Electronic excitation energy transfer between molecules of carbocyanine dyes in complexes with DNA

Electronic excitation energy transfer has been carried out between molecules of carbocyanine dyes bound noncovalently to DNA. 3,3′,9-Triethyl-5,5′-dimethyloxacarbocyanine iodide was used as an energy donor and 3,3′-diethylthiacarbocyanine iodide as an acceptor dye. In this process, the band belonging to the donor is observed in the fluorescence excitation spectrum of the acceptor. Donor fluorescence quenching by the acceptor in the presence of DNA was studied. The results of the experiments are discussed in terms of the Dye-DNA stoichiometric complex formation and with respect to concentrating the dyes in the microphase (pseudophase) of the biopolymer.     

Distribution of distances in donor-acceptor pairs of cyanine dyes upon electronic excitation energy transfer in the presence of DNA

Electronic excitation energy transfer (EEET) between molecules of carbocyanine dyes, which form noncovalent complexes with DNA, has been studied by picosecond spectroscopy. Three oxacarbocyanine dyes have been used as electronic excitation energy donors, and 3,3′-diethylthiacarbocyanine iodide has served as an acceptor dye. An analysis of the kinetic dependences permitted obtaining the data on distribution of the distances in donor-acceptor pairs upon EEET. The effect of the acceptor concentration on the parameters of distribution of its molecules in the quenching microphase has been revealed.     

Study of cis-trans equilibrium of oxacarbocyanine dyes in solution and in a complex with DNA

Cis-trans equilibrium for a number of meso-substituted oxacarbocyanine dyes, 3,3′-diethyloxacarbocyanine iodide (K1), 3,3′-diethyl-9-methyloxacarbocyanine iodide (K2), 3,3′-dimethyl-9-ethyloxacarbocyanine iodide (K3), 3,3′,9-triethyl-6,6′-dimethoxyoxacarbocyanine iodide (K4), and 3,3′,9-triethyl-5,5′-dimethyloxacarbocyanine iodide (K5), has been studied in solutions and in a complex with DNA by spectral and fluorescent methods. A shift of the cis-trans isomer equilibrium toward the formation of the trans-isomer was observed in the presence of DNA, which determined in many respects the spectral effects observed upon the complexation of the oxacarbocyanine dyes. A steep rise of fluorescence (due to binding of the trans-isomer) in a complex with DNA is favorable for using oxacarbocyanine dyes to determine DNA.     

DNA Effect on Cis–Trans Equilibrium and Fluorescent Properties of 3,3′-Diethyl-9-thiomethylthiacarbocyanine Iodide in Aqueous Solution

The influence of DNA on the cis–trans equilibrium and fluorescent properties of 3,3-diethyl-9-thiomethylthiacarbocyanine iodide (DTTC) in a phosphate buffer (pH 7) was studied by various photochemical techniques. The interaction of dye molecules with DNA leads to the formation of stable noncovalently bonded complexes. Data obtained from DTTC absorption and fluorescence spectra suggest that complexation proceeds primarily through the cis-form of the dye. Complexation with DNA leads to a substantial increase in the quantum yield of the triplet state of DTTC molecules. The rate constant for quenching the dye triplet state by oxygen turned out to be significantly lower than the diffusion-controlled value.     

Spectral characteristics of CdS quantum dots and their associates with dye molecules dispersed in gelatin

A sol–gel method for the production of open quantum dots of CdS measuring 2-5 nm and their associates with dye molecules [methylene blue and the pyridinium salt of 3,3′-di(γ-sulfopropyl)-9-ethyl-4,5,4′,5′-dibenzothiacarbocyaninebetaine] dispersed in gelatin is described. Their spectral characteristics are analyzed. Evidence is obtained for the formation of hybrid associates of CdS quantum dots with monomers of the first and J-aggregates of the second dye.     

Specifics of the formation of J-aggregates of cyanine dyes in solutions of AOT/water/hexane reverse micelles

The behavior of a cyanine dye (3,3′-di-(gamma-sulfopropyl)-4,5,4′,5′-dibenzo-9-ethylthiacarbocyanine betaine pyridinium salt) was studied in AOT/water/hexane reverse micelles over a wide range of W at various concentrations of the dye, AOT, and reverse micelles. The processes occurring during the formation of the AOT/water/hexane micellar solution were studied in detail. It has been shown that, before the formation of the stable microemulsion, the dye aggregation processes occur by virtue of the interaction of the dye with the AOT anion. The amount of J-aggregates is proportional to the logarithm of the ratio of the amount of AOT molecules to the amount of dye molecules. The time behavior of J-aggregates after the formation of a micellar structure depends on the concentration of reverse micelles, thereby indicating an important role of intermicellar exchange.     

Dye J-aggregate—semiconductor nanocrystal hybrid nanostructures in reverse micelles: an experimental study

Reverse micelle solutions can be used for the assembly of hybrid nanostructures of the composition dye monomer—Ag₂S nanocrystal, dye J-aggregate—CuI nanocrystal, and dye J-aggregate—PbI₂ nanocrystal. The assembly is effected by means of adsorption of the dye (3,3′-di-(γ-sulfopropyl)-4,5,4′,5′-dibenzo-9-ethylthiacarbocyanine betaine pyridinium salt) onto the nanocrystal surface. Factors responsible for the dye adsorption onto semiconductor nanocrystals in reverse micelle solutions are analyzed. It is suggested that adsorption can be the outcome of forces induced by both van der Waals and chemical interactions. The surfactants used for stabilization of reverse micelle solutions also influence the assembly of the hybrid nanostructures.     

Effect of donor-acceptor interaction strength on excitation energy migration and diffusion at high donor concentrations

The migration and diffusion modulated excitation energy transfer has been studied in a new dye pair 7-diethylamino-4-methylcoumarin (donor) to 3,3'-dimethyloxacarbocyanine iodide (acceptor) by steady-state and picosecond time-resolved spectroscopy. To reduce the artifact of self-absorption, at high donor concentrations, the time-resolved studies have been carried out in thin films of polyvinyl alcohol (solid matrix) and in methanol (liquid phase) at front-face geometry of excitation. The Forster-type (nonradiative) energy transfer [Discuss. Faraday Soc. 27, 7 (1959)] takes place directly from donor to acceptor in case of solid matrix, while Yokota-Tanimoto model [J. Phys. Soc. Jpn. 22, 779 (1967)] for diffusion has been found to be operating in the liquid phase. It has been found here that the high interaction strength between donor and acceptor molecules as compared to that among donors masks the effect of energy migration and diffusion at high donor concentrations. The rate and efficiency of energy transfer increase with increasing the acceptor concentration. This has been confirmed by the study of acceptor kinetics.     

Quenching of the triplet state of meso-substituted thiacarbocyanine dyes by nitroxyl radicals, iodide ions, and oxygen in solutions and in complexes with DNA

Using the flash photolysis method, the spectral and kinetic characteristics of triplet states of a number of meso-substituted thiacarbocyanine dyes (3,3′-diethyl-9-methoxythiacarbocyanine iodide, 3,3′,9-triethylthiacarbocyanine iodide, 3,3′-diethyl-9-methylthiacarbocyanine iodide, and 3,3′-diethyl-9-thiomethylthiacarbocyanine iodide) were studied, and the rate constants of triplet quenching by a stable nitroxyl radical, iodide ion, and oxygen were determined in solutions and in complexes with DNA. The results obtained show the formation of two types of dye-DNA complexes: formed by binding of the dye in the groove of a DNA molecule and by intercalation of the dye between base pairs. The complexation creates steric hindrances upon quenching of the triplet states of the ligands and causes great differences between the rate constants of the quenching processes.     

Photochemical properties of meso-substituted thiacarbocyanine dyes in solutions and in complexes with DNA

The processes of cis-trans photoisomerization and thermal back isomerization as well as the effect of DNA on the spectral and kinetic characteristics of the triplet state of a number of meso-substituted thiacarbocyanine dyes: 3,3’-diethyl-9-methoxythiacarbocyanine iodide (K1), 3,3’,9-triethylthiacarbocyanine iodide (K2), 3,3’-diethyl-9-methylthiacarbocyanine iodide (K3), and 3,3’-diethyl-9-chlorothiacarbocyanine perchlorate (K4), were studied by the flash photolysis method. Upon flash photoexcitation, the processes of trans-cis and cis-trans photoisomerization were observed for dye K1; the data on the structure of the absorption bands of the photoisomers were obtained. Complexation with DNA leads to an increase in the quantum yield of the triplet state of the dyes, which is explained by growing rigidity of the bound molecules. In the presence of DNA, triplet state deactivation follows the two-exponential law, thus showing that the dyes form complexes of two different types. The processes of quenching of the dye triplet state by oxygen were studied in solutions and in complexes with DNA. The rate constants for oxygen quenching of the triplet state of the dyes in complexes with DNA were found to be much lower than the values expected for the diffusion-controlled reactions (with allowance for the spin statistical factor, $k_{qO_2 } < 1/9k_{dif} $ ), which is explained by the steric factor of the complexation.     

The Study of <Emphasis Type="Italic">cis-trans</Emphasis> Equilibrium and Complexation with DNA of <Emphasis Type="Italic">meso</Emphasis>-Substituted Carbocyanine Dyes

The effect of DNA was studied on cis-trans equilibrium and spectral and fluorescent properties of a number of meso-substituted carbocyanine dyes: 3,3′-diethyl-9-thiomethylthiacarbocyanine iodide (K1), 3,3′-diethyl-9-methoxythiacarbocyanine iodide (K2), 3,3′-9-triethylthiacarbocyanine iodide (K3), 3,3′-dimethyl-9-ethyloxacarbocyanine iodide (K4), 3,3′-9-triethyl-5,5′-dimethyloxacarbocyanine iodide (K5), and 3,3′,9-triethyl-6,6′-dimethoxyoxacarbocyanine iodide (K6). Equilibrium between the cis and trans isomeric forms was detected for the thiacarbocyanine dyes in a number of organic solvents, with a shift of the equilibrium toward the cis-isomer caused by an increase in the solvent polarity. The oxacarbocyanines are present only in the form of trans-isomers in both polar and nonpolar solvents. Interaction of the dyes with DNA leads to the formation of stable noncovalent complexes. The complexation of the thiacarbocyanine dyes results in a shift of the isomeric equilibrium and occurs predominantly via the cis-form of the dye. The oxacarbocyanine dyes produce complexes with DNA in the initial trans-form.__________Translated from Khimiya Vysokikh Energii, Vol. 39, No. 4, 2005, pp. 280–286.Original Russian Text Copyright © 2005 by Pronkin, Tatikolov, Anikovskii, Kuz’min.     

Primary photoprocesses of 3,3’-diethylthiacarbocyanine in the presence of cucurbit[7]uril: Laser flash photolysis and quantum chemical calculations

The effect of cucurbit[7]uril on the phototransformation of 3,3′-diethylthiacarbocyanine iodide dye in aqueous solution has been investigated by nanosecond laser flash photolysis. The presence of cucurbit[7]uril results in the formation of its complex with the dye molecule producing a dimer. The dimer formation is evident from the ground and triplet-triplet absorption spectra. The dimers in the triplet state are capable of electron transfer. The structure of the complexes is suggested on the basis of quantum chemical calculations.     

Fast and sensitive DNA analysis using changes in the FRET signals of molecular beacons in a PDMS microfluidic channel

A new DNA hybridization analytical method using a microfluidic channel and a molecular beacon-based probe (MB-probe) is described. A stem-loop DNA oligonucleotide labeled with two fluorophores at the 5′ and 3′ termini (a donor dye, TET, and an acceptor dye, TAMRA, respectively) was used to carry out a fast and sensitive DNA analysis. The MB-probe utilized the specificity and selectivity of the DNA hairpin-type probe DNA to detect a specific target DNA of interest. The quenching of the fluorescence resonance energy transfer (FRET) signal between the two fluorophores, caused by the sequence-specific hybridization of the MB-probe and the target DNA, was used to detect a DNA hybridization reaction in a poly(dimethylsiloxane) (PDMS) microfluidic channel. The azoospermia gene, DYS 209, was used as the target DNA to demonstrate the applicability of the method. A simple syringe pumping system was used for quick and accurate analysis. The laminar flow along the channel could be easily controlled by the 3-D channel structure and flow speed. By injecting the MB-probe and target DNA solutions into a zigzag-shaped PDMS microfluidic channel, it was possible to detect their sequence-specific hybridization. Surface-enhanced Raman spectroscopy (SERS) was also used to provide complementary evidence of the DNA hybridization. Our data show that this technique is a promising real-time detection method for label-free DNA targets in the solution phase. Figure FRET-based DNA hybridization detection using a molecular beacon in a zigzag-shaped PDMS microfluidic channel     

Experimental and Theoretical Thermodynamic Studies of the Adsorption of Polyhalogenated Organic Compounds from Aqueous Solution by Chemically Modified Multi-walled Carbon Nanotubes

Multi-walled carbon nanotubes (MWCNTs) were chemically modified with octadecyl amine or polyethyleneglycol and then used as solid phase adsorbents for the adsorption from aqueous solution of different polyhalogenated organic pollutants: pentachlorophenol, 2,4,5-trichlorophenol, 3,3′,4,4′-tetrachlorobiphenyl and 2,2′,5,5′-tetrabromobiphenyl from model aqueous solutions. The effects of temperature were measured and thus the Gibbs energy, enthalpy, and entropy of adsorption were calculated. In general, the Gibbs energy of adsorption was negative for the target analytes, indicating that adsorption was spontaneous at all temperatures. On the other hand, the values of the enthalpy and entropy of adsorption were significantly dependent on the type of modified MWCNTs as well as the analytes used. Computer modeling was used to simulate the adsorption process and calculate the Gibbs energies of adsorption. The results showed moderate agreement with the experimentally determined values.     

A new method for the detection of ATP using a quantum-dot-tagged aptamer

Fluorescence resonance energy transfer (FRET) between a quantum dot as donor and an organic fluorophore as acceptor has been widely used for detection of nucleic acids and proteins. In this paper, we developed a new method, characterized by 605-nm quantum dot (605QD) fluorescence intensity increase and corresponding Cy5 fluorescence intensity decrease, to detect adenosine triphosphate (ATP). The new method involved the use of three different oligonucleotides: 3′-biotin-modified DNA that binds to streptavidin-conjugated 605QD; 3′-Cy5-labelled DNA; and a capture DNA consisting of an ATP aptamer and a sequence which could hybridize with both 3′-biotin-modified DNA and 3′-Cy5-labelled DNA. In the absence of the target ATP, the capture DNA binds to 3′-biotin-modified DNA and 3′-Cy5-labelled DNA, bringing quantum dot and Cy5 into close proximity for greater FRET efficiency. When ATP is introduced, the release of the 3′-Cy5-labelled DNA from the hybridization complex took place, triggering 605QD fluorescence intensity increase and corresponding Cy5 fluorescence intensity decrease. Taken together, the virtue of FRET pair 605QD/Cy5 and the property of aptamer-specific conformation change caused by aptamer–ATP interaction, combined with the fluorescence intensity change of both 605QD and Cy5, provide prerequisites for simple and convenient ATP detection. Zhang Chen and Guang Li contributed equally to this work.     

Ellagic acid derivatives from the stem bark of <Emphasis Type="Italic">Dipentodon sinicus</Emphasis>

Ellagic acid derivatives were isolated from Dipentodon sinicus and their structures were identified as 3,3′,4′-tri-O-methylellagic acid (1), 3,3′-di-O-methylellagic acid (2), 4,4′-di-O-methylellagic acid (3), 3,3′-di-O-methylellagic acid-4′-O-α-L-rhamnopyranoside (4), 3,3′,4′-tri-O-methylellagic acid-4′-O-β-D-glucopyranoside (5), 3,3′-di-O-methylellagic acid-4′-O-β-D-glucopyranoside (6), and ellagic acid (7). All the compounds were isolated for the first time from the title plant. Published in Khimiya Prirodnykh Soedinenii, No. 2, pp. 106–107, March–April, 2007.     

