Probing biotin receptors in cancer cells with rationally designed fluorogenic squaraine dimers

Fluorogenic probes enable imaging biomolecular targets with high sensitivity and maximal signal-to-background ratio under non-wash conditions. Here, we focus on the molecular design of biotinylated dimeric squaraines that undergo aggregation-caused quenching in aqueous media through intramolecular H-type dimerization, but turn on their fluorescence in apolar environment due to target-mediated disaggregation. Our structure–property study revealed that depending on the linkers used to connect the squaraine dyes, different aggregation patterns could be obtained (intramolecular dimerization versus intermolecular aggregation) leading to different probing efficiencies. Using a relatively short l-lysine linker we developed a bright fluorogenic probe, Sq2B, displaying only intramolecular dimerization-caused quenching properties in aqueous media. The latter was successfully applied for imaging biotin receptors, in particular sodium-dependent multivitamin transporter (SMVT), which are overexpressed at the surface of cancer cells. Competitive displacement with SMVT-targets, such as biotin, lipoic acid or sodium pantothenate, showed Sq2B targeting ability to SMVT. This fluorogenic probe for biotin receptors could distinguish cancer cells (HeLa and KB) from model non-cancer cell lines (NIH/3T3 and HEK293T). The obtained results provide guidelines for development of new dimerization-based fluorogenic probes and propose bright tools for imaging biotin receptors, which is particularly important for specific detection of cancer cells.

Rational design of self-quenched squaraine dimers bearing biotin yielded a bright fluorogenic probe that can distinguish cancerous from non-cancerous cells.     

BODIPY 493 acts as a bright buffering fluorogenic probe for super-resolution imaging of lipid droplet dynamics

The need for temporal resolution and long-term stability in super-resolution fluorescence imaging has motivated research to improve the photostability of fluorescent probes. Due to the inevitable photobleaching of fluorophores, it is difficult to obtain long-term super-resolution imaging regardless of the self-healing strategy of introducing peroxide scavengers or the strategy of fluorophore structure modification to suppress TICT formation. The buffered fluorogenic probe uses the intact probes in the buffer pool to continuously replace the photobleached ones in the target, which greatly improves the photostability and enables stable dynamic super-resolution imaging for a long time. But the buffering capacity comes at the expense of reducing the number of fluorescent probes in targets, resulting in low staining fluorescence intensity. In this paper, we selected BODIPY 493, a lipid droplet probe with high fluorescence brightness, to explore the dynamic process of lipid droplet staining of this probe in cells. We found that BODIPY 493 only needs very low laser power for lipid droplet imaging due to the high molecular accumulation in lipid droplets and the high brightness, and the spatiotemporal resolution is greatly improved. More importantly, we found that BODIPY 493 also has a certain buffering capacity, which enables BODIPY 493 to be used for super-resolution imaging of lipid droplet dynamics. This work reminds researchers to coordinate the buffering capacity and brightness of fluorogenic probes.     

Reversible Live-Cell Labeling with Retro-engineered HaloTags Enables Long-Term High- and Super-Resolution Imaging

Self-labeling enzymes (SLE) such as the HaloTag have emerged as powerful tools in high and super-resolution fluorescence microscopy. Newly developed fluorogenic SLE substrates enable imaging in the presence of excess dye. To exploit this feature for reversible labeling, we engineered two variants of HaloTag7 with restored dehalogenase activity. Kinetic studies in vitro showed different turnover kinetics for reHaloTagS (≈0.006 s⁻¹) and reHaloTagF (≈0.055 s⁻¹). Imaging by confocal and stimulated emission depletion microscopy yielded 3-5-time enhanced photostability of reHaloTag labeling. Prominently, single molecule imaging with reHaloTags enabled controlled and stable labeling density over extended time periods. By combination with structured illumination, simultaneous visualization of single molecule diffusion and organellar dynamics was achieved. These applications highlight the potential of reHaloTag labeling for pushing the limits of advanced fluorescence microscopy techniques.     

