rotor dyes and nucleic acid stains

We show that covalent labelling of sialic acids on live cell surfaces or mucin increases the fluorescence of the fluorescence molecular rotors (FMRs) CCVJ, Cy3 and thioazole orange, enabling wash-free imaging of cell surfaces. Dual labelling with an FMR and an environmentally insensitive dye allows detection of changes that occur, for example, when cross-linking is altered.

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

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

A chloromethyl-triazole fluorescent chemosensor for O6-methylguanine DNA methyltransferase

Fluorescent chemosensors offer a direct means of measuring enzyme activity for cancer diagnosis, predicting drug resistance, and aiding in the discovery of new anticancer drugs. O6-methylguanine DNA methyltransferase (MGMT) is a predictor of resistance towards anticancer alkylating agents such as temozolomide. Using the fluorescent molecular rotor, 9-(2-carboxy-2-cyanovinyl)julolidine (CCVJ), we synthesized, and evaluated a MGMT fluorescent chemosensor derived from a chloromethyl-triazole covalent inhibitor, AA-CW236, a non-pseudosubstrate of MGMT. Our fluorescence probe covalently labelled the MGMT active site C145, producing a 18-fold increase in fluorescence. Compared to previous fluorescent probes derived from a substrate-based inhibitor, our probe had improved binding and reaction rate. Overall, our chloromethyl triazole-based fluorescence MGMT probe is a promising tool for measuring MGMT activity to predict temozolomide resistance.

Integration of Demethylation-Activated DNAzyme with a Single Quantum Dot Nanosensor for Sensitive Detection of O6-Methylguanine DNA Methyltransferase in Breast Tissues

O6-Methylguanine-DNA-methyltransferase (MGMT) is a demethylation protein that dynamically regulates the O6-methylguanine modification (O6 MeG), and dysregulated MGMT is implicated in various malignant tumors. Herein, we integrate demethylation-activated DNAzyme with a single quantum dot nanosensor to sensitively detect MGMT in breast tissues. The presence of MGMT induces the demethylation of the O6 MeG-caged DNAzyme and the restoration of catalytic activity. The activated DNAzyme then specifically cleaves the ribonucleic acid site of hairpin DNA to expose toehold sequences. The liberated toehold sequence may act as a primer to trigger a cyclic exponential amplification reaction for the generation of enormous signal strands that bind with the Cy5/biotin-labeled probes to form sandwich hybrids. The assembly of sandwich hybrids onto 605QD obtains 605QD-dsDNA-Cy5 nanostructures, inducing efficient FRET between the 605QD donor and Cy5 acceptor. Notably, the introduction of a mismatched base in hairpin DNA can greatly minimize the background and improve the signal-to-noise ratio. This nanosensor achieves a dynamic range of 1.0 × 10-8 to 0.1 ng/μL and a detection limit of 155.78 aM, and it can screen MGMT inhibitors and monitor cellular MGMT activity with single-cell sensitivity. Moreover, it can distinguish the MGMT level in tissues of breast cancer patients and healthy persons, holding great potential in clinical diagnostics and epigenetic research studies.

Imaging of Carbonic Anhydrase Level in Epilepsy with an Environment-Sensitive Fluorescent Probe

Carbonic anhydrases (CAs) participate in various physiological and pathological activities by catalyzing the interconversion between carbon dioxide and bicarbonate ions. Under normal circumstances, they guarantee that the relevant biological reactions in our body occur within an appropriate time scale. Abnormal expression or activity alteration of CAs is closely related to the pathogenesis of diverse diseases. This work reports an inhibitor-directed fluorescent probe FMRs-CA for the detection of CAs. Excellent selectivity, favorable biocompatibility, and desirable blood-brain barrier (BBB) penetration endow the probe with the ability to image the fluctuation of CAs in cells and mice. We achieved in situ visualization of the increased CAs in hypoxic cells with this probe. Additionally, probe FMRs-CA was mainly enriched within the liver and gradually metabolized by the liver. With the help of FMRs-CA, the increase of CAs in epileptic mouse brains was revealed first from the perspective of imaging, providing the mechanism connection between abnormal CA expressions and epilepsy.

Design of a palette of SNAP-tag mimics of fluorescent proteins and their use as cell reporters

Naturally occurring fluorescent proteins (FPs) are the most widely used tools for tracking cellular proteins and sensing cellular events. Here, we chemically evolved the self-labeling SNAP-tag into a palette of SNAP-tag mimics of fluorescent proteins (SmFPs) that possess bright, rapidly inducible fluorescence ranging from cyan to infrared. SmFPs are integral chemical-genetic entities based on the same fluorogenic principle as FPs, i.e., induction of fluorescence of non-emitting molecular rotors by conformational locking. We demonstrate the usefulness of these SmFPs in real-time tracking of protein expression, degradation, binding interactions, trafficking, and assembly, and show that these optimally designed SmFPs outperform FPs like GFP in many important ways. We further show that the fluorescence of circularly permuted SmFPs is sensitive to the conformational changes of their fusion partners, and that these fusion partners can be used for the development of single SmFP-based genetically encoded calcium sensors for live cell imaging.

Molecular rotors in haemoglobin and bovine serum albumin proteins

Molecular rotors are fluorescent viscosity probes and their response in simple fluids is known to be a Förster-Hoffman power law, allowing the viscosity of the medium to be quantified by its fluorescence intensity. They are attractive probes in biological media, usually consisting of proteins, but how does a molecular rotor behave in a protein solution? The response of the DASPI molecular rotor is compared in two globular protein solutions of similar size, haemoglobin (Hb) and bovine serum albumin, one absorbent, the other not. In absorbent Hb, a model validated by experiments in triangular geometry allows one to correct the absorbing effect and to compare the rotor response in both proteins. With concomitant microrheology measurements, we investigate the relation between the DASPI fluorescence intensity and solution viscosity. In protein solutions, we show that viscosity is no longer the parameter determining the rotor response in contrast to simple fluids. Varying the viscosity by concentration or temperature is not equivalent, and the Förster-Hoffmann power laws do not apply when the solution concentration varies. We show that the concentration regime of the protein solution, semi-dilute or concentrated, determines the sensitivity of the rotor to its environment.

A small molecule antagonist of SMN disrupts the interaction between SMN and RNAP II

Survival of motor neuron (SMN) functions in diverse biological pathways via recognition of symmetric dimethylarginine (Rme2s) on proteins by its Tudor domain, and deficiency of SMN leads to spinal muscular atrophy. Here we report a potent and selective antagonist with a 4-iminopyridine scaffold targeting the Tudor domain of SMN. Our structural and mutagenesis studies indicate that both the aromatic ring and imino groups of compound 1 contribute to its selective binding to SMN. Various on-target engagement assays support that compound 1 specifically recognizes SMN in a cellular context and prevents the interaction of SMN with the R1810me2s of RNA polymerase II subunit POLR2A, resulting in transcription termination and R-loop accumulation mimicking SMN depletion. Thus, in addition to the antisense, RNAi and CRISPR/Cas9 techniques, potent SMN antagonists could be used as an efficient tool to understand the biological functions of SMN.

A NIR molecular rotor photosensitizer for efficient PDT and synchronous mitochondrial viscosity imaging

Herein, two mitochondria-targeting photosensitizers (PSs, CCVJ-Mito-1 and CCVJ-Mito-2) that exhibit a turn-on fluorescence response towards increasing viscosity are reported. Notably, CCVJ-Mito-2 exhibits absorption in the near-infrared (NIR) region, and can be employed as a NIR PS targeting mitochondria and a fluorescent probe for tracking mitochondrial viscosity changes during photodynamic therapy (PDT). This dual functional PS can help to shed light on the dynamic changes of the cellular microenvironment during PDT and further guide the PDT process.

A simple and rapid mix-and-read assay for sensitive detection of O6-methylguanine DNA methyltransferase

We have developed a simple and rapid mix-and-read assay for the sensitive detection of O⁶-methylguanine DNA methyltransferase (MGMT) activity based on exonuclease III-assisted signal amplification under completely isothermal conditions (37 °C). This method is very simple and rapid (60 min) with ultrahigh sensitivity and good specificity, and it can detect MGMT activity at the single-cell level. Moreover, this method can be applied for the screening of MGMT inhibitors and the discrimination of MGMT in different cancer cells.

An expanded palette of fluorogenic HaloTag probes with enhanced contrast for targeted cellular imaging

We report the development of HaloTag fluorogens based on dipolar flexible molecular rotor structures. By modulating the electron donating and withdrawing groups, we have tuned the absorption and emission wavelengths to design a palette of fluorogens with emissions spanning the green to red range, opening new possibilities for multicolor imaging. The probes were studied in glycerol and in the presence of HaloTag and exhibited good fluorogenic properties thanks to a viscosity-sensitive emission. In live-cell confocal imaging, the fluorogens yielded only a very low non-specific signal that enabled wash-free targeted imaging of intracellular organelles and proteins with good contrast. Combining experimental studies and theoretical investigation of the protein/fluorogen complexes by molecular dynamics, these results offer new insight into the design of molecular rotor-based fluorogenic HaloTag probes in order to improve reaction rates and the imaging contrast.

Harnessing an emissive guanine surrogate to design small-molecule fluorescent chemosensors of O6-methylguanine-DNA-methyltransferase (MGMT)

The fluorescence properties of an emissive guanine surrogate, thienoguanine (thGN, 2-aminothieno[3,4-d]pyrimidin-4(3H)-one), were exploited to design two real-time chemosensors of O6-methylguanine-DNA-methyltransferase (MGMT), a key DNA repair enzyme involved in the resistance to DNA-alkylating anti-cancer drugs though direct reversal of O6-alkylated guanine adducts.

Design and Synthesis of Fluorophore-Tagged Disparlure Enantiomers to Study Pheromone Enantiomer Discrimination in the Pheromone-Binding Proteins from the Gypsy Moth, Lymantria dispar

Fluorescent analogues of the gypsy moth sex pheromone (+)-disparlure (1) and its enantiomer (-)-disparlure (ent-1) were designed, synthesized, and characterized. The fluorescently labelled analogues 6-FAM (+)-disparlure and 1a 6-FAM (-)-disparlure ent-1a were prepared by copper-catalyzed azide-alkyne cycloaddition of disparlure alkyne and 6-FAM azide. These fluorescent disparlure analogues 1a and ent-1a were used to measure disparlure binding to two pheromone-binding proteins from the gypsy moth, LdisPBP1 and LdisPBP2. The fluorescence binding assay showed that LdisPBP1 has a stronger affinity for 6-FAM (-)-disparlure ent-1a, whereas LdisPBP2 has a stronger affinity for 6-FAM (+)-disparlure 1a, consistent with findings from previous studies with disparlure enantiomers. The 6-FAM disparlure enantiomers appeared to be much stronger ligands for LdisPBPs, with binding constants (K_d) in the nanomolar range, compared to the fluorescent reporter 1-NPN (which had K_d values in the micromolar range). Fluorescence competitive binding assays were used to determine the displacement constant (K_i) for the disparlure enantiomers in competition with fluorescent disparlure analogues binding to LdisPBP1 and LdisPBP2. The K_i data show that disparlure enantiomers can effectively displace the fluorescent disparlure from the binding pocket of LdisPBPs and, therefore, occupy the same binding site.

Excimer-monomer fluorescence changes by supramolecular disassembly for protein sensing and quantification

A protein binding-induced supramolecular dissociation strategy is developed with the ratio of monomer and excimer fluorescence as the tool for protein sensing and quantification. Due to the "lock-and-key" strategy based on specific ligand-protein binding, the probe exhibits excellent selectivity and quantification accuracy to the protein of interest. The ratiometric approach is immune to interference from extrinsic quenchers, while preserving the opportunity to be protein specific.

"Repaired and Activated" DNAzyme Enables the Monitoring of DNA Alkylation Repair in Live Cells

Direct measurement of DNA repair is critical for the annotation of their clinical relevance and the discovery of drugs for cancer therapy. Here we reported a "repaired and activated" DNAzyme (RADzyme) by incorporating a single methyl lesion (O⁶ MeG, 3MeC, or 1MeA) at designated positions through systematic screening. We found that the catalytic activity of the RADzyme was remarkably suppressed and could be restored via enzyme-mediated DNA repair. Benefit from these findings, a fluorogenic RADzyme sensor was developed for the monitoring of MGMT-mediated repair of O⁶ MeG lesion. Importantly, the sensor allowed the evaluation of MGMT repair activity in different cells and under drugs treatment. Furthermore, another RADzyme sensor was engineered for the monitoring of ALKBH2-mediated repair of 3MeC lesion. This strategy provides a simple and versatile tool for the study of the basic biology of DNA repair, clinical diagnosis and therapeutic assessment.

Fluorescent Probes for Imaging Protein Disulfides in Live Organisms

Cellular redox homeostasis is predominantly controlled by the ratio of thiols and disulfides, and reversible thiol-disulfide exchange reactions are fundamental of the biological redox regulation. However, due to the dynamic exchanges of thiols and disulfides, the detection, especially the in situ detection, of protein disulfides (PDS) is challenging. We employ the strategy, i.e., the increase of emission upon an environment-sensitive dye binding to proteins, to design PDS probes and discover a two-photon probe PDSTP590 (S6) that selectively recognizes PDS in live organisms. With the aid of the probe, we further disclose the elevation of PDS in brains of the mouse stroke model.

A fluorescent molecular rotor probe for tracking plasma membranes and exosomes in living cells

A rotor-based probe MRMP-1 was designed and synthesized. MRMP-1 can bind to plasma membranes very quickly and stably with remarkable fluorescence enhancement. It can be used to monitor the dynamic changes in cell membranes in real-time under stimuli conditions. Importantly, MRMP-1 is the first rotor-based fluorescent sensor to label exosomes in living cells.

Self-Immolative Difluorophenyl Ester Linker for Affinity-Based Fluorescence Turn-on Protein Detection

Currently most fluorogenic probes are developed for the analysis of enzymes, where a bond breaking or rearrangement reaction is required to transform a nonfluorescent enzymatic substrate into a fluorescent product. However, this approach cannot be used for proteins that do not possess enzymatic activities. In this article, we show that fluorogenic probes with a self-immolative difluorophenyl ester linker can mimic the bond disassembly processes of fluorogenic enzyme substrates for the rapid analysis of nonenzymatic proteins. Although numerous self-immolative reagents have shown promising applications in sensors, drug delivery systems, and material chemistry, all of them are triggered by either enzymes or small reactive molecules. In our strategy, the probe binds to the protein via a specific protein-ligand interaction, inducing a chemical reaction between the self-immolative linker and an amino acid of the protein, thereby triggering a cascade reaction that leads to the activation and release of the fluorogenic reporter. In contrast, a phenyl ester linker without the difluoro substituent cannot be triggered to release the fluorogenic reporter. With this probe design, live-cell imaging of extracellular and intracellular endogenous tumor marker proteins can be achieved with high selectivity and sensitivity.

A General Strategy to Control Viscosity Sensitivity of Molecular Rotor-Based Fluorophores

Molecular rotor-based fluorophores (RBFs) have been widely used in many fields. However, the lack of control of their viscosity sensitivity limits their application. Herein, this problem is resolved by chemically installing extended π-rich alternating carbon-carbon linkages between the rotational electron donors and acceptors of RBFs. The data reveal that the length of the linkage strongly influences the viscosity sensitivity, likely resulting from varying height of the energy barriers between the fluorescent planar and the dark twisted configurations. Three RBF derivatives that span a wide range of viscosity sensitivities were designed. These RBFs demonstrated, through a dual-color imaging strategy, that they can differentiate misfolded protein oligomers and insoluble aggregates, both in test tubes and live cells. Beyond RBFs, it is envisioned that this chemical mechanism might be generally applicable to a wide range of photoisomerizable and aggregation-induced emission fluorophores.

Fluorogenic Protein Probes with Red and Near-Infrared Emission for Genetically Targeted Imaging*

Fluorogenic probes are important tools to image proteins with high contrast and no wash protocols. In this work, we rationally designed and synthesized a small set of four protein fluorogens with red or near-infrared emission. The fluorophores were characterized in the presence of albumin as a model protein environment and exhibited good fluorogenicity and brightness (fluorescence quantum yield up to 36 %). Once conjugated to a haloalkane ligand, the probes reacted with the protein self-labeling tag HaloTag with a high fluorescence enhancement (up to 156-fold). The spectroscopic properties of the fluorogens and their reaction with HaloTag were investigated experimentally in vitro and with the help of molecular dynamics. The two most promising probes, one in the red and one in the near-infrared range, were finally applied to image the nucleus or actin in live-cell and in wash-free conditions using fluorogenic and chemogenetic targeting of HaloTag fusion proteins.

AggFluor: Fluorogenic Toolbox Enables Direct Visualization of the Multi-Step Protein Aggregation Process in Live Cells

Aberrantly processed or mutant proteins misfold and assemble into a variety of soluble oligomers and insoluble aggregates, a process that is associated with an increasing number of diseases that are not curable or manageable. Herein, we present a chemical toolbox, AggFluor, that allows for live cell imaging and differentiation of complex aggregated conformations in live cells. Based on the chromophore core of green fluorescent proteins, AggFluor is comprised of a series of molecular rotor fluorophores that span a wide range of viscosity sensitivity. As a result, these compounds exhibit differential turn-on fluorescence when incorporated in either soluble oligomers or insoluble aggregates. This feature allows us to develop, for the first time, a dual-color imaging strategy to distinguish unfolded protein oligomers from insoluble aggregates in live cells. Furthermore, we have demonstrated how small molecule proteostasis regulators can drive formation and disassembly of protein aggregates in both conformational states. In summary, AggFluor is the first set of rationally designed molecular rotor fluorophores that evenly cover a wide range of viscosity sensitivities. This set of fluorescent probes not only change the status quo of current imaging methods to visualize protein aggregation in live cells but also can be generally applied to study other biological processes that involve local viscosity changes with temporal and spatial resolutions.

Visualizing and Manipulating Biological Processes by Using HaloTag and SNAP-Tag Technologies

Visualizing and manipulating the behavior of proteins is crucial to understanding the physiology of the cell. Methods of biorthogonal protein labeling are important tools to attain this goal. In this review, we discuss advances in probe technology specific for self-labeling protein tags, focusing mainly on the application of HaloTag and SNAP-tag systems. We describe the latest developments in small-molecule probes that enable fluorogenic (no wash) imaging and super-resolution fluorescence microscopy. In addition, we cover several methodologies that enable the perturbation or manipulation of protein behavior and function towards the control of biological pathways. Thus, current technical advances in the HaloTag and SNAP-tag systems means that they are becoming powerful tools to enable the visualization and manipulation of biological processes, providing invaluable scientific insights that are difficult to obtain by traditional methodologies. As the multiplex of self-labeling protein tag systems continues to be developed and expanded, the utility of these protein tags will allow researchers to address previously inaccessible questions at the forefront of biology.

Molecular Mechanism of Viscosity Sensitivity in BODIPY Rotors and Application to Motion-Based Fluorescent Sensors

Viscosity in the intracellular microenvironment shows a significant difference in various organelles and is closely related to cellular processes. Such microviscosity in live cells is often mapped and quantified with fluorescent molecular rotors. To enable the rational design of viscosity-sensitive molecular rotors, it is critical to understand their working mechanisms. Herein, we systematically synthesized and investigated two sets of BODIPY-based molecular rotors to study the relationship between intramolecular motions and viscosity sensitivity. Through experimental and computational studies, two conformations (i.e., the planar and butterfly conformations) are found to commonly exist in BODIPY rotors. We demonstrate that the transformation energy barrier from the planar conformation to the butterfly conformation is strongly affected by the molecular structures of BODIPY rotors and plays a critical role in viscosity sensitivity. These findings enable rational structure modifications of BODIPY molecular rotors for highly effective protein detection and recognition.

Twisted intramolecular charge transfer (TICT) based fluorescent probe for lighting up serum albumin with high sensitivity in physiological conditions

Accurate detection of human serum albumin (HSA) in biological samples is quite meaningful for early disease diagnosis and treatment. Herein, a novel fluorescent probe 1-ethyl-4-[2-[4-(diethylamino)-2-hydroxyphenyl]ethenyl]]-pyridinium salt (DEHP) was developed for HSA determination. The inherent fluorescence of DEHP is essentially negligible at physiological conditions assigned to the well-developed twisted intramolecular charge transfer (TICT) protocol. An intriguing fluorescence light up is triggered as the addition of HSA, on account of the inhibited TICT procedure when DEHP enters the hydrophobic cavity of protein HSA. This combination leads to a turn on fluorescent response for HSA with a detection limit of 4.8 nM. After an overall investigation, it has been proved that the strong binding between DEHP and HSA is specific-site-related. In additional, the probe implies a great potential to assist clinical diagnosis due to the usage in actual serum detection. Cell imaging also shows that the probe is expected to monitor HSA production process at cell level.

Ultrafast Oxime Formation Enables Efficient Fluorescence Light-up Measurement of DNA Base Excision

DNA glycosylases constitute a biologically and biomedically important group of DNA repair enzymes responsible for initiating base excision repair (BER). Measuring their activities can be useful for studying the mechanisms DNA damage and repair and for practical applications in cancer diagnosis and drug screening. Previous fluorescence methods for assaying DNA glycosylases are often complex and/or limited in scope to a single enzyme type. Here we report a universal base excision reporter (UBER) fluorescence probe design that implements an unprecedentedly rapid oxime reaction (>150 M^-1 s^-1) with high specificity for the abasic (AP) site of DNA. The molecular rotor design achieves a robust >250-500-fold increase in fluorescence upon reaction with AP sites in DNA. By using the fluorescence reporter in concert with specific DNA lesion-containing substrates, the UBER probe can be used in a coupled assay in principle with any DNA glycosylase. We demonstrate the utility of the UBER probe by assaying five different glycosylases in real time as well as profiling glycosylase activity in cell lysates. We anticipate that the UBER probe will be of considerable utility to researchers studying DNA repair biology owing to its high level of generalizability, ease of use, and compatibility with biologically derived samples.

Solvent viscosity induces twisted intramolecular charge transfer state lifetime tunable of Thioflavin-T

Excited-state deactivation dynamics of Thioflavin-T (ThT) in gradual viscosity solvents were investigated. Femtosecond transient absorption spectra and dynamic decay curves both present significant distinction of ThT in different volume ratios binary mixtures solvents. Dynamics fitting lifetime of twisted intramolecular charge transfer (TICT) state is strongly dependent on solvents viscosity. Compared to rotation corresponding time of ThT in low viscosity solvent (0.6 cp) experimentally coincident well with Stokes-Einstein-Debye (SED) equation, the relation between rotation corresponding time and relatively high viscosity (5.9 cp to 1091.2 cp) is more consistent with fractional SED equation. Combined with optimized geometric structures of ThT by density functional theory and time-dependent density functional theory, further understand TICT state lifetime increases with increasing solvents viscosity. Our work provides a comprehensive understanding of fluorescence molecular rotor (FMR) deactivation process in different viscosity solvents and is helpful to design new FMR.

Fluorogenic D-amino acids enable real-time monitoring of peptidoglycan biosynthesis and high-throughput transpeptidation assays

Peptidoglycan (PG) is an essential cell wall component that maintains the morphology and viability of nearly all bacteria. Its biosynthesis requires periplasmic transpeptidation reactions which construct peptide cross-linkages between polysaccharide chains to endow mechanical strength. However, tracking transpeptidation reaction in vivo and in vitro is challenging, mainly due to the lack of efficient, biocompatible probes. Here, we report the design, synthesis, and application of rotor-fluorogenic D-amino acids (RfDAAs) enabling real-time, continuous tracking of transpeptidation reactions. These probes enable monitoring PG biosynthesis in real time through visualizing transpeptidase reactions in live cells, as well as real-time activity assays of D,D-, L,D-transpeptidases, and sortases in vitro. The unique ability of RfDAAs to become fluorescent when incorporated into PG provides a powerful new tool to study PG biosynthesis with high temporal resolution and prospectively enable high-throughput screening for inhibitors of PG biosynthesis.

An aptamer-based four-color fluorometic method for simultaneous determination and imaging of alpha-fetoprotein, vascular endothelial growth factor-165, carcinoembryonic antigen and human epidermal growth factor receptor 2 in living cells

The extraordinary fluorescence quenching capability of graphene oxide (GO) was coupled to the specific recognition capability of aptamers to design a four-color fluorescent nanoprobe for multiplexed detection and imaging of tumor-associated proteins in living cells. Specifically, alpha-fetoprotein (AFP), vascular endothelial growth factor-165 (VEGF₁₆₅), carcinoembryonic antigen (CEA), and human epidermal growth factor receptor 2 (HER2) were detected. Due to strong π interaction, the fluorescence of labeled aptamers is quenched by GO. Four fluorophore-labeled aptamers that bind the tumor-associated proteins were adsorbed on GO to form the four-color nanoprobe with quenched fluorescence. The nanoprobes were internalized into cells via endocytosis, where the aptamer/GO nanoprobes bind the intracellular tumor-associated proteins. The aptamer-protein complexes thus formed detach from GO, and fluorescence recovers. Each analyte has its typical color (AFP: blue; VEGF165: green; CEA: yellow; HER2: red). As a result, simultaneous detection and imaging of multiple tumor-associated proteins in living cells were achieved. This nanoprobe has a fast response and is highly specific and biocompatible. The linear ranges for AFP, VEGF₁₆₅, CEA, and HER2 are 0.8 nM-160 nM, 0.5 nM-100 nM, 1.0 nM-200 nM, and 1.2 nM-240 nM, respectively. Detection limits were 0.45 nM for AFP, 0.30 nM for VEGF₁₆₅, 0.62 nM for CEA, and 0.96 nM for HER2. The probe allows for a fast distinction between tumor cells and normal cells via imaging. Graphical abstract Schematic presentation of the development of a four-color fluorometic method based on aptamer and graphene oxide for simultaneous detection and imaging of alpha-fetoprotein, vascular endothelial growth factor-165, carcinoembryonic antigen and human epidermal growth factor receptor 2 in living cells.

A SNAP-tag fluorogenic probe mimicking the chromophore of the red fluorescent protein Kaede

Self-labelling protein tags with fluorogenic probes serve as great fluorescence imaging tools to understand key questions of protein dynamics and functions in living cells. In the present study, we report a SNAP-tag fluorogenic probe 4c mimicking the chromophore of the red fluorescent protein Kaede. The molecular rotor properties of 4c were utilized as a fluorogenic probe for SNAP-tag, such that conjugation with SNAPf protein leads to inhibition of twisted intramolecular charge transfer, triggering fluorogenecity. Upon conjugation with SNAPf, 4c exhibited approximately a 90-fold enhancement in fluorescence intensity with fast labelling kinetics (k2 = 15 000 M-1 s-1). Biochemical and spectroscopic studies confirmed that fluorescence requires formation of folded SNAPf·4c covalent conjugate between Cys 145 and 4c. Confocal microscopy and flow cytometry showed that 4c is capable of detecting SNAPf proteins or SNAPf fused with a protein of interest in living cells. This work provides a framework to develop the large family of FP chromophores into fluorogenic probes for self-labelling protein tags.

Depletion of protein thiols and the accumulation of oxidized thioredoxin in Parkinsonism disclosed by a red-emitting and environment-sensitive probe

Protein sulfhydryl groups play a vital role in maintaining cellular redox homeostasis and protein functions and have attracted increasing interests for the selective detection of protein thiols over low-molecular-weight thiols (LMWTs).

