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

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

Journey of Poly(ethylene Glycol) in Living Cells.

As the gold standard for stealth polymer materials, poly(ethylene glycol) (PEG) has been widely used in drug delivery with excellent properties such as low toxicity, reduced immunogenicity, good water solubility, and so forth. However, lack of understanding for the fate of PEG and PEGylated delivery systems at the cellular level has limited the application of PEGylated molecules in diagnosis and therapy. Here, we chose linear PEG 5k as a representative model and focused on the internalization behavior and mechanism, intracellular trafficking, sub-cellular localization, and cellular exocytosis of PEG and PEGylated molecules in living cells. Our investigation showed that PEG could be internalized into cells in 1 h. The internalized PEG was localized to lysosome, cytosol, endoplasmic reticulum (ER) and mitochondria. Importantly, the fate of PEG in cells could be regulated by conjugating different small molecules. PEGylated rhodamine B (PEG-RB) as the positively charged macromolecule was internalized into cells by micropinocytosis and then transported in lysosomes, ER, and mitochondria via vesicles sequentially. In contrast, PEGylated pyropheophorbide-a (PEG-PPa) as the negatively charged macromolecule was internalized into cells and transported to lysosomes ultimately. PEGylation slowed down the exocytosis process of RB and PPa and significantly prolonged their residence time inside the cells. These findings improve the understanding of how PEG and PEGylated molecules interact with the biological system at cellular and sub-cellular levels, which is of significance to rational PEGylation design for drug delivery.

Probing Variations of Reduction Activity at the Plasma Membrane Using a Targeted Ratiometric FRET Probe.

Plasma membrane (PM) is the turntable of various reactions that regulate essential functionalities of cells. Among these reactions, the thiol disulfide exchange (TDE) reaction plays an important role in cellular processes. We herein designed a selective probe, called membrane reduction probe (MRP), that is able to report TDE activity at the PM. MRP is based on a green emitting BODIPY PM probe connected to rhodamine through a disulfide bond. MRP is fluorogenic as it is turned off in aqueous media due to aggregation-caused quenching, and once inserted in the PM, it displays a bright red signal due to an efficient fluorescence energy resonance transfer (FRET) between the BODIPY donor and the rhodamine acceptor. In the PM model, the MRP can undergo TDE reaction with external reductive agents as well as with thiolated lipids embedded in the bilayer. Upon TDE reaction, the FRET is turned off and a bright green signal appears allowing a ratiometric readout of this reaction. In cells, the MRP quickly labeled the PM and was able to probe variations of TDE activity using ratiometric imaging. With this tool in hand, we were able to monitor variations of TDE activity at the PM under stress conditions, and we showed that cancer cell lines presented a reduced TDE activity at the PM compared to noncancer cells.

Synthesis of Catechol Derived Rosamine Dyes and Their Reactivity toward Biogenic Amines.

Functional organic dyes play a key role in many fields, namely in biotechnology and medical diagnosis. Herein, we report two novel 2,3- and 3,4-dihydroxyphenyl substituted rosamines (3 and 4, respectively) that were successfully synthesized through a microwave-assisted protocol. The best reaction yields were obtained for rosamine 4, which also showed the most interesting photophysical properties, specially toward biogenic amines (BAs). Several amines including n- and t-butylamine, cadaverine, and putrescine cause spectral changes of 4, in UV-Vis and fluorescence spectra, which are indicative of their potential application as an effective tool to detect amines in acetonitrile solutions. In the gas phase, the probe response is more expressive for spermine and putrescine. Additionally, we found that methanolic solutions of rosamine 4 and n-butylamine undergo a pink to yellow color change over time, which has been attributed to the formation of a new compound. The latter was isolated and identified as 5 (9-aminopyronin), whose solutions exhibit a remarkable increase in fluorescence intensity together with a shift toward more energetic wavelengths. Other 9-aminopyronins 6a, 6b, 7a, and 7b were obtained from methanolic solutions of 4 with putrescine and cadaverine, demonstrating the potential of this new xanthene entity to react with primary amines.

Iridium-Triggered Allylcarbamate Uncaging in Living Cells.

Designing a metal catalyst that addresses the major issues of solubility, stability, toxicity, cell uptake, and reactivity within complex biological milieu for bioorthogonal controlled transformation reactions is a highly formidable challenge. Herein, we report an organoiridium complex that is nontoxic and capable of the uncaging of allyloxycarbonyl-protected amines under biologically relevant conditions and within living cells. The potential applications of this uncaging chemistry have been demonstrated by the generation of diagnostic and therapeutic agents upon the activation of profluorophore and prodrug in a controlled fashion within HeLa cells, providing a valuable tool for numerous potential biological and therapeutic applications.

Development of Novel Rhodanine Analogs as Anticancer Agents: Design, Synthesis, Evaluation and CoMSIA Study.

BACKGROUND: A series of novel 5-substituted benzylidene rhodanine derivatives using four different amines were designed based on our previously developed CoMSIA (Comparative molecular similarity indices analysis) model for the anticancer activity. METHODS: The designed rhodanines were synthesized via dithiocarbamate formation, cyclization and Knoevenagel condensation. The structures of the synthesized compounds were confirmed and analyzed by spectral studies. RESULTS: The synthesized rhodanines were investigated for in vitro anticancer activities and the analogs have displayed mild to significant cytotoxicity against MCF-7 breast cancer cells. The compounds with benzyloxy substitution at the fifth position of rhodanine ring (Compounds 20, 33 and 38) system showed significant cytotoxic activity against MCF-7 cells. CoMSIA, a three-dimensional quantitative structureactivity relationship (3D-QSAR) technique was accomplished to elucidate structure-activity relationships. CONCLUSION: Based on the information derived from CoMSIA contour plots, some key features for increasing the activity of compounds have been identified and used to design new anti-cancer agents. The present developed CoMSIA model displayed good external predictability, r2pred of 0.841 and good statistical robustness.

NIR-II pH Sensor with a FRET Adjustable Transition Point for In Situ Dynamic Tumor Microenvironment Visualization.

Monitoring the pH in tumor lesions provides abundant physiological information. However, currently developed pH sensors only achieve sensitive detection in the settled response region around the pH transition point (pHt ). To realize tumor pH monitoring with high sensitivity within a wider response region, reported here are serial pHt adjustable sensors (pTAS) that simply regulate the component ratio of second near-infrared (NIR-II) emission aza-BODIPY (NAB) donor and pH sensitive rhodamine-based pre-acceptor (NRh) in Förster resonance energy transfer system. Combining the pH response regions of pTAS, a twofold widened pH detection range (6.11-7.22) is obtained compared to the pHt settled sensor (6.38-6.94). With an adjustable pHt , in vivo tumor pH increase and decrease processes could be dynamically visualized through dual-channel ratiometric bioimaging within the NIR-II window, with a coefficient of variation under 1 % compared to the standard pH meter.

Fluorescent dATP for DNA Synthesis In Vivo.

Fluorescent nucleoside triphosphates are powerful probes of DNA synthesis, but their potential use in living animals has been previously underexplored. Here, we report the synthesis and characterization of 7-deaza-(1,2,3-triazole)-2'-deoxyadenosine-5'-triphosphate (dATP) derivatives of tetramethyl rhodamine ("TAMRA-dATP"), cyanine ("Cy3-dATP"), and boron-dipyrromethene ("BODIPY-dATP"). Upon microinjection into live zebrafish embryos, all three compounds were incorporated into the DNA of dividing cells; however, their impact on embryonic toxicity was highly variable, depending on the exact structure of the dye. TAMRA-EdATP exhibited superior characteristics in terms of its high brightness, low toxicity, and rapid incorporation and depletion kinetics in both a vertebrate (zebrafish) and a nematode (Caenorhabditis elegans). TAMRA-EdATP allows for unprecedented, real-time visualization of DNA replication and chromosome segregation in vivo.

A rapid response near-infrared ratiometric fluorescent probe for the real-time tracking of peroxynitrite for pathological diagnosis and therapeutic assessment in a rheumatoid arthritis model.