Synthesis,structural and catalytic activity of binaphthyl macrocyclic complexes

The binaphthyl macrocyclic ligand, N,N′-diethyl-[3,3′-(2,2′-dihydroxy-1,1′-binaphthyl)carboxamide]-2,2′-dihydroxy-1,1′-binaphthyl-3,3′-dicarboxylic acid (DDCDB), has been synthesized and investigated. The ligand (DDCDB) and its metal complexes involving Cu^II, Zn^II, UO ₂ ^II , Th^IV, Ce^III, Mo^VI and W^VI ions have been prepared and characterized by spectral (i.r., u.v.–vis.), elemental analyses, magnetic moments and thermal analyses measurements. DDCDB behaves as a tridentate ligand towards Cu^II, Zn^II and UO ₂ ^II ions coordinating via CO, NH and the deprotonated naphthyl OH groups in a ratio of 2:1 (M:L). On the other hand, DDCDB behaves in a bidentate manner coordinatingvia the NH and the deprotonated naphthyl OH groups only in case of the Th^IV, Ce^III, Mo^VI, and W^IV ions and in ratio 1:1 (M:L). Results of thermal measurements confirm the existence of solvent molecules inside and outside the coordination sphere. Th^VI complex has been applied for the hydrolysis of phosphodiester and the results show a significant rate enhancement of ~5.8 million fold with respect to the auto-hydrolysis of bis-(p-nitrophenyl) phosphate (BNPP) under the same conditions Also, Cu^II complex accelerates the photodegradation of the hazardous pollutant (acid green dye) in the presence of hydrogen peroxide by degrading 90% of the dye within 23 min.     

Synthesis, structures, and conductivities of salts (BEDT-TTF)[9,9′(12′)-I2-3,3′-Co(1,2-C2B9H10)2] and (TTF)[9,9′,12,12′-I4-3,3′-Co(1,2-C2B9H9)2]

The radical cation salts of tetrathiafulvalene (TTF) and bis(ethylenedithio)tetrathiafulvalene (BEDT-TTF) with iodo derivatives of cobalt bis(dicarbollide), (TTF)[9,9′,12,12′-I₄-3,3′-Co(1,2-C₂B₉H₉)₂] and (BEDT-TTF)[9,9′(12′)-I₂-3,3′-Co(1,2-C₂B₉H₁₀)₂], respectively, were synthesized and their crystal structures were determined. The introduction of iodine atoms into the lower rim of the dicarbollide ligands, unlike the substitution at the upper rim, leads to insignificant changes in the crystal structure and the conductivity of the radical cation salts compared to the analogous salts based on unsubstituted cobalt bis(dicarbollide).     

Synthesis and spectral properties of 3,3′-bis(dipyrrolylmethene)

Bis(2,4,7,8,9-pentamethyldipyrrolylmethene-3-yl)(4′-methoxyphenyl)methane dihydrobromide was synthesized and its spectral properties were studied. It was found that the basicity of the ligand 3,3′-bis-(dipyrrolylmethene) decreases upon insertion of the methoxyphenyl group in the 3,3′-spacer.     

MP2 Study on the Stacking Interactions Between 2-Hydroxyadenine and Four DNA Bases

MP2 calculations were used to perform an energy scan of 2-hydroxyadenine (2-OH-A) stacked with four canonical DNA bases. The structures that were studied correspond to potential energy surface points of B-DNA. Eight stacking complexes were analyzed in detail: 5′-2-OH-A/A-3′, 5′-2-OH-A/C-3′, 5′-2-OH-A/G-3′, 5′-2-OH-A/T-3′, 5′-A/2-OH-A-3′, 5′-C/2-OH-A-3′, 5′-G/2-OH-A-3′, and 5′-T/2-OH-A-3′. The stabilization energy, including electron correlation terms, suggests that the 5′-G/2-OH-A-3′ pair is the most stable among all of the studied complexes. The dependence of the stacking energy on the vertical separation and on the twist angle between the two stacked bases were studied in great detail.