carbocyanines and tetramethylrhodamine

Topics: Base Sequence; Biomedical Enhancement; Biosensing Techniques; Carbocyanines; DNA; Fluorescence Resonance Energy Transfer; Fluorescent Dyes; Gold; Metal Nanoparticles; Models, Molecular; Rhodamines; Surface Plasmon Resonance; Surface Properties

Herein, a DNAzyme-powered nanomachine responsive to multiple hepatocellular carcinoma (HCC)-related miRNAs derived from clinical samples was designed. Initially, three types of nanomachines were constructed with dye molecule [(fluorescein (FAM), tetramethylrhodamin (TMR), and Cyanine 5 (Cy5)]-labeled DNA-RNA chimeric substrates and a specific recognized probe for the corresponding miRNAs target. Once the target miRNAs were captured by two recognizing probes, the DNA nanomachine was initiated, leading to the hybridization between the DNAzyme and the substrates. With the help of a cofactor, the automatic operation of the nanomachine was driven by cyclic cleavage of the DNAzyme. Meanwhile, we also explored the recognition behavior between the recognizing probe and the target miRNA. Subsequently, these DNAzyme-powered nanomachines were developed for the homogeneous and simultaneous detection of three target miRNAs at the femtomloar level. Furthermore, the potential in clinical diagnosis was proven by the successful determination of target miRNA in real clinical samples. Thus, this nanomachine-based strategy possesses significant potential to be an innovation in miRNA analysis methodology.

Topics: Biosensing Techniques; Carbocyanines; Carcinoma, Hepatocellular; DNA, Catalytic; Fluorescein; Fluorescent Dyes; Gold; Humans; Liver Neoplasms; Metal Nanoparticles; MicroRNAs; Nucleic Acid Hybridization; Rhodamines

Estrogen conjugates with a polyamidoamine (PAMAM) dendrimer have shown remarkably selective regulation of the nongenomic actions of estrogens in target cells. In response to pH changes, however, these estrogen-dendrimer conjugates (EDCs) display a major morphological transition that alters the accessibility of the estrogen ligands that compromises the bioactivity of the EDC. A sharp break in dynamic behavior near pH 7 occurs for three different ligands on the surface of a PAMAM-G6 dendrimer: a fluorophore (tetramethylrhodamine [TMR]) and two estrogens (17α-ethynylestradiol and diphenolic acid). Collisional quenching and time-resolved fluorescence anisotropy experiments with TMR-PAMAM revealed high ligand shielding above pH 7 and low shielding below pH 7. Furthermore, when the pH was cycled from 8.5 (conditions of ligand-PAMAM conjugation) to 4.5 (e.g., endosome/lysosome) and through 6.5 (e.g., hypoxic environment) back to pH 8.5, the 17α-ethynylestradiol- and diphenolic acid-PAMAM conjugates experienced a dramatic, irreversible loss in cell stimulatory activity; dynamic NMR studies indicated that the hormonal ligands had become occluded within the more hydrophobic core of the PAMAM dendrimer. Thus, the active state of these estrogen-dendrimer conjugates appears to be metastable. This pH-dependent irreversible masking of activity is of considerable relevance to the design of drug conjugates with amine-bearing PAMAM dendrimers.

Topics: Carbocyanines; Dendrimers; Drug Carriers; Ethinyl Estradiol; Fluorescence Polarization; Fluorescent Dyes; Gene Expression; Humans; Hydrogen-Ion Concentration; Ligands; Magnetic Resonance Spectroscopy; MCF-7 Cells; Microscopy, Fluorescence; Pentanoic Acids; Phenols; Receptors, Estrogen; Rhodamines

We demonstrate a polyion complex (PIC) nanoparticle that contains both a responsive fluorophore and an "internal standard" fluorophore for quantitative measurement of protein kinase (PK) activity. The PK-responsive fluorophore becomes more fluorescent with PK-catalyzed phosphorylation of substrate peptides incorporated in the PIC, while fluorescence from the internal standard remains unchanged during phosphorylation. This new concept will be useful for quantitative PK assays and the discovery of PK inhibitors.

Topics: Biocatalysis; Carbocyanines; Enzyme Activation; Enzyme Assays; Fluorescence; Fluorescent Dyes; Ions; Models, Molecular; Molecular Structure; Nanoparticles; Peptides; Phosphorylation; Protein Kinase C-alpha; Reference Standards; Rhodamines

Decreases in mitochondrial membrane potential (MMP) have been associated with mitochondrial dysfunction that could lead to cell death. The MMP is generated by an electrochemical gradient via the mitochondrial electron transport chain coupled to a series of redox reactions. Measuring the MMP in living cells is commonly used to assess the effect of chemicals on mitochondrial function; decreases in MMP can be detected using lipophilic cationic fluorescent dyes. To identify an optimal dye for use in a high-throughput screening (HTS) format, we compared the ability of mitochondrial membrane potential sensor (Mito-MPS), 5,5',6,6'-tetrachloro-1,1',3,3' tetraethylbenzimidazolylcarbocyanine iodide, rhodamine 123, and tetramethylrhodamine to quantify a decrease in MMP in chemically exposed HepG2 cells cultured in 1,536-well plates. Under the conditions used, the optimal dye for this purpose is Mito-MPS. Next, we developed and optimized a homogenous cell-based Mito-MPS assay for use in 1,536-well plate format and demonstrated the utility of this assay by screening 1,280 compounds in the library of pharmacologically active compounds in HepG2 cells using a quantitative high-throughput screening platform. From the screening, we identified 14 compounds that disrupted the MMP, with half-maximal potencies ranging from 0.15 to 18 μM; among these, compound clusters that contained tyrphostin and 3'-substituted indolone analogs exhibited a structure-activity relationship. Our results demonstrate that this homogenous cell-based Mito-MPS assay can be used to evaluate the ability of large numbers of chemicals to decrease mitochondrial function.

Topics: Benzimidazoles; Carbocyanines; Cell Survival; Dose-Response Relationship, Drug; Equipment Design; Fluorescent Dyes; Fluorometry; Hep G2 Cells; High-Throughput Screening Assays; History, Medieval; Humans; Inhibitory Concentration 50; Membrane Potential, Mitochondrial; Microscopy, Fluorescence; Miniaturization; Mitochondria; Molecular Structure; Reproducibility of Results; Rhodamine 123; Rhodamines; Structure-Activity Relationship

A new numerical analysis method for experimental single-pair fluorescence resonance energy transfer (sp-FRET) data is proposed. In this method, every single data point was plotted in a style of a cumulative distribution function and dedicated to curve-fitting analysis, so that the analysis does not depend on bin size. A series of numerical simulations showed that this analysis has a more efficient and accurate resolvability of components than a fitting method based on Gaussian functions to a histogram plot. A simulated data based on experimental FRET distributions were also used to discuss the fitting errors of this method. The proposed method was applied to sp-FRET experiments of doubly dye-labeled double-strand DNA with a short sequence. Mixtures of up to three species were analyzed, and the contributions up to four subpopulations were successfully resolved.

Topics: Algorithms; Biotin; Carbocyanines; Computer Simulation; DNA; Fluorescence Resonance Energy Transfer; Fluorescent Dyes; Microscopy, Confocal; Polydeoxyribonucleotides; Rhodamines; Statistical Distributions

In F1F0-ATP synthase, the subunit b2delta complex comprises the peripheral stator bound to subunit a in F0 and to the alpha3beta3 hexamer of F1. During catalysis, ATP turnover is coupled via an elastic rotary mechanism to proton translocation. Thus, the stator has to withstand the generated rotor torque, which implies tight interactions of the stator and rotor subunits. To quantitatively characterize the contribution of the F0 subunits to the binding of F1 within the assembled holoenzyme, the isolated subunit b dimer, ab2 subcomplex, and fully assembled F0 complex were specifically labeled with tetramethylrhodamine-5-maleimide at bCys64 and functionally reconstituted into liposomes. Proteoliposomes were then titrated with increasing amounts of Cy5-maleimide-labeled F1 (at gammaCys106 and analyzed by single-molecule fluorescence resonance energy transfer. The data revealed F1 dissociation constants of 2.7 nm for the binding of F0 and 9-10 nm for both the ab2 subcomplex and subunit b dimer. This indicates that both rotor and stator components of F0 contribute to F1 binding affinity in the assembled holoenzyme. The subunit c ring plays a crucial role in the binding of F1 to F0, whereas subunit a does not contribute significantly.

Topics: Adenosine Triphosphate; ATP Synthetase Complexes; Bacterial Proton-Translocating ATPases; Carbocyanines; Dimerization; Escherichia coli; Fluorescence Resonance Energy Transfer; Fluorescent Dyes; Hydrolysis; Kinetics; Liposomes; Mitochondrial Proton-Translocating ATPases; Mutagenesis, Site-Directed; Protein Binding; Protein Subunits; Rhodamines; Spectrometry, Fluorescence; Substrate Specificity

The EF(0)F(1)-ATP synthase mutants bQ64C and gamma T106C were labelled selectively with the fluorophores tetramethylrhodamine (TMR) at the b-subunit and with a cyanine (Cy5) at the gamma-subunit. After reconstitution into liposomes, these double-labelled enzymes catalyzed ATP synthesis at a rate of 33 s(-1). Fluorescence of TMR and Cy5 was measured with a confocal set-up for single-molecule detection. Photon bursts were detected, when liposomes containing one enzyme traversed the confocal volume. Three states with different fluorescence resonance energy transfer (FRET) efficiencies were observed. In the presence of ATP, repeating sequences of those three FRET-states were identified, indicating stepwise rotation of the gamma-subunit of EF(0)F(1).

Topics: Adenosine Triphosphate; Carbocyanines; Energy Transfer; Fluorescence; Fluorescent Dyes; Hydrolysis; Liposomes; Microscopy, Confocal; Models, Molecular; Mutation; Protein Conformation; Protein Subunits; Proton-Translocating ATPases; Rhodamines; Rotation; Spectrometry, Fluorescence

An immunohistochemical technique was developed to visualize nitric oxide synthase (NOS)-immunopositive neurons in fresh-frozen tissue sections of rat brain for laser capture microdissection (LCM) and mRNA analysis. The effect of tissue fixation and the choice of fluorophore were investigated. Here we describe a rapid immunofluorescence protocol that allows the processing of fresh-frozen tissue sections within eight minutes and subsequent mRNA extraction and real-time PCR from pools of 20 NOS-immunopositive LCM neurons. The cellular complement of a subset of ionotropic glutamate receptors, specifically N-methyl-D-aspartate receptor subunit mRNAs, was examined because these receptor complexes are thought to mediate the effects of fast and slow glutamate excitotoxicity. Real-time PCR data revealed that striatal NOS interneurons express the mRNAs encoding NR1, NR2A, NR2B, and NR2D but not NR2C. These LCM mRNA data are consistent with previous in situ hybridization studies and demonstrate the utility of rapid immuno-LCM with real-time quantitative PCR for the study of mRNA abundance in discrete populations of neurons within the mammalian brain.

Topics: Animals; Carbocyanines; Cell Separation; Computer Systems; Corpus Striatum; Fluorescent Antibody Technique, Indirect; Fluorescent Dyes; Frozen Sections; Hydrazines; Interneurons; Isoenzymes; Lasers; Nerve Tissue Proteins; Nitric Oxide Synthase; Nitric Oxide Synthase Type I; Polymerase Chain Reaction; Rats; Rats, Sprague-Dawley; Receptors, N-Methyl-D-Aspartate; Rhodamines; RNA, Messenger; Specimen Handling; Time Factors

The ability to distinguish and identify specific subcellular compartments is essential to understanding organelle function, biogenesis, and maintenance within cells and to defining protein trafficking pathways. Fluorescent dyes and/or fluorescently labeled lipid derivatives can be used to identify ER, Golgi complex, and mitochondria. Specific conditions for labeling each of these compartments are described.

Topics: 4-Chloro-7-nitrobenzofurazan; Animals; Carbocyanines; Cells, Cultured; Ceramides; Coloring Agents; Endoplasmic Reticulum; Fluorescent Dyes; Golgi Apparatus; Intracellular Membranes; Mitochondria; Rhodamines; Specimen Handling; Sphingosine; Staining and Labeling; Tissue Fixation

We present results of an approach in which low-density labeled DNA itself provides an amplification of the cross-correlated fluorescent signal in the two-color cross-correlation function. Tetramethylrhodamine-4-dUTP and Cy5-dCTP are incorporated by polymerase chain reaction at multiple positions of the same 217 bp target DNA. We call this novel approach the 'two-color FCS signal amplification'. The signal amplification is an example for interactions of two ligands with different colors at multiple positions of the same target.

Topics: Carbocyanines; Deoxyuracil Nucleotides; DNA; Fluorescent Dyes; Models, Theoretical; Polymerase Chain Reaction; Rhodamines; Spectrometry, Fluorescence

The early events in signal transduction from the epidermal growth factor (EGF) receptor (EGFR) are dimerization and autophosphorylation of the receptor, induced by binding of EGF. Here we observe these events in living cells by visualizing single molecules of fluorescent-dye-labelled EGF in the plasma membrane of A431 carcinoma cells. Single-molecule tracking reveals that the predominant mechanism of dimerization involves the formation of a cell-surface complex of one EGF molecule and an EGFR dimer, followed by the direct arrest of a second EGF molecule, indicating that the EGFR dimers were probably preformed before the binding of the second EGF molecule. Single-molecule fluorescence-resonance energy transfer shows that EGF-EGFR complexes indeed form dimers at the molecular level. Use of a monoclonal antibody specific to the phosphorylated (activated) EGFR reveals that the EGFR becomes phosphorylated after dimerization.