Imaging and Quantification of Secreted Peroxynitrite at the Cell Surface by a Streptavidin-Biotin-Controlled Binding Probe

The ability to detect and image secreted peroxynitrite (ONOO^- ) along the extracellular surface of a single cell is biologically significant, as ONOO^- generally exerts its function for host defense and signal transductions at the plasma membrane. However, as a result of the short lifetime and fast diffusion rate of small ONOO^- , precise determination of the ONOO^- level at the cell surface remains a challenging task. In this paper, the use of a membrane-anchored streptavidin-biotin-controlled binding probe (CBP), ONOO-CBP, to determine quantitatively the ONOO^- level at the cell surface and to investigate the effect of different stimulants on the production of ONOO^- along the plasma membrane of macrophages is reported. Our results revealed that the combination of NO synthase (iNOS) and NADPH oxidase (NOX) activators was highly effective in inducing ONOO^- secretion, achieving more than a 25-fold increase in ONOO^- relative to untreated cells. After 1 h of phorbol-12-myristate-13-acetate (PMA) stimulation, the amount of ONOO^- secreted by RAW264.7 macrophages was similar to the condition treated with 25 μm 3-morpholinosydnonimine hydrochloride (SIN-1), which was estimated to release about 20 μm of ONOO^- into Dulbecco's modified Eagle's medium (DMEM) in 1 h. This novel approach should open up new opportunities to image various reactive oxygen and nitrogen species secreted at the plasma membrane that cannot be simply achieved by conventional analytical methods.

Fluorescent Probes of DNA Repair

DNA repair is now understood to play a key role in a variety of disease states, most notably cancer. Tools for studying DNA have typically relied on traditional biochemical methods which are often laborious and indirect. Efforts to study the biology and therapeutic relevance of DNA repair pathways can be limited by such methods. Recently, specific fluorescent probes have been developed to aid in the study of DNA repair. Fluorescent probes offer the advantage of being able to directly assay for DNA repair activity in a simple, mix-and-measure format. This review will summarize the distinct classes of probe designs and their potential utility in varied research and preclinical settings.

Reversibly Switching Molecular Spectra

Manipulation of light transmission/absorbance and reflection/emission has a great significance in smart windows and displaying media like liquid crystal. Here, we report the usage of an external electric field to reversibly switch the molecular spectra of a model molecule on the basis of its interaction with an electroresponsible polymer brush. Both the UV-vis absorbance spectrum and the fluorescence emission spectrum of the model molecule were confirmed to be electroswitchable. The electroswitchable spectra were experimentally demonstrated to be induced by the electroswitchable statuses of medium anionic poly-allyloxy hydroxypropyl sulfonate (poly-AHPS) brush. Insightfully, the molecular aggregated status of model proflavine molecules could be electrically controlled via the electroresponsible poly-AHPS brushes and then the molecular spectra of the model proflavine molecule also could be electrically and controllably shifted. The success in the manipulation of molecular spectra opens up a wide range of applications not only for displaying but also for nonlinear optics, in vivo imaging, sensors, and environmental inspection.

A new probe for detecting zinc-bound carbonic anhydrase in cell lysates and cells

We report the synthesis and application of a small molecule probe for carbonic anhydrase (CA) to track holo-CA in cell lysates and live-cell models of zinc dyshomeostasis. The probe displays a 12-fold increase in fluorescence upon binding to bovine CA and also responds to human CA isoforms.

Rational design of substituted maleimide dyes with tunable fluorescence and solvafluorochromism

A series of maleimide derivatives were systematically designed and synthesized with tunable fluorescent properties. The facile modifications herein provide a simple methodology to expand the scope of maleimide-based dyes and also provide insight into the relationship between substitution pattern and optical properties.

Recent progresses in small-molecule enzymatic fluorescent probes for cancer imaging

An overview of recent advances in small-molecule enzymatic fluorescent probes for cancer imaging, including design strategies and cancer imaging applications.