Peroxynitrite (ONOO-) is a potent bio-oxidant involved in many physiological and pathological processes; however, most of the pathological effects associated with ONOO-in vivo are still ambiguous. Herein, we designed and synthesized two near-infrared ratiometric fluorescent probes, Ratio-A and Ratio-B, for the detection and biological evaluation of ONOO-. The recognition unit diene in the probes could be specifically cleaved by ONOO- with a 94-fold enhancement in the ratiometric fluorescence signal. By imaging ONOO- in immune stimulated cells and acute inflammation mice model using Ratio-A, we investigated the fluctuations of ONOO- levels in a rheumatoid arthritis (RA) model of mice. Ratio-A could be applied for the effective imaging of RA and could rapidly evaluate the response of the RA treatment with methotrexate (MTX). Thus, Ratio-A can be considered as a promising tool for pathological diagnosis and the therapeutic assessment of a wide range of diseases including RA.

Synthesis of some steroidal mitocans of nanomolar cytotoxicity acting by apoptosis.

Several steroids (abiraterone, prednisone, testosterone, cholesterol) and the BCL-2 inhibitor bexarotene were used as starting materials to synthesize iperazinyl-spacered rhodamine B conjugates. The conjugates were screened for their cytotoxicity in SRB assays against several human tumor cell lines and found to be active in a low µM to nM range. The conjugate derived from testosterone held an EC50 = 59 nM against MCF-7 tumor cells and acted mainly by necrosis. The prednisone conjugate, however, was less cytotoxic but acted mainly by apoptosis and held a moderate selectivity against MCF-7 tumor cells.

Thiol-responsive pro-fluorophore labeling: Synthesis of a pro-fluorescent labeled oligonucleotide for monitoring cellular uptake.

Pro-fluorescent labeled oligonucleotides are potential alternative tools to classical fluorescently labeled oligonucleotides for monitoring cellular uptake. Here, we report the design and synthesis of a thiol-responsive pro-fluorophore labeled oligonucleotide, and its fluorescence responsivity to glutathione in the test tube and live cells.

Site-Specific Fluorogenic Protein Labelling Agent for Bioconjugation.

Many clinically relevant therapeutic agents are formed from the conjugation of small molecules to biomolecules through conjugating linkers. In this study, two novel conjugating linkers were prepared, comprising a central coumarin core, functionalized with a dimaleimide moiety at one end and a terminal alkyne at the other. In our first design, we developed a protein labelling method that site-specifically introduces an alkyne functional group to a dicysteine target peptide tag that was genetically fused to a protein of interest. This method allows for the subsequent attachment of azide-functionalized cargo in the facile synthesis of novel protein-cargo conjugates. However, the fluorogenic aspect of the reaction between the linker and the target peptide was less than we desired. To address this shortcoming, a second linker reagent was prepared. This new design also allowed for the site-specific introduction of an alkyne functional group onto the target peptide, but in a highly fluorogenic and rapid manner. The site-specific addition of an alkyne group to a protein of interest was thus monitored in situ by fluorescence increase, prior to the attachment of azide-functionalized cargo. Finally, we also demonstrated that the cargo can also be attached first, in an azide/alkyne cycloaddition reaction, prior to fluorogenic conjugation with the target peptide-fused protein.

Polypeptide-rhodamine B probes containing laminin/fibronectin receptor-targeting sequence (YIGSR/RGD) for fluorescent imaging in cancers.

Currently, fluorescent imaging is one of the most promising diagnostic approaches for facile detection of cancers in situ in thanks to a fluorescent probe. Two novel polypeptide-based fluorescent probes for different biomarkers to cancers are reported here. These probes focused on tyrosine-isoleucine-glycine-serine-arginine (YIGSR) and arginine-glycine-aspartic (RGD), which receptors play an important role in the extracellular matrix and are overexpressed in tumor cells and then can be used as tumor-targeting groups in fluorescent imaging. In this work, the pentpeptide-rhodamine B derivative (YIGSR-RhB) and tripeptide-rhodamine B derivative (RGD-RhB) were synthesized respectively by using the solid phase synthesis methods. These derivatives were further characterized by 1HNMR, MS, UV and IR, etc. Their fluorescent and biocompatibility properties, such as the cell cytotoxicity, cell uptake and fluorescent imaging of tumor cells, and fluorescent imaging in BALB/c female mice with 4T1 tumors and C57 mice with B16F10 tumor in vivo, were also measured. Experiment results demonstrated that YIGSR-RhB and RGD-RhB possessed the low cell cytotoxicity, good tumor-targeting property and fluorescent properties similar to rhodamine B. Moreover, YIGSR-RhB and RGD-RhB can be taken up highly by the B16F10 melanoma cells and 4T1 breast cancer cells, and then achieve the good fluorescent imaging in these tumor cells in vitro and tumors of mice in vivo. Therefore, YIGSR-RhB and RGD-RhB can be used as the potential tumor-targeting probes for fluorescent imaging. They can directly attach the cell membrane and specifically target to the tumor cells.

