carbocyanines and 3-3--diethylthiacarbocyanine-iodide

Changes in microscopic viscosity represent an important characteristic of structural transitions in soft matter systems. Here we demonstrate the use of molecular rotors to explore the changes in microrheology accompanying the transition of proteins from their soluble states into a gel phase composed of amyloid fibrils. The formation of beta-sheet rich protein aggregates, including amyloid fibrils, is a hallmark of a number of neurodegenerative disorders, and as such, the mechanistic details of this process are actively sought after. In our experiments, molecular rotors report an increase in rigidity of approximately three orders of magnitude during the aggregation reaction. Moreover, phasor analysis of the fluorescence decay signal from the molecular rotors suggests the presence of multiple distinct mechanistic stages during the aggregation process. Our results show that molecular rotors can reveal key microrheological features of protein systems not observable through classical fluorescent probes operating in light switch mode.

Topics: Amyloid; Animals; Benzothiazoles; Carbocyanines; Cattle; Chickens; Egg Proteins; Gels; Insulin; Microfluidics; Microscopy, Fluorescence, Multiphoton; Muramidase; Phase Transition; Protein Multimerization; Protein Structure, Secondary; Solubility; Solutions; Thiazoles; Viscosity

This paper presents wavelength configurable on-chip solid-state ring lasers fabricated by a single-mask standard lithography. The single- and coupled-ring resonator hosts were fabricated on a fused-silica wafer and filled with 3,3'-Diethyloxacarbocyanine iodide (CY3), Rhodamine 6G (R6G), and 3,3'-Diethylthiadicarbocyanine iodide (CY5)-doped polymer as the reconfigurable gain media. The recorded lasing threshold was ~220 nJ/mm(2) per pulse for the single-ring resonator laser with R6G, marking the lowest threshold shown by solid-state dye-doped polymer lasers fabricated with a standard lithography process on a chip. A single-mode lasing from a coupled-ring resonator system with the lasing threshold of ~360 nJ/mm(2) per pulse was also demonstrated through the Vernier effect. The renewability of the dye-doped polymer was examined by removing and redepositing the dye-doped polymer on the same resonator hosts for multiple cycles. We recorded consistent emissions from the devices for all trials, suggesting the feasibility of employing this technology for numerous photonic and biochemical sensing applications that entail for sustainable, reconfigurable, and low lasing threshold coherent light sources on a chip.

Topics: Benzothiazoles; Biosensing Techniques; Carbocyanines; Equipment Design; Fluorescent Dyes; Lasers, Solid-State; Optics and Photonics; Polymers; Reproducibility of Results; Rhodamines; Silicon Dioxide

In many settings, molecular testing is needed but unavailable due to complexity and cost. Simple, rapid, and specific DNA detection technologies would provide important alternatives to existing detection methods. Here we report a novel, rapid nucleic acid detection method based on the accelerated photobleaching of the light-sensitive cyanine dye, 3,3'-diethylthiacarbocyanine iodide (DiSC(2)(3) I(-)), in the presence of a target genomic DNA and a complementary peptide nucleic acid (PNA) probe. On the basis of the UV-vis, circular dichroism, and fluorescence spectra of DiSC(2)(3) with PNA-DNA oligomer duplexes and on characterization of a product of photolysis of DiSC(2)(3) I(-), a possible reaction mechanism is proposed. We propose that (1) a novel complex forms between dye, PNA, and DNA, (2) this complex functions as a photosensitizer producing (1)O(2), and (3) the (1)O(2) produced promotes photobleaching of dye molecules in the mixture. Similar cyanine dyes (DiSC(3)(3), DiSC(4)(3), DiSC(5)(3), and DiSC(py)(3)) interact with preformed PNA-DNA oligomer duplexes but do not demonstrate an equivalent accelerated photobleaching effect in the presence of PNA and target genomic DNA. The feasibility of developing molecular diagnostic assays based on the accelerated photobleaching (the smartDNA assay) that results from the novel complex formed between DiSC(2)(3) and PNA-DNA is under way.

Topics: Benzothiazoles; Carbocyanines; Catalysis; Circular Dichroism; Coloring Agents; DNA; Molecular Diagnostic Techniques; Oligonucleotide Probes; Peptide Nucleic Acids; Photobleaching; Sequence Analysis, DNA; Spectrophotometry, Ultraviolet

The human genome contains thousands of regions, including that of the telomere, that have the potential to form quadruplex structures. Many of these regions are potential targets for therapeutic intervention. There are many different folding patterns for quadruplex DNAs and the loops exhibit much more variation than do the quartets. The successful targeting of a particular quadruplex structure requires distinguishing that structure from all of the other quadruplex structures that may be present. A mix and measure fluorescent screening method has been developed, that utilizes multiple reporter molecules that bind to different features of quadruplex DNA. The reporter molecules are used in combination with DNAs that have a variety of quadruplex structures. The screening is based on observing the increase or decrease in the fluorescence of the reporter molecules. The selectivity of a set of test molecules has been determined by this approach.

Topics: Benzothiazoles; Binding, Competitive; Carbocyanines; Circular Dichroism; DNA; Fluorescent Dyes; G-Quadruplexes; Ligands; Mesoporphyrins; Spectrometry, Fluorescence

The pore-forming activity of Cry1Ab, Cry1Fa and Cry1Ca toxins and their interaction with leucine transport mediated by the K(+)/leucine cotransporter were studied in brush border membrane vesicles (BBMVs) isolated from the midgut of Ostrinia nubilalis and Sesamia nonagrioides. In both species, as in other Lepidoptera, leucine uptake by BBMVs can take place in the absence of cations, but it can also be driven by a K(+) gradient. Experiments with the voltage-sensitive fluorescent dye 3,3'-diethylthiacarbocyanine iodide proved that Cry1Ab, a Bacillus thuringiensis toxin active in vivo, enhanced the membrane permeability to potassium in O. nubilalis BBMVs. This result is in agreement with similar effects observed in S. nonagrioides BBMV incubated with various Cry1 toxins active in vivo. The effect of the above toxins was tested on the initial rate of 0.1 mM: leucine influx. Instead of an increase in leucine influx, a reduction was observed with the Cry1 toxins active in vivo. Cry1Ab and Cry1Fa, but not the inactive toxin Cry1Da, inhibited in a dose-dependent manner leucine uptake both in the absence and in the presence of a K(+) gradient, a clear indication that their effect is independent of the channel formed by the toxins and that this effect is exerted directly on the amino acid transport system.

Topics: Animals; Bacillus thuringiensis; Bacillus thuringiensis Toxins; Bacterial Proteins; Bacterial Toxins; Benzothiazoles; Biological Transport, Active; Carbocyanines; Cell Membrane Permeability; Endotoxins; Fluorescent Dyes; Hemolysin Proteins; Intestinal Mucosa; Larva; Lepidoptera; Leucine; Membrane Potentials; Microvilli; Potassium; Transport Vesicles

Optical spectroscopy and molecular dynamics simulations have been used to study the interaction between a cationic cyanine dye and peptide nucleic acid (PNA)-DNA duplexes. This recognition event is important because it leads to a visible color change, signaling successful hybridization of PNA with a complementary DNA strand. We previously proposed that the dye recognized the minor groove of the duplex, using it as a template for the assembly of a helical aggregate. Consistent with this, we now report that addition of isobutyl groups to the PNA backbone hinders aggregation of the dye when the substituents project into the minor groove but have a weaker effect if directed out of the groove. UV-Visible and circular dichroic spectroscopy were used to compare aggregation on the different PNA-DNA duplexes, while molecular dynamics simulations were used to confirm that the substituents block the minor groove to varying degrees, depending on the configuration of the starting amino acid. In addition to a simple steric blockage effect of the substituent, the simulations suggest that directing the isobutyl group into the minor groove causes the groove to narrow and the duplex to become more rigid, structural perturbations that are relevant to the growing interest in backbone-modified PNA for applications in the biological and materials sciences.

Topics: Benzothiazoles; Carbocyanines; Circular Dichroism; Coloring Agents; Computer Simulation; DNA; Models, Molecular; Nucleic Acid Heteroduplexes; Peptide Nucleic Acids; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; Spectrophotometry, Ultraviolet; Thermodynamics

A symmetrical cyanine dye was previously shown to bind as a cofacial dimer to alternating A-T sequences of duplex DNA. Indirect evidence suggested that dimerization of the dye occurred in the minor groove. 1H NMR experiments reported here verify this model based on broadening and shifting of signals due to protons on carbon 2 of adenine and imino protons at the central five A-T pairs of the 11 base pair duplex: 5'-GCGTATATGCG-3'/3'-CGCATATACGC-5'. This binding mode is similar to that of distamycin A, even though the dye lacks the hydrogen-bonding groups used by distamycin for sequence-specific recognition. Surprisingly, the third base pair (G-C) was also implicated in the binding site. UV-vis experiments were used to compare the extent of dimerization of the dye for 11 different sequence variants. These experiments verified the importance of a G-C pair at the third position: replacing this pair with A-T suppressed dimerization. These results indicate that the dye binding site spans six base pairs: 5'-GTATAT-3'. The initial G-C pair seems to be important for widening the minor groove rather than for making important contacts with the dye molecules since inverting its orientation to C-G or replacing it with I-C still led to favorable dimerization of the dye.

Topics: Benzothiazoles; Carbocyanines; Dimerization; DNA; Nuclear Magnetic Resonance, Biomolecular; Oligodeoxyribonucleotides

Topics: Base Pair Mismatch; Benzothiazoles; Carbocyanines; Colorimetry; DNA; Peptide Nucleic Acids; Staining and Labeling

In this study the effect of a transmembrane electrical potential on the phospholipid headgroup conformation was investigated using the 2H-NMR technique. Large unilamellar vesicles were prepared of dioleoylphosphatidylcholine, specifically 2H-labeled at the alpha- or beta-position of the choline group. No conformational change of the phosphocholine headgroup could be detected after induction of a valinomycin-induced K(+)-diffusion potential across the bilayer. However, this method could be used to measure the redistribution of tetraphenylphosphonium across the bilayer in response to delta psi, which reorients the phosphocholine headgroups in the opposite bilayer-water interfaces.

Topics: Benzothiazoles; Carbocyanines; Coloring Agents; Deuterium; Lipid Bilayers; Liposomes; Magnetic Resonance Spectroscopy; Membrane Potentials; Molecular Conformation; Onium Compounds; Organophosphorus Compounds; Phosphatidylcholines; Phosphatidylglycerols; Phosphorylcholine; Tetraphenylborate

All symmetrical dialkylthiacarbocyanine dyes, with the exception of the diethyl derivatives, are incorporated into liposomes. Absorption and fluorescence data indicate a solubilization site close to the bilayer surface with the alkyl chains penetrating into the lipid bilayer. Incorporation into organized assemblies affects the photophysical parameters of these dyes. Photoisomerization occurring from the first excited state becomes more difficult as the restrictive effect of the solubilization site increases. As a consequence, competing deactivation processes, such as fluorescence and triplet formation, become more efficient with the result that fluorescence quantum yields, triplet yields and singlet oxygen quantum yields are larger in liposomes than in homogeneous solution. Dihexylthiacarbocyanine iodide has a fluorescence quantum yield of 0.27 and 0.10 (25 degrees C) in dimyristoylphosphatidyl-choline liposomes and ethanol, respectively, and the singlet oxygen yield increases by a factor three to 0.006 on going from ethanol to liposomes. The effect of a highly organized environment is even more pronounced in thin polymer films. In these systems, photoisomerization is completely inhibited and only triplet formation is observed in the transient absorption spectrum.

Topics: Benzothiazoles; Carbocyanines; Coloring Agents; Dimyristoylphosphatidylcholine; Lasers; Light; Liposomes; Membranes; Photolysis; Polymers; Spectrophotometry

Calcium and membrane potential sensitive dyes have been widely used to study the biochemical effects of the intracellular calcium concentration and of the membrane potential on diverse biochemical processes. However, due to the discontinuous measurement techniques applied, it was until now impossible to get an insight into the sequence and dynamics of the induced biological reactions. In order to study the relationship between the intracellular calcium concentration and the membrane potential, an apparatus was developed capable of measuring both biological processes simultaneously. Potassium chloride induced changes of the synaptosomal membrane potential and of the intracellular calcium concentration are presented.

Topics: Aniline Compounds; Animals; Benzothiazoles; Calcium; Carbocyanines; Coloring Agents; Female; Fluorescent Dyes; Kinetics; Membrane Potentials; Potassium Chloride; Rats; Rats, Inbred Strains; Synaptic Membranes; Xanthenes