Homodimeric monomethine cyanine dyes as fluorescent probes of biopolymers

The fluorescence properties of newly synthesized homodimeric monomethine cyanine dyes in the presence of biopolymers are investigated. They do not fluoresce in TE buffer and bidistilled water but become strongly fluorescent (Q(F)=0.3-0.9) in the region 530-650 nm when bound to dsDNA and ssDNA. The detection limit of dsDNA is about 1.7 ng/ml. Some of dyes studied are able to distinguish between dsDNA and ssDNA, RNA, BSA in solution and gel electrophoresis. The influence of different factors (temperature, pH and viscosity of the medium, presence of histone) on the formation of the dye-biopolymer complexes is investigated. The results of steady-state and dynamic fluorescence measurements concerning the different types of binding between dyes and biopolymers show that the new dyes are applicable in molecular biology as highly sensitive fluorescence labels.     

Photophysical properties of fluorescent DNA-dyes bound to single- and double-stranded DNA in aqueous buffered solution.

The absorption and fluorescence spectra, fluorescence quantum yields, lifetimes and time-resolved fluorescence spectra are reported for nine different fluorescent DNA-dyes. The work was initiated in search of a quantitative method to detect the ratio of single-to-double stranded DNA (ssDNA/dsDNA) in solution based on the photophysics of dye-DNA complexes; the result is a comprehensive study providing a vast amount of information for users of DNA strains. The dyes examined were the bisbenzimide or indole-derived stains (Hoechst 33342, Hoechst 33258 and 4',6-diamidino-2-phenylindole), phenanthridinium stains (ethidium bromide and propidium iodide) and cyanine dyes (PicoGreen, YOYO-1 iodide, SYBR Green I and SYBR Gold). All were evaluated under the same experimental conditions in terms of ionic strength, pH and dye-DNA ratio. Among the photophysical properties evaluated only fluorescence lifetimes for the cyanine stilbene dyes allowed a convenient differentiation between ssDNA and dsDNA. The bisbenzimide dyes showed multiexponential decays when bound to either form of DNA, making lifetime-based analysis cumbersome with inherent errors. These dyes also presented biexponential decay when free in aqueous buffered solutions at different pH. A mechanism for their deactivation is proposed based on two different conformers decaying with different kinetics. The phenanthridinