Dimerization of Organic Dyes on Luminescent Gold Nanoparticles for Ratiometric pH Sensing

Synergistic effects arising from the conjugation of organic dyes onto non‐luminescent metal nanoparticles (NPs) have greatly broadened their applications in both imaging and sensing. Herein, we report that conjugation of a well‐known pH‐insensitive dye, tetramethyl‐rhodamine (TAMRA), to pH‐insensitive luminescent gold nanoparticles (AuNPs) can lead to an ultrasmall nanoindicator that can fluorescently report local pH in a ratiometric way. Such synergy originated from the dimerization of TAMRA on AuNPs, of which geometry was very sensitive to surface charges of the AuNPs and can be reversely modulated through protonation of surrounding glutathione ligands. Not limited to pH‐insensitive dyes, this pH‐dependent dimerization can also enhance the pH sensitivity of fluorescein, a well‐known pH‐sensitive dye, within a larger pH range, opening up a new pathway to design ultrasmall fluorescent ratiometric nanoindicators with tunable wavelengths and pH response ranges.     

Supramolecular Translation of Enzymatically Triggered Disassembly of Micelles into Tunable Fluorescent Responses

The need for advanced fluorescent imaging and delivery platforms has motivated the development of smart probes that change their fluorescence in response to external stimuli. Here a new molecular design of fluorescently labeled PEG–dendron hybrids that self‐assemble into enzyme‐responsive micelles with tunable fluorescent responses is reported. In the assembled state, the fluorescence of the dyes is quenched or shifted due to intermolecular interactions. Upon enzymatic cleavage of the hydrophobic end‐groups, the labeled polymeric hybrids become hydrophilic, and the micelles disassemble. This supramolecular change is translated into a spectral response as the dye–dye interactions are eliminated and the intrinsic fluorescence is regained. We demonstrate the utilization of this molecular design to generate both Turn‐On and spectral shift responses by adjusting the type of the labeling dye. This approach enables transformation of non‐responsive labeling dyes into smart fluorescent probes.     

Excitonic interaction: another photophysical process for fluorescence‐controlled nucleic acid sensing

An excitonic interaction caused by the H‐aggregation of fluorescent dyes is a new type of useful photophysical process for fluorescence‐controlled nucleic acid sensing. We designed a fluorescence‐labeled nucleotide in which two thiazole orange dyes were linked covalently. A DNA strand containing this fluorescence‐labeled nucleotide showed absorption at 480 nm before hybridization, whereas an absorption band at 510 nm became predominant when the DNA was hybridized with the complementary strand. The shift in the absorption bands shows the existence of an excitonic interaction between dyes in the nucleotide, and as a result, emission from the doubly thiazole orange‐labeled DNA was well controlled. This clear change in fluorescence intensity depending on hybridization is applicable to multicolor RNA imaging in living cells. © 2010 The Japan Chemical Journal Forum and Wiley Periodicals, Inc. Chem Rec 10: 188–196; 2010: Published online in Wiley InterScience ( www.interscience.wiley.com ) DOI 10.1002/tcr.201000003     

“Stainomics”: Identification of mitotracker labeled proteins in mammalian cells

Organelle‐specific cell‐permeable fluorescent dyes are invaluable tools in cell biology as they reveal intracellular dynamics in living cells. Mitrotracker is a family of dyes that strongly label the mitochondrion, a key organelle associated with many crucial cellular functions. Despite the popularity of these dyes, little is known about the molecular mechanism behind their staining specificity. Here, we aimed to identify the protein targets of one member of this dye family, mitotracker red (MTR), by 2DE and MS. MTR bound to cellular proteins covalently, and its fluorescence persisted even after cell lysis, protein solubilization, denaturation, and electrophoresis. This enabled us to display MTR‐labeled proteins by 2DE. The MTR‐specific fluorescent signals on the gel revealed the spots that contained MTR‐conjugated proteins. These spots were analyzed by MS, resulting into the identification of ten proteins. We discovered that one major target is the mitochondrial protein HSP60 and that MTR staining could induce production of HSP60, predisposing cells to heat shock‐like responses. The identification of the molecular targets of biological dyes, or “stainomics,” can help correlate their intracellular staining properties with biochemical affinities. We believe this approach can be applied to a wide range of fluorescent probes.     

Keto‐benzo[h]‐Coumarin‐Based Near‐Infrared Dyes with Large Stokes Shifts for Bioimaging Applications

Fluorescence imaging is a promising tool for the visualization of biomolecules in living systems and there is great demand for new fluorescent dyes that absorb and emit in the near‐infrared (NIR) region. Herein, we constructed three new fluorescent dyes ( NBC dyes) based on keto‐benzo[h]coumarin ( k‐BC ) and benzopyrilium salts. These dyes showed large Stokes shifts (>100 nm) and NIR emission (>800 nm). The relationship between the structures and optical properties of these dyes was further investigated by using density functional theory calculations at the B3LYP/6‐3G level of theory. Fluorescence images indicated that the fabricated dyes exhibited good photostability and low cytotoxicity and, thus, have potential applications as imaging agents in living cells and animals.     

Micelle-like macromolecular systems for controlled release of daunomycin

Soluble macromolecular conjugates for the delivery of the strongly hydrophobic anticancer drug daunomycin (DM) or rubomycin with its controlled release were prepared. The solution properties of these conjugates consisting of DM bonded to copolymer of maleic anhydride and divinyl ether (DIVEMA) and a few model compounds were investigated using adsorbance spectroscopy, as well as surface activity and solubilization of water-insoluble dye measurements. The data of these studies indicated that in water solutions conjugates are associated, probably intramolecularly. This micellization in parallel with an H-bonded ionic complex between DM and polymer carrier determines the DM release. It is concluded that the desirable drug release can be achieved through changing the structure of conjugates by means of varying the constituents hydrophobicity. © 1998 John Wiley & Sons, Ltd.     

Fluorescently Labeled Substrates for Monitoring α1,3‐Fucosyltransferase IX Activity

Fucosylation is often the final process in glycan biosynthesis. The resulting glycans are involved in a variety of biological processes, such as cell adhesion, inflammation, or tumor metastasis. Fucosyltransferases catalyze the transfer of fucose residues from the activated donor molecule GDP‐β‐L ‐fucose to various acceptor molecules. However, detailed information about the reaction processes is still lacking for most fucosyltransferases. In this work we have monitored α1,3‐fucosyltransferase activity. For both donor and acceptor substrates, the introduction of a fluorescent ATTO dye was the last step in the synthesis. The subsequent conversion of these substrates into fluorescently labeled products by α1,3‐fucosyltransferases was examined by high‐performance thin‐layer chromatography coupled with mass spectrometry as well as dual‐color fluorescence cross‐correlation spectroscopy, which revealed that both fluorescently labeled donor GDP‐β‐L ‐fucose‐ATTO 550 and acceptor N‐acetyllactosamine‐ATTO 647N were accepted by recombinant human fucosyltransferase IX and Helicobacter pylori α1,3‐fucosyltransferase, respectively. Analysis by fluorescence cross‐correlation spectroscopy allowed a quick and versatile estimation of the progress of the enzymatic reaction and therefore this method can be used as an alternative method for investigating fucosyltransferase reactions.     

Ex Vivo and In Vitro Studies on the Cytotoxicity and Immunomodulative Properties of Poly(2‐isopropenyl‐2‐oxazoline) as a New Type of Biomedical Polymer

Poly(2‐alkenyl‐2‐oxazoline)s are promising functional polymers for a variety of biomedical applications, such as drug delivery systems, peptide conjugates, or gene delivery. In this study, poly(2‐isopropenyl‐2‐oxazoline) (PIPOx) is prepared through free‐radical polymerization initiated with azobisisobutyronitrile. Reactive 2‐oxazoline units in the side chain support an addition reaction with different compounds containing a carboxylic group, which facilitates the preparation of polymers labeled with two different fluorescent dyes. The cytotoxicities of 2‐oxazoline monomers, PIPOx, and fluorescently labeled PIPOx are evaluated in vitro using an 3‐(4,5‐Dimethyldiazol‐2‐yl)‐2,5‐diphenyl tetrazolium bromide assay and ex vivo using a cell proliferation assay with adenosine triphosphate bioluminescence. The cell uptake of labeled PIPOx is used to determine the colocalization of PIPOx with cell organelles that are part of the endocytic pathway. For the first time, it is shown that poly(2‐isopropenyl‐2‐oxazoline) is a biocompatible material and is suitable for biomedical applications; further, its immunomodulative properties are evaluated.

     

A General Strategy for Development of Near‐Infrared Fluorescent Probes for Bioimaging

Near‐infrared (NIR) fluorescent dyes with favorable photophysical properties are highly useful for bioimaging, but such dyes are still rare. The development of a unique class of NIR dyes via modifying the rhodol scaffold with fused tetrahydroquinoxaline rings is described. These new dyes showed large Stokes shifts (>110 nm). Among them, WR3, WR4, WR5, and WR6 displayed high fluorescence quantum yields and excellent photostability in aqueous solutions. Moreover, their fluorescence properties were tunable by easy modifications on the phenolic hydroxy group. Based on WR6, two NIR fluorescent turn‐on probes, WSP‐NIR and SeSP‐NIR, were devised for the detection of H₂S. The probe SeSP‐NIR was applied in visualizing intracellular H₂S. These dyes are expected to be useful fluorophore scaffolds in the development of new NIR probes for bioimaging.     

Histone‐Deacetylase‐Targeted Fluorescent Ruthenium(II) Polypyridyl Complexes as Potent Anticancer Agents

Histone deacetylases inhibitors (HDACis) have gained much attention as a new class of anticancer agents in recent years. Herein, we report a series of fluorescent ruthenium(II) complexes containing N¹‐hydroxy‐N⁸‐(1,10‐phenanthrolin‐5‐yl)octanediamide ( L ), a suberoylanilide hydroxamic acid (SAHA) derivative, as a ligand. As expected, these complexes show interesting chemiphysical properties, including relatively high quantum yields, large Stokes shifts, and long emission lifetimes. The in vitro inhibitory effect of the most effective drug, [Ru(DIP)₂ L ](PF₆)₂ ( 3 ; DIP: 4,7‐diphenyl‐1,10‐phenanthroline), on histone deacetylases (HDACs) is approximately equivalent in activity to that of SAHA, and treatment with complex 3 results in increased levels of the acetylated histone H3. Complex 3 is highly active against a panel of human cancer cell lines, whereas it shows relatively much lower toxicity to normal cells. Further mechanism studies show that complex 3 can elicit cell cycle arrest and induce apoptosis through mitochondria‐related pathways and the production of reactive oxygen species. These data suggest that these fluorescent ruthenium(II)–HDACi conjugates may represent a promising class of anticancer agents for potential dual imaging and therapeutic applications targeting HDACs.     

Biological Imaging with Medium‐Sensitive Bichromatic Flexible Fluorescent Dyes

A family of environment‐sensitive shape‐shifting molecules have been developed as flexible fluorescent (FlexFluor) dyes for biological imaging applications. These compounds feature a flexible bithiophene‐based fluorophore that gives rise to different emission colors in lipophilic or hydrophilic environments, as well as side groups that can be synthetically modified with ease. FlexFluor dyes are the first fluorescent dyes in which emission color can be used to indicate lipid/water environments. The behavior of these dyes in different solvents was studied, and used to simultaneously highlight lipid and water contents in adipose and brain tissues using optical fluorescence microscopy.     

A Homogenous Assay of FAD Using a Binding Between Apo‐Glucose Oxidase and FAD Labeled with an Electroactive Compound

A homogenous assay of FAD using a binding between glucose oxidase (apo‐GOD) and FAD labeled with an electroactive compound was developed. Because daunomycin is sensitively detected with voltammetry, daunomycin was connected to FAD with a cross‐linker. The peak current decreased due to the apo‐GOD‐labeled FAD binding. Competitive reaction to the apo‐GOD between FAD and the labeled FAD produces the increase of peak current. Accordingly, FAD is detected on the basis of the reaction. The merit of this method is that the influence from FMN and riboflavin in the measurement of FAD can be suppressed by the high selective binding.     

Bioconjugatable Azo‐Based Dark‐Quencher Dyes: Synthesis and Application to Protease‐Activatable Far‐Red Fluorescent Probes

We describe the efficient synthesis and one‐step derivatization of novel, nonfluorescent azo dyes based on the Black Hole Quencher‐3 (BHQ‐3) scaffold. These dyes were equipped with various reactive and/or bioconjugatable groups (azido, α‐iodoacetyl, ketone, terminal alkyne, vicinal diol). The azido derivative was found to be highly reactive in the context of copper‐catalyzed azide–alkyne cycloaddition (CuAAC) reactions and allowed easy synthetic access to the first water‐soluble (sulfonated derivative) and aldehyde‐modified BHQ‐3 dyes, the direct preparation of which failed by means of conventional azo‐coupling reactions. The aldehyde‐ and α‐iodoacetyl‐containing fluorescence quenchers were readily conjugated to aminooxy‐ and cysteine‐containing peptides by the formation of a stable oxime or thioether linkage, respectively. Further fluorescent labeling of the resultant peptide conjugates with red‐ or far‐red‐emitting rhodamine or cyanine dyes through sequential and/or one‐pot bioconjugations, led to novel Förster resonance energy transfer (FRET) based probes suitable for the in vivo detection and imaging of urokinase plasminogen activator, a key protease in cancer invasion and metastasis.     

Size‐matched alkyne‐conjugated cyanine fluorophores to identify differences in protein glycosylation

Currently, there are few methods to detect differences in posttranslational modifications (PTMs) in a specific manner from complex mixtures. Thus, we developed an approach that combines the sensitivity and specificity of click chemistry with the resolution capabilities of 2D‐DIGE. In “Click‐DIGE”, posttranslationally modified proteins are metabolically labeled with azido‐substrate analogs, then size‐ and charge‐matched alkyne‐Cy3 or alkyne‐Cy5 dyes are covalently attached to the azide of the PTM by click chemistry. The fluorescently‐tagged protein samples are then multiplexed for 2DE analysis. Whereas standard DIGE labels all proteins, Click‐DIGE focuses the analysis of protein differences to a targeted subset of posttranslationally modified proteins within a complex sample (i.e. specific labeling and analysis of azido glycoproteins within a cell lysate). Our data indicate that (i) Click‐DIGE specifically labels azido proteins, (ii) the resulting Cy‐protein conjugates are spectrally distinct, and (iii) the conjugates are size‐ and charge‐matched at the level of 2DE. We demonstrate the utility of this approach by detecting multiple differentially expressed glycoproteins between a mutant cell line defective in UDP‐galactose transport and the parental cell line. We anticipate that the diversity of azido substrates already available will enable Click‐DIGE to be compatible with analysis of a wide range of PTMs.     

Repurposing Antiviral Drugs for Orthogonal RNA‐Catalyzed Labeling of RNA

In vitro selected ribozymes are promising tools for site‐specific labeling of RNA. Previously known nucleic acid catalysts attached fluorescently labeled adenosine or guanosine derivatives through 2′,5′‐branched phosphodiester bonds to the RNA of interest. Herein, we report new ribozymes that use orthogonal substrates, derived from the antiviral drug tenofovir, and attach bioorthogonal functional groups, as well as affinity handles and fluorescent reporter units through a hydrolytically more stable phosphonate ester linkage. The tenofovir transferase ribozymes were identified by in vitro selection and are orthogonal to nucleotide transferase ribozymes. As genetically encodable functional RNAs, these ribozymes may be developed for potential cellular applications. The orthogonal ribozymes addressed desired target sites in large RNAs in vitro, as shown by fluorescent labeling of E. coli 16S and 23S rRNAs in total cellular RNA.     

BODIPYs as Chemically Stable Fluorescent Tags for Synthetic Glycosylation Strategies towards Fluorescently Labeled Saccharides

A series of fluorescent boron-dipyrromethene (BODIPY, 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene) dyes have been designed to participate, as aglycons, in synthetic oligosaccharide protocols. As such, they served a dual purpose: first, by being incorporated at the beginning of the process (at the reducing-end of the growing saccharide moiety), they can function as fluorescent glycosyl tags, facilitating the detection and purification of the desired glycosidic intermediates, and secondly, the presence of these chromophores on the ensuing compounds grants access to fluorescently labeled saccharides. In this context, a sought-after feature of the fluorescent dyes has been their chemical robustness. Accordingly, some BODIPY derivatives described in this work can withstand the reaction conditions commonly employed in the chemical synthesis of saccharides; namely, glycosylation and protecting-group manipulations. Regarding their photophysical properties, the BODIPY-labeled saccharides obtained in this work display remarkable fluorescence efficiency in water, reaching quantum yield values up to 82 %, as well as notable lasing efficiencies and photostabilities.     

Visible‐Light‐Induced Annihilation of Tumor Cells with Platinum–Porphyrin Conjugates

Despite the extensive use of porphyrins in photodynamic therapy (PDT), tetraplatinated porphyrins have so far not been studied for their anticancer properties. Herein, we report the synthesis of such novel platinum–porphyrin conjugates as well as their photophysical characterization and in vitro light‐induced anticancer properties. These conjugates showed only minor cytotoxicity in the dark, but IC₅₀ values down to 19 nM upon irradiation with light at 420 nm.These values correspond to an excellent phototoxic index (PI=IC₅₀ in the dark/IC₅₀ in light), which reached 5000 in a cisplatin‐resistant cell line. After incubation with HeLa cells, nuclear Pt concentrations were 30 times higher than with cisplatin. All of these favorable characteristics imply that tetraplatinated porphyrin complexes are worthy of exploration as novel PDT anticancer agents in vivo.     

Well‐Defined Polymer–Paclitaxel Prodrugs by a Grafting‐from‐Drug Approach

We report on the design of a polymeric prodrug of the anticancer agent paclitaxel (PTX) by a grafting‐from‐drug approach. A chain transfer agent for reversible addition fragmentation chain transfer (RAFT) polymerization was efficiently and regioselectively linked to the C2′ position of paclitaxel, which is crucial for its bioactivity. Subsequent RAFT polymerization of a hydrophilic monomer yielded well‐defined paclitaxel–polymer conjugates with high drug loading, water solubility, and stability. The versatility of this approach was further demonstrated by ω‐end post‐functionalization with a fluorescent tracer. In vitro experiments showed that these conjugates are readily taken up into endosomes where native PTX is efficiently cleaved off and then reaches its subcellular target. This was confirmed by the cytotoxicity profile of the conjugate, which matches those of commercial PTX formulations based on mere physical encapsulation.     

Red‐Emitting Rhodamines with Hydroxylated,Sulfonated, and Phosphorylated Dye Residues and Their Use in Fluorescence Nanoscopy

Fluorescent dyes emitting red light are frequently used in conventional and super‐resolution microscopy of biological samples, although the variety of the useful dyes is limited. We describe the synthesis of rhodamine‐based fluorescent dyes with absorption and emission maxima in the range of 621–637 and 644–660 nm, respectively and demonstrate their high performance in confocal and stimulated emission depletion (STED) microscopy. New dyes were prepared by means of reliable chemical transformations applied to a rhodamine scaffold with three variable positions. They feature polarity, water solubility, variable net charges, improved stabilities of N‐hydroxysuccinimidyl (NHS) esters, as well as large fluorescence quantum yields in dye solutions and antibody conjugates. The photophysical and imaging properties of dyes containing three different polar groups, namely primary phosphate, sulfonic acid (in two different positions), and hydroxyl were compared. A dye with two primary phosphate groups was explored as a valuable alternative to dyes with “classical” sulfonic acid groups. Due to the increased net charge of the phosphorylated dye (q=?4 at pH 8), it demonstrated a far better electrophoretic mobility compared with analogues with two sulfonic acid groups (q=?2). As an example, one fluorescent dye was designed to be especially convenient for practical use. It is characterized by sufficiently high chemical stability of the NHS ester, its simple isolation, handling, and solubility in aqueous buffers, as well as in organic solvents. All these features, accompanied by a zero net charge in conjugates, were accomplished by the introduction of hydrophilic groups of two types: two hydroxyl groups and one sulfonic acid residue.     

Cell‐Derived Vesicles for Single‐Molecule Imaging of Membrane Proteins

A new approach is presented for the application of single‐molecule imaging to membrane receptors through the use of vesicles derived from cells expressing fluorescently labeled receptors. During the isolation of vesicles, receptors remain embedded in the membrane of the resultant vesicles, thus allowing these vesicles to serve as nanocontainers for single‐molecule measurements. Cell‐derived vesicles maintain the structural integrity of transmembrane receptors by keeping them in their physiological membrane. It was demonstrated that receptors isolated in these vesicles can be studied with solution‐based fluorescence correlation spectroscopy (FCS) and can be isolated on a solid substrate for single‐molecule studies. This technique was applied to determine the stoichiometry of α3β4 nicotinic receptors. The method provides the capability to extend single‐molecule studies to previously inaccessible classes of receptors.