Time-gated luminescence probe for ratiometric and luminescence lifetime detection of Hypochorous acid in lysosomes of live cells.

Time-gated luminescence (TGL) probes based on lanthanide complexes have appealed wide attention in the detection of biologically relevant analytes because of their inimitable photophysical properties. In this work, a TGL probe (TR-HOCl) based on intramolecular Förster resonance energy transfer (FRET) system for specific determination of hypochlorous acid (HOCl) was designed and synthesized, in which a rhodamine derivative (energy acceptor) was conjugated to a luminescent Tb3+ complex (energy donor). After reacting with HOCl, the Tb3+ emission of TR-HOCl at 540 nm declined while the rhodamine emission at 580 nm increased, which leaded to an increase of the TGL intensity ratio of rhodamine to Tb3+ complex (I560/I540) up to ~9-fold. The dose-dependent increase of I560/I540 gives a nice linearity in HOCl concentration range of 0.5-45 µM. The detection limit of for HOCl was determined to be 0.34 µM. Interestingly, the average luminescence lifetime of the Tb3+ emission decreased (from 588 µs to 254 µs) accompanied with the FRET process and the value gave a fine linearity to the variation of HOCl concentration. Additionally, TR-HOCl showed great selectivity for recognition of HOCl over other ROS, RNS, biothiols and other interference. These properties endow TR-HOCl to be conveniently applied for high accurate recognition of HOCl with ratiometric TGL and luminescence lifetime dual-signal output. Finally, TR-HOCl was successfully applied for the TGL determination of HOCl in HepG2 cells. The co-localization experiments of TR-HOCl with LysoSensor Green revealed the lysosome-localizing property of the probe in live cells. The study demonstrated that TR-HOCl could be a competent tool for investigating roles of HOCl in various physiological processes.

A near-infrared fluorescent probe based on a novel rectilinearly π-extended rhodamine derivative and its applications.

We designed and synthesized a novel near-infrared (NIR) mitochondria-targeted fluorescent probe RQNA for the specific detection of mitochondrial Cu2+ because mitochondria are important reservoirs of intracellular copper. For the preparation of this probe, a novel π-extended fluorescent xanthene dye RQN was firstly synthesized via an intramolecular nucleophilic substitution of aromatic hydrogen (SNArH) strategy. Then, probe RQNA was prepared by the reaction of RQN and hydrazine hydrate, followed by treatment with acetone. RQNA exhibited selectivity, sensitivity (22 nM), and fast response time (20 s) for the detection of Cu2+via a specific Cu2+-triggered ring-opening and hydrolysis cascade reaction. RQNA is cell-membrane permeable and mitochondria-targetable, and can be used for monitoring mitochondrial Cu2+ in living cells.

Single-Chain Nanoparticle Delivers a Partner Enzyme for Concurrent and Tandem Catalysis in Cells.

Combining synthetic chemistry and biocatalysis is a promising but underexplored approach to intracellular catalysis. We report a strategy to codeliver a single-chain nanoparticle (SCNP) catalyst and an exogenous enzyme into cells for performing bioorthogonal reactions. The nanoparticle and enzyme reside in endosomes, creating engineered artificial organelles that manufacture organic compounds intracellularly. This system operates in both concurrent and tandem reaction modes to generate fluorophores or bioactive agents. The combination of SCNP and enzymatic catalysts provides a versatile tool for intracellular organic synthesis with applications in chemical biology.

One-step synthesis of rhodamine-based Fe3+ fluorescent probes via Mannich reaction and its application in living cell imaging.

Four rhodamine-based fluorescent probes M1-M4 were synthesized in one step using Mannich reaction. The Mannich reaction based approach has the advantages of simplicity, good yield and excellent atomic economy. The structures were determined by 1H NMR, 13C NMR, IR and HRMS. The probe M3 as a representative compound was characterized by single-crystal X-ray analyses. The fluorescence and absorbance spectra research of the probes demonstrated that they could be used as Fe3+-selective fluorescent probes with good sensitivity, excellent linearity, and outstanding anti-interference in acetonitrile/Tris-HCl buffer solution (3:7, V/V; pH = 7.4). Moreover, confocal laser scanning microscopy experiments have proven that the probe M3 was successfully used for fluorescence imaging in MCF-7 cells.

A selective and sensitive turn-on chemosensor for detection of Fe3+ in aqueous solution and its cell imaging in dorsal root ganglia neurons and MKN-45 cells.

A new turn-on fluorescent chemosensor (RBTM) for Fe3+ was designed based on Rhodamine B and a thiocarbonylimidazole moiety. The spectroscopic probe used for characterization of the synthesized system showed 300-fold fluorescence enhancement for the detection of Fe3+ with a 1:1 stoichiometry in EtOH/H2O solution (2:1, v/v, HEPES buffer, 1 mM, pH 7.30). Upon addition of Fe3+ in aqueous ethanol, the probe displayed a significant fluorescence enhancement and a distinct color change (colorless to pink) that can be detected by the naked eye. The binding constant between the probe and Fe3+ was determined to be 1.16 × 104 M-1 and the corresponding detection limit was calculated to be 0.256 µM. In addition, the energy gaps between the HOMO and LUMO in RBTM and RBTM-Fe3+ were calculated using DFT calculations to be 92.93 kcal/mol and 37.49 kcal/mol, respectively. The results indicate that binding of Fe3+ to RBTM lowered the HOMO-LUMO energy gap of the complex and stabilized the system. Fluorescence imaging experiments demonstrated that RBTM can be used as a fluorescent probe to detect Fe3+ in MKN-45 cells and dorsal root ganglia, thus revealing that RBTM could be used for biological applications.

A novel cell-penetrating Janus nanoprobe for ratiometric fluorescence detection of pH in living cells.

pH regulates the function of many organelles and plays a pivotal role in requiring multitud cellular behaviors. Compared with single fluorescent probes, ratio fluorescent probes have higher sensitivity and immunity to interference. Herein, a novel Janus ratio nanoprobe was developed for intracellular pH detection. Modified rhodamine B probe and fluorescein isothiocyanate (FITC) were individually encapsulated in the independent hemispheres of Janus microparticles fabricated via Pickering emulsion. Moreover, it exhibits a satasified ratiometric detection of pH compared to the previous core-shell structure and organic small molecule probe. Accordingly, the Janus nanoprobe possesses many important features as an attractive sensor, including high anti-jamming capability, excellent stability, good reversibility and low cytotoxicity. Variations of the two fluorescence intensities (Fgreen/Fred) resulted in a ratiometric pH fluorescent sensor, which can respond to wide range of pH values from 3 to 8. To be more specific, with a single excitation wavelength of 488 nm, there are dual emission bands centered at 538 nm and 590 nm. Also the Janus nanoprobe displays a excellent linear relationship in the physiologically relevant pH range of 4.0-6.0. Consequently, detecting of pH and imaging was successfully achieved in living cells, which provides a simple and reliable method for detecting intracelluar pH and other similar substances.

A Fluorescent Probe for Rapid, High-Contrast Visualization of Folate-Receptor-Expressing Tumors In†Vivo.

Folate receptors (FRs) are membrane proteins involved in folic acid uptake, and the alpha isoform (FR-α) is overexpressed in ovarian and endometrial cancer cells. For fluorescence imaging of FRs in vivo, the near-infrared (NIR) region (650-900 nm), in which tissue penetration is high and autofluorescence is low, is optimal, but existing NIR fluorescent probes targeting FR-α show high non-specific tissue adsorption, and require prolonged washout to visualize tumors. We have designed and synthesized a new NIR fluorescent probe, FolateSiR-1, utilizing a Si-rhodamine fluorophore having a carboxy group at the benzene moiety, coupled to a folate ligand moiety through a negatively charged tripeptide linker. This probe exhibits very low background fluorescence and afforded a tumor-to-background ratio (TBR) of up to 83 in FR-expressing tumor-bearing mice within 30 min. Thus, FolateSiR-1 has the potential to contribute to the research in the field of biology and the clinical medicine.