Topics: Antibodies, Monoclonal; Calcium; Carbocyanines; Carcinoma; Cell Membrane; Dimerization; Energy Transfer; Epidermal Growth Factor; ErbB Receptors; Fluorescent Dyes; Humans; Intracellular Fluid; Microscopy, Fluorescence; Phosphorylation; Rhodamines; Signal Transduction; Tumor Cells, Cultured

To understand the mechanism of GroEL-assisted protein folding, we observed the interaction of fluorescence-labeled GroEL with fluorescence-labeled substrate proteins at the single molecule level by total internal reflection fluorescence microscopy. GroEL with a A133C mutation in the equatorial domain was labeled with a fluorescent dye, tetramethylrhodamine. As substrate proteins, we used the largely denatured and partly denatured forms of bovine beta-lactoglobulin, both labeled with another fluorescent dye, Cy5. The complexes formed by GroEL with these substrates were characterized by size-exclusion gel chromatography. The recovered complexes were then observed by fluorescence microscopy. For both substrates, agreement of the fluorescent spots for tetramethylrhodamine and Cy5 indicated formation of the complex at the single molecule level. Similar observation of macroscopic binding by size-exclusion chromatography and microscopic binding by the fluorescence microscopy was done for the folding intermediate of Cy5-labeled bovine rhodanese. The fluorescence microscopy opens a new avenue for studying the interaction of GroEL with substrate proteins.

Topics: Adenosine Triphosphate; Amino Acid Substitution; Animals; Carbocyanines; Cattle; Chaperonin 60; Dimerization; Disulfides; Escherichia coli; Lactoglobulins; Microscopy, Fluorescence; Models, Molecular; Protein Binding; Protein Conformation; Protein Denaturation; Protein Folding; Rhodamines; Salts; Static Electricity; Thiosulfate Sulfurtransferase

It is commonly accepted that mitochondria undergo major changes early during the apoptotic process and that these alterations are critical for the death/life decision. Here we report that Jurkat T cell leukemia cells exhibit a perturbed incorporation of potential-sensitive fluorochromes. After 6 h of CD95/Fas/APO-1 crosslinking, a significant fraction of still normal-sized Jurkat cells exhibit a decreased incorporation of three different cationic lipophilic dyes commonly used for the quantitation of the mitochondrial transmembrane potential (deltapsi(m)): DiOC6(3), chloromethyl-X-rosamine, and tetramethylrhodaminemethylester. In contrast, upon induction of apoptosis, cells tend to exhibit an increase in the fluorescence obtained with rhodamine 123. The increased rhodamine 123 fluorescence into cells undergoing apoptosis is not affected by labeling in the presence of the protonophore m-chlorophenylhydrazone and thus cannot be attributed to a change in the deltapsi(m). Six hours after CD95 ligation no changes are found among normal-sized cells in the incorporation of mitotracker green and nonylacridine orange, which both measure mitochondrial mass. However, a fraction of cells exhibit an increased staining with the Apo2.7 antibody which detects a mitochondrial antigen generated during apoptosis. These findings underline the importance of using adequate fluorochromes for the quantitation of mitochondrial changes occurring during early apoptosis. Moreover, they cast doubts on those studies that, using rhodamine 123, hypothesized that apoptosis would be associated with a stable or increased deltapsi(m).

Topics: Aldehydes; Aminoacridines; Antibodies, Monoclonal; Apoptosis; Carbocyanines; fas Receptor; Flow Cytometry; Fluorescence; Fluorescent Dyes; Humans; Jurkat Cells; Membrane Potentials; Mitochondria; Organic Chemicals; Rhodamine 123; Rhodamines

We measured the lateral mobility of two fluorescent lipid probes dioctadecylindocarbocyanine (diI) and tetramethyl rhodamine phosphatidylethanolamine (R-PE) in the plasma membranes of Saccharomyces cerevisiae ino1 and opi3 spheroplasts. These are well-characterized strains with mutations in the inositol and phosphatidylcholine biosynthetic pathways. Membrane phospholipid composition was altered by growing these mutants in the presence or absence of inositol and choline. Lateral mobility was measured by fluorescence recovery after photobleaching (FRAP). Microscopic fluorescence polarization employing CCD digital imaging produced an ordered orientation distribution of the lipid probe diI, confirming that at least one of the probes was largely incorporated into the bilayer membrane. Our results demonstrated anomalously slow mobility of both lipid probes for both mutants, regardless of whether the lipid composition was near normal or dramatically altered in relative composition of phosphatidylinositol and phosphatidylcholine. Trypsinization of the spheroplasts to remove surface proteins resulted in markedly increased lateral mobility. However, even in trypsinized spheroplasts, mobility was still somewhat lower than the mobility observed in the membrane of mammalian cells, such as rat smooth muscle culture cells tested here for comparison.

Topics: Carbocyanines; Cell Membrane; Fluorescence Polarization; Fluorescent Dyes; Membrane Lipids; Phosphatidylethanolamines; Rhodamines; Saccharomyces cerevisiae