Ultrafluorogenic Coumarin–Tetrazine Probes for Real‐Time Biological Imaging

We have developed a series of new ultrafluorogenic probes in the blue‐green region of the visible‐light spectrum that display fluorescence enhancement exceeding 11 000‐fold. These fluorogenic dyes integrate a coumarin fluorochrome with the bioorthogonal trans‐cyclooctene(TCO)–tetrazine chemistry platform. By exploiting highly efficient through‐bond energy transfer (TBET), these probes exhibit the highest brightness enhancements reported for any bioorthogonal fluorogenic dyes. No‐wash, fluorogenic imaging of diverse targets including cell‐surface receptors in cancer cells, mitochondria, and the actin cytoskeleton is possible within seconds, with minimal background signal and no appreciable nonspecific binding, opening the possibility for in vivo sensing.     

A Far-Red Molecular Rotor Fluorogenic Trehalose Probe for Live Mycobacteria Detection and Drug-Susceptibility Testing

Increasing the speed, specificity, sensitivity, and accessibility of mycobacteria detection tools are important challenges for tuberculosis (TB) research and diagnosis. In this regard, previously reported fluorogenic trehalose analogues have shown potential, but their green-emitting dyes may limit sensitivity and applications in complex settings. Here, we describe a trehalose-based fluorogenic probe featuring a molecular rotor turn-on fluorophore with bright far-red emission (RMR-Tre). RMR-Tre, which exploits the unique biosynthetic enzymes and environment of the mycobacterial outer membrane to achieve fluorescence activation, enables fast, no-wash, low-background fluorescence detection of live mycobacteria. Aided by the red-shifted molecular rotor fluorophore, RMR-Tre exhibited up to a 100-fold enhancement in M. tuberculosis labeling compared to existing fluorogenic trehalose probes. We show that RMR-Tre reports on M. tuberculosis drug resistance in a facile assay, demonstrating its potential as a TB diagnostic tool.     

Redesign of a Fluorogenic Labeling System To Improve Surface Charge,Brightness, and Binding Kinetics for Imaging the Functional Localization of Bromodomains

Protein labeling with fluorogenic probes is a powerful method for the imaging of cellular proteins. The labeling time and fluorescence contrast of the fluorogenic probes are critical factors for the precise spatiotemporal imaging of protein dynamics in living cells. To address these issues, we took mutational and chemical approaches to increase the labeling kinetics and fluorescence intensity of fluorogenic PYP‐tag probes. Because of charge‐reversal mutations in PYP‐tag and probe redesign, the labeling reaction was accelerated by a factor of 18 in vitro, and intracellular proteins were detected with an incubation period of only 1 min. The brightness of the probe both in vitro and in living cells was enhanced by the mutant tag. Furthermore, we applied this system to the imaging analysis of bromodomains. The labeled mutant tag successfully detected the localization of bromodomains to acetylhistone and the disruption of the bromodomain–acetylhistone interaction by a bromodomain inhibitor.     

Redesign of a Fluorogenic Labeling System To Improve Surface Charge,Brightness, and Binding Kinetics for Imaging the Functional Localization of Bromodomains

Protein labeling with fluorogenic probes is a powerful method for the imaging of cellular proteins. The labeling time and fluorescence contrast of the fluorogenic probes are critical factors for the precise spatiotemporal imaging of protein dynamics in living cells. To address these issues, we took mutational and chemical approaches to increase the labeling kinetics and fluorescence intensity of fluorogenic PYP‐tag probes. Because of charge‐reversal mutations in PYP‐tag and probe redesign, the labeling reaction was accelerated by a factor of 18 in vitro, and intracellular proteins were detected with an incubation period of only 1 min. The brightness of the probe both in vitro and in living cells was enhanced by the mutant tag. Furthermore, we applied this system to the imaging analysis of bromodomains. The labeled mutant tag successfully detected the localization of bromodomains to acetylhistone and the disruption of the bromodomain–acetylhistone interaction by a bromodomain inhibitor.     

