Dicarbocyanine Dyes Research Articles

DNA Photocleavage in the Near-Infrared Wavelength Range by 2-Quinolinium Dicarbocyanine Dyes.

Here, we report the syntheses of two pentamethine cyanine dyes containing quinolinium rings and substituted with either hydrogen (3) or bromine (4) at the meso carbon. The electron withdrawing bromine atom stabilizes dye 4 in aqueous buffer, allowing complex formation to occur between the dye and double-helical DNA. UV–visible, CD, and fluorescence spectra recorded at low DNA concentrations suggest that dye 4 initially binds to the DNA as a high-order aggregate. As the ratio of DNA to dye is increased, the aggregate is converted to monomeric and other low-order dye forms that interact with DNA in a non-intercalative fashion. The brominated dye 4 is relatively unreactive in the dark, but, under 707–759 nm illumination, generates hydroxyl radicals that cleave DNA in high yield (pH 7.0, 22 °C). Dye 4 is also taken up by ES2 ovarian carcinoma cells, where it is non-toxic under dark conditions. Upon irradiation of the ES2 cells at 694 nm, the brominated cyanine reduces cell viability from 100 ± 10% to 14 ± 1%. Our results suggest that 2-quinolinium-based carbocyanine dyes equipped with stabilizing electron withdrawing groups may have the potential to serve as sensitizing agents in long-wavelength phototherapeutic applications.

Novel Simple Cyanine, Carbocyanine, and Dicarbocyanine Dyes: Synthesis, Characterization and Application on Polyester Fabric

Novel Simple Cyanine, Carbocyanine, and Dicarbocyanine Dyes: Synthesis, Characterization and Application on Polyester Fabric

Single photon DNA photocleavage at 830 nm by quinoline dicarbocyanine dyes.

We have synthesized symmetrical carbocyanine dyes in which two 4-quinolinium rings are joined by a pentamethine bridge that is meso-substituted with H or Cl. Irradiation of the halogenated dye at 830 nm produces hydroxyl radicals that generate DNA direct strand breaks. This represents the first reported example of DNA photocleavage upon single photon excitation of a chromophore at wavelengths above 800 nm.

Template‐Free Self‐Assembly of Dimeric Dicarbocyanine Dyes

AbstractSymmetrical dicarbocyanine dyes are known to cooperatively assemble on DNA templates. With the goal of developing dyes that are capable of template‐free self‐assembly, two N‐linked dimeric benzothiazole containing pentamethine cyanine dyes have been synthesized. UV‐visible spectroscopy of the dimeric dyes reveals very strong propensities for self‐assembly unlike their monomeric dye counterparts. The N‐propyl linked dye exhibits pronounced H‐aggregation at micromolar dye concentrations with the absorption maxima blue‐shifted by nearly 200 nm. In contrast, an N‐hexyl linked dye preferentially folds into H‐dimers. Similar aggregates of the monomeric dicarbocyanine dyes are known to be observed at much higher dye concentrations or in presence of suitable templates such as DNA molecules. The aggregate species of the dimeric dyes are identified based on shifts in their absorbance maxima and quenched fluorescence. The calculated electronic structure of the dimeric dyes supports their observed aggregation behaviour. Further, introduction of DNA molecules with AT‐tracts leads to transformation of the spontaneously formed dimeric dye H‐aggregates and H‐dimers into DNA‐bound dye species.

Optical properties and component composition of layers of cyanine dyes on dielectric supports: influence of asymmetry of the molecular electron density distribution

The component composition of molecular layers of dicarbocyanine dyes of cationic type on glass is determined by the absorption spectroscopy methods. For symmetric and asymmetric molecules the component composition depends on the chemical structure of a molecule and its interaction with the substrate, which are responsible for the electron density distribution in a molecule. The interaction with the substrate depends on the thickness of a layer and the orientation of a layer molecule on the substrate. The increase in the separation between the molecule and the substrate in thicker layers decreases the interaction with the substrate and the asymmetry of a molecule. In symmetric and slightly asymmetric dyes the value of the charge difference on the end groups decreases with increasing layer thickness, whereas in dyes with a large asymmetry, both the value and the sign of the charge difference change. The above results are confirmed by data on the computer simulation of the charge distribution in a dicarbocyanine cation upon its interaction with the oxygen anion on the substrate.

Studies of thermally stimulated reversible restructuring and variation of the optical parameters of molecular layers of polymethine dyes

This paper discusses the thermally stimulated restructuring of the molecular components of layers of symmetric polymethine dicarbocyanine dyes. Heating the layer to a temperature above 100°C causes a partially reversible conversion of the dimers into monomeric stereoisomers (the all-trans isomer and the β-cis isomer) and into J aggregates, as well as restructuring the β-cis isomer into the all-trans isomer. The restructuring time is tens of minutes. The rate of such conversions depends on the components present in the layer, the structure of the heterocyclic end groups of the monomeric molecules, and the temperature.

How temperature affects the stereoisomerization variations of the optical properties of solutions of polymethine dyes

The influence of temperature on the absorption and fluorescence properties of solutions of dicarbocyanine dyes and on stereoisomerization processes is studied in the range from −60 to 60 °C. It is shown that the optical density and the absorption spectrum vary as a result of temperature redistribution of the concentration of four stereoisomeric forms. The fluorescence-intensity variations are determined by variations of both the concentration of the isomers and the quenching rates associated with photoisomerization of the molecules in the excited state. It is concluded that recording the changes of the optical density and fluorescence intensity makes it possible to investigate the temperature distribution in a solution. It is shown that the fluorescence technique of investigation is several times more sensitive than the absorption technique.

Effect of the thickness of a dicarbocyanine dye layer on the conformational composition and spatial orientation of layer components

The conformational and aggregate structure and the spatial orientation of polyatomic organic molecules on solid substrates are investigated by the example of molecular layers of symmetric and asymmetric dicarbocyanine dyes. It is shown that the structure of a dicarbocyanine dye layer is determined by two mechanisms: (i) the change in the symmetry of the intramolecular charge distribution in the monomeric components of the layer as a result of the intermolecular interaction with the substrate, which leads to closer values of the equilibrium concentrations of two monomers with different spatial structure (rotational stereoisomers), and (ii) the association of monomer molecules with formation of dimers and J aggregates. The relative position of the spectra of the layer components, the spatial orientation of the components, and the concentration ratio of different monomeric forms depend on the structure and the electron-donating ability of terminal groups. In going from a monomolecular layer to multilayered structures, the asymmetry of the intramolecular charge distribution induced by the substrate and the ratio of different stereoisomeric forms first change and then become stabilized.

Step photoisomerization of dicarbocyanine dyes

Step photostereoisomerization of solutions of dicarbocyanine dyes was studied by laser photolysis. It is shown that, due to excitation, primary mono-cis-photoisomers are formed (a one-step process), whose excitation results in the formation of a γβ-di-cis-isomer (a two-step process). It was proved that the γβ-di-cis-isomer is formed mainly from a γ-mono-cis-isomer. The relaxation of the ground state of the γβ-di-cis-isomer to the ground state of a stable all-trans-isomer occurs in steps via two channels, in which γ-and β-mono-cis-isomers arise as intermediate products. The relaxation rates of both channels are different. The shift of the wavelength related to the maximum of absorption in the spectra of the primary and secondary isomers relative to that of the all-trans-isomer depends on the electron-donor ability of terminal groups. Quantum-chemical calculations of changes in the energies of the ground and first excited singlet states of a molecule, caused by the rotation around several bonds in the methine chain, were carried out.

Photosensitized processes in dicarbocyanine dyes induced by energy transfer: delayed fluorescence, trans→ cis isomerization and electron transfer

The triplet-induced photoprocesses of 3,3′-diethylthiadicarbocyanine ( 1), 3,3′-diethyloxadicarbocyanine ( 2), its methyl ( 3), ethyl ( 4) and phenyl ( 5) derivatives as well as of 1,1′,3,3,3′,3′-hexamethylindodicarbocyanine ( 6) and its chlorine ( 7), bromine ( 8) and methyl ( 9) derivatives were studied in deoxygenated acetonitrile upon anthracene-sensitized excitation by conventional and ns-flash photolysis. The emission is attributed to the sensitized (mixed) type rather than E- or P-type delayed fluorescence. The triplet state of the dyes, radicals and a cis isomer with absorption maxima at 650–1000, 450–500 and 620–695 nm, respectively, were spectroscopically and kinetically distinguished. The trans→ cis photoisomerization can be initiated by both triplet (mostly) and singlet states of the dyes.

Dicarbocyanine dyes in methanol solution probed by depolarized Rayleigh and hyper-Rayleigh light scattering

The hyper-Rayleigh scattering (HRS) intensity of two symmetric carbocyanine dyes (1122 DEDC and 1144 DEDC, full names given in the text) in methanol is measured as a function of dye concentration. These dye molecules at equilibrium show a negligible permanent dipole moment. The low concentration data showing that the HRS intensity is proportional to the dye concentration are used to determine the first hyperpolarizability for each of these dyes. However, above a concentration ρb=0.1×10−3 M, the HRS intensity shows an anomalous concentration dependence. Above ρb, the HRS intensity shows a saturation behavior and it even decreases with increasing concentration at high dye concentration. The depolarization ratio of the HRS intensity is also measured as a function of dye concentration. At lowest concentration, the depolarization ratio is 0.18. As the dye concentration increases, the depolarization ratio also rapidly increases but the increase quickly saturates as the concentration exceeds ρb. The concentration dependence of the HRS intensity and depolarization ratio are interpreted as due to formation of molecular aggregates. The depolarized Rayleigh scattering (DRS) intensity is also measured as a function of dye concentration. The result of DRS corroborates well with that found in HRS.

Chapter 7 Imaging Endoplasmic Reticulum in Living Sea Urchin Eggs

This chapter describes a way to label the endoplasmic reticulum (ER) of living sea urchin eggs so that it can be imaged by confocal microscopy. This involves intracellular injection of the dicarbocyanine DiI dissolved in oil. DiI spreads in the ER of the egg and then is observed by confocal microscopy. The name DiI refers to either DiIC 16 or DiIC 18 . These are dicarbocyanine dyes that consist of a fluorescent portion and two long alkyl chains. Both dyes seem to behave similarly in labeling the ER. The method labels membranes that are part of the ER, including the nuclear envelope and the cortical ER network, and the method produces similar staining as seen with immunocytochemical localization of a calsequestrin-like protein that was isolated from sea urchin egg microsomes. DiI does not label yolk platelets or cortical granules, which are abundant in sea urchin eggs. There are two significant precautions about the use of this method. First, bright punctuate labeling accumulates with time and may represent dye leaving the ER network via membrane traffic with the Golgi apparatus. Second, it is not possible to show that DiI labels all of the ER. If the ER is a single interconnected membrane, then this method probably labels all of the ER.

The relation between dicarbocyanine dye fluorescence and the membrane potential of human red blood cells set at varying Donnan equilibria.

The fluorescence, F, of two dicarbocyanine dyes, diS-C3(5) and diI-C3(5), depends both on the membrane potential, E, and on the intracellular pH, pHc, or human red blood cells. Compositions of isotonic media have been devised in which the equilibrium Donnan potential, E, varies at constant pHc and in which pHc varies at constant E. Dye fluorescence measurements in these suspensions yield calibrations of +1.7 % delta F/mV for diS-C3(5) and +0.6 % delta F/mV for diI-C3 (5). While pHo does not affect F of either dye, changes in pHc of 0.1 unit at constant E cause changes of F equivalent to those induced by 2--3mV. Based on these results, a method is given for estimating changes in E from dye fluorescence in experiments in which E and pHc co-vary. The relation of F to E also depends in a complex way on the type and concentration of cells and dye, and the wavelengths employed. The equilibrium calibration of dye fluorescence, when applied to diffusion potentials induced by 1 microM valinomycin, yields a value for the permeability ratio, PK.VAL/PCl, of 20 +/- 5, in agreement with previous estimates by other methods. The calibration of F is identical both for diffusion potentials and for equilibrium potentials, implying that diC-C3(5) responds to changes in voltage independently of ionic fluxes across the red cell membrane. Changes in the absorption spectra of dye in the presence of red cells in response to changes in E show that formation of nonfluorescent dimers contributes to fluorescence quenching of diS-C3(5). In contrast, only a hydrophobic interaction of dye monomers need be considered for diI-C3(5), indicating the occurrence of a simpler mechanism of fluorescence quenching.

Dicarbocyanine fluorescent probes of membrane potential block lymphocyte capping, deplete cellular ATP and inhibit respiration of isolated mitochondria

3,3′-Dipropylthiodicarbocyanine iodide, a widely used fluorescent probe of membrane potential, was found to inhibit anti-Ig antibody, induced capping of mouse lymphocytes. The dye also lowered the cell ATP content. Experiments with isolated mitochondria revealed that the probe had a potent inhibitory action at site I of the respiratory chain. This mitochondrial blockade helps to explain the ATP depletion and blockade of capping, and gives cause for caution in the use of this dye as a probe of cell membrane potential. Three related dicarbocyanine dyes had similar toxic effects, but two cyanine dyes with much longer alkyl side chains, which have been used as probes of membrane fluidity, did not.

Laser photolysis of dicarbocyanine dyes

1. The photoisomerization of the indolenine dicarbocyanine dyes leads to the formation of ordinary long-lived trans photoisomers and short-lived sterically hindered di-cis photoisomers. 2. The dye photoisomers do not fluoresce. This leads to induced loss in resonators using dyes as active laser media.

Study of sterically hindered short-lived isomers of polymethine dyes by laser photolysis

Steric hindrance in carbocyanine dyes disturbs the coplanarity of the molecules and markedly shortens the lifetimes of the isomers. The relaxation rate constants of photoisomers in solution are determined by the possible rotation angles of the molecule's heterofragments. Long-lived trans photoisomers and short-lived sterically hindered di-cis photoisomers have been observed upon photoexcitation of dicarbocyanine dyes.

Synthesis of polymethine dyes from ?-alkoxy-?-phenylbutadienyl salts of heterocyclic bases

β-Phenyl-substituted dicarbocyanine dyes or β-phenyl-substituted hemicyanine dyes, respectively, are obtained in the condensation of δ ethoxy-β-phenylbutadienyl salts of heterocyclic bases (I) with quaternary salts of heterocyclic bases or amines. Depending on the reaction conditions, α-phenyl-γ-ethoxyallylidene derivatives of ketomethylene compounds or γ-phenyl-substituted tetramethylidynemerocyanine dyes are obtained in the condensation of I with ketomethylene compounds.