A High-Affinity “Synthavidin” Receptor for Squaraine Dyes

Strong-binding host–guest pairings in aqueous media have potential as “supramolecular glues” in biomedical techniques, complementing the widely-used (strept)avidin-biotin combination. We have previously found that squaraine dyes are bound very strongly by tetralactam macrocycles possessing anthracenyl units as cavity walls. Here we show that replacing the anthracenes with pentacyclic 5,7,12,14-tetrahydro-5,7,12,14-tetraoxapentacene (TOP) units generates receptors which bind squaraines with increased affinities (around K_a=10¹⁰ m ⁻¹) and improved selectivities. Binding can be followed through changes to squaraine fluorescence and absorbance. The TOP units are easy to prepare and potentially variable, while the TOP-based receptor shows improved photostability, both in itself and in complex with squaraines. The results suggest that this system could prove valuable in the further development of practical “synthavidin” chemistry.     

Rational Design of Fluorescent Bioimaging Probes by Controlling the Aggregation Behavior of Squaraines: A Special Effect of Ionic Liquid Pendants

We herein present an effective strategy to create water‐soluble fluorescent bioimaging dyes by introducing the imidazolium‐based ionic liquid (IL) pendants into a fluorescent skeleton. A new type of water‐soluble imidazolium‐anchored squaraine dye was synthesized accordingly. The relationship between the aggregate of squaraines and their fluorescent cell imaging application was elucidated in detail. Firstly, the aggregation behavior of squaraines in water solutions could be suppressed by varying the alkyl chain attached to the imidazolium unit. Secondly, the capability of cellular uptake and staining of dyes was also dramatically enhanced upon increasing the length of the paraffinic chain. These squaraine dyes displayed an excellent photostability that could permit real‐time fluorescence bioimaging experiments to be monitored over a long time period with constant sample irradiation. Additionally, we designed for the first time an Fe^II‐ion probe on the basis of an attack of the hydroxyl radical to the four‐membered ring of squaraine. The results demonstrated that the imidazolium‐anchored squaraines could perform “naked‐eye” detection of the Fe²⁺ ion over a wide range of other interfering metals in aqueous media. More surprisingly, this process showed a fluorescence “turn‐off” and “‐on” response through the regeneration of squaraines in cells.     

Trianionic 1,3,2-Dioxaborine-Containing Polymethines: Bright Near-Infrared Fluorophores

Trianionic polymethines of the A′-π-A-π-A-π-A′ type comprising dioxaborine rings (A) and different electron-accepting end groups (A′) have been synthesized. The obtained dyes absorb and emit light in the near-infrared region with remarkably high molar attenuation coefficients (ϵ up to 495 000 M⁻¹ cm⁻¹ in DMF) and fluorescence quantum yields (Φ_f up to 0.73 in DMF). Thus, the novel trianionic dyes stand among the brightest individual fluorophores known to date – with a magnitude of fluorescence brightness (ϵ⋅Φ_f) of 313 000 M⁻¹ cm⁻¹ in DMF. The synthesized dyes demonstrate a minor negative solvatochromism and small Stokes shifts. X-ray data reveal the nearly planar geometry of the trianionic chromophore. All the obtained compounds are stable in the solid state and in a solution, although the relative stability is much higher in polar aprotic than in protic solvents.     

A General Strategy for Through-Bond Energy Transfer Fluorescence Probes Combining Intramolecular Charge Transfer: A Silyl Ether System for Endogenous Peroxynitrite Sensing

A general strategy is reported for developing through-bond energy transfer (TBET) fluorescence probes by combining intramolecular charge transfer (ICT). The strategy uses a coplanar donor-π-bridge-acceptor system (SiOPh-PyOH) without spirolactam. The off-on switch of TBET and ICT is controlled by coplanar structure changes in the sensing process instead of spirolactam ring-opening in traditional TBET probes. DFT calculations showed that the energy and charge transfers from SiOPh to PyOH are prohibited. Since the SiOPh has no fluorescence, the probe SiOPh-PyOH shows fluorescence properties similar to that of pyrene. After sensing ONOO⁻, the silyl ether is removed and the probe changes into ⁻OPh-PyO⁻. Electron-donating ICT from ⁻OPh to PyO⁻ induces a large redshift of emission to 594 nm (179 nm shift). TBET from ⁻OPh to PyO⁻ ensures the probe exhibits a large pseudo-Stokes shift of 213 nm. Furthermore, the probe was successfully used in endogenous ONOO⁻ detection. This study offers a new strategy for the construction of TBET probes emitting in the red region without spirolactam ring-opening, a new ONOO⁻ sensing system using silyl ether as a reaction site, and a method for the deprotection of silyl ethers with ONOOH under mild conditions.     

Synthesis of a Far‐Red Photoactivatable Silicon‐Containing Rhodamine for Super‐Resolution Microscopy

The rhodamine system is a flexible framework for building small‐molecule fluorescent probes. Changing N‐substitution patterns and replacing the xanthene oxygen with a dimethylsilicon moiety can shift the absorption and fluorescence emission maxima of rhodamine dyes to longer wavelengths. Acylation of the rhodamine nitrogen atoms forces the molecule to adopt a nonfluorescent lactone form, providing a convenient method to make fluorogenic compounds. Herein, we take advantage of all of these structural manipulations and describe a novel photoactivatable fluorophore based on a Si‐containing analogue of Q‐rhodamine. This probe is the first example of a “caged” Si‐rhodamine, exhibits higher photon counts compared to established localization microscopy dyes, and is sufficiently red‐shifted to allow multicolor imaging. The dye is a useful label for super‐resolution imaging and constitutes a new scaffold for far‐red fluorogenic molecules.     

A Double‐Clicking Bis‐Azide Fluorogenic Dye for Bioorthogonal Self‐Labeling Peptide Tags

Herein, we give the very first example for the development of a fluorogenic molecular probe that combines the two‐point binding specificity of biarsenical‐based dyes with the robustness of bioorthogonal click‐chemistry. This proof‐of‐principle study reports on the synthesis and fluorogenic characterization of a new, double‐quenched, bis‐azide fluorogenic probe suitable for bioorthogonal two‐point tagging of small peptide tags by double strain‐promoted azide–alkyne cycloaddition. The presented probe exhibits remarkable increase in fluorescence intensity when reacted with bis‐cyclooctynylated peptide sequences, which could also serve as possible self‐labeling small peptide tag motifs.     

Design and synthesis of squaraine based near infrared fluorescent probes

A novel class of dialkylanthracene containing squaraine dyes (Sq1-3) possessing intense absorption and emission in the NIR region has been synthesized. Structural and electronic features investigated using DFT methods suggest that the significant bathochromic shifts observed on replacing dialkylaniline by dialkylanthracene in this class of molecules can be attributed to a reduction in the HOMO-LUMO gap mainly due to enhanced hydrogen bonding between the carbonyl group of the cyclobutane ring and the neighboring aromatic hydrogen in the dyes containing the anthracene moiety. The absence of fluorescence in aqueous media and high fluorescence when encapsulated into hydrophobic domains make this class of dyes especially useful as probes for mapping such domains in biological systems.     

Bright,Color-Tunable Fluorescent Dyes in the Vis/NIR Region: Establishment of New “Tailor-Made” Multicolor Fluorophores Based on Borondipyrromethene

A new series of high-performance fluorophores named Keio Fluors (KFL), which are based on borondipyrromethene (BODIPY), are reported. The KFL dyes cover a wide spectral range from the yellow (547 nm) to the near-infrared (NIR, 738 nm) region, and their emission wavelength could be easily and subtly controlled based on simple molecular modifications only, without losing their optical properties. This “tailor-made” synthetic strategy for tuning the emission wavelength enabled the creation of fourteen KFL dyes with well-controlled emission colors (yellow, orange, red, far-red, and NIR). Moreover, these KFL dyes also retain their excellent optical properties, such as spectral bands sharper than quantum dots, high extinction coefficients (140 000–316 000 M ⁻¹ cm⁻¹), and high quantum yields (0.56–0.98), without any critical solvent polarity dependent decrease of their brightness. These advantageous characteristics make the KFL dyes potentially useful as new candidates of fluorescent standard dyes to substitute or to complement existing long-wavelength fluorescent dyes, such as cyanines, oxazines, rhodamines, or other BODIPY dyes.     

方酸菁荧光探针的应用研究进展

功能性方酸菁染料具有独特的D-A-D共轭结构,其在可见光和近红外区域有强烈的吸收和荧光发射。方酸菁染料作为近红外荧光探针母体被应用于蛋白质、氨基酸、一些生物小分子、环境污染物及金属离子等的检测。本文结合课题组近几年工作综述了方酸菁染料在蛋白质、氨基酸、生物小分子、阳离子和其它物质检测方面的应用。     

Recent Progress of Small-Molecule Ratiometric Fluorescent Probes for Peroxynitrite in Biological Systems

Peroxynitrite (ONOO⁻) as a major reactive oxygen species plays important roles in cellular signal transduction and homeostatic regulation. Precise detection of ONOO⁻ in biological systems is vital for exploring its physiological and pathological function. Among numerous detection methods, fluorescence imaging technology using fluorescent probes offers some advantages, including simple operation, high sensitivity and selectivity, as well as real-time and nondestructive detection. In particular, ratiometric fluorescent probes, in which the built-in calibration of the two emission bands prevents interference from the biological environment, have been extensively employed to monitor the fluctuation of bioactive species. In this review, we will discuss small-molecule ratiometric fluorescent probes for ONOO⁻ in live cells or in vivo, which involves chemical structures, response mechanisms, and biological applications. Moreover, the challenges and future prospects of ONOO⁻-responsive ratiometric fluorescent probe are also proposed.     

Mechanism-based molecular design of highly selective fluorescence probes for nitrative stress

Nitrative stress is implicated in various pathogenic processes, including neurodegenerative disorders, but there is no practical fluorescence probe which can monitor the generation of nitrative stress with high selectivity. To design a suitable fluorescence probe, we have first focused on the fluorescence quenching mechanism of the nitro group, which has been believed to be a unique quencher of fluorescent dyes. We found that nitro group-based fluorescence quenching could be explained in terms of an electron transfer process, from the excited fluorophore to the electron-deficient aromatic nitro moiety. By utilizing this result, we succeeded in developing novel fluorogenic probes, NiSPYs, which can selectively monitor the generation of nitrative stress based on aromatic nitration. NiSPYs showed strong fluorescence enhancement upon the reaction with nitrating agents, including peroxynitrite, but showed little or no fluorescence augmentation in the presence of other reactive oxygen species. NiSPYs should be potentially useful as tools to study the role of nitrative stress in various biological applications.     

Sensitive and Selective Detection of Enterococcus faecalis Using a New Turn-on Fluorogenic β-glucosidase Substrate Combined with a Modified Selective Broth

A new, simple-to-synthesize and sensitive turn-on fluorogenic substrate ( CFMU-Glu ) for β-glucosidase activity was developed. This probe was based on a 7-hydroxycoumarin derivative ( CFMU ) that could emit green fluorescence and had the low pK_a value of 5.61 ± 0.01. CFMU-Glu could be used for sensitive monitoring of the almond βGLU and Enterococcus faecalis (E. faecalis) at the optimal pHs of 6.50 and 7.00, respectively. Moreover, a new sensitive and selective fluorogenic broth (PBF-B) for E. faecalis, utilizing CFMU-Glu and polymyxin B, was also developed. Polymyxin B was discovered to can significantly improve the detection selectivity and signal intensity. The proposed 4-four method using PBF-B and a microcentrifuge tube could provide fluorogenic detection limits of 5.01 × 10⁴ and 1.0 × 10⁵ CFU mL⁻¹ by fluorescence microplate reader and naked eye, respectively; it could also provide a turn-on chromogenic detection limit of 1.0 × 10⁶ CFU mL⁻¹ by naked eye. The proposed method could detect 8 CFU mL⁻¹ of E. faecalis in drinking water, Liangcha (herbal tea) and milk samples within 10 h, without pre-enrichment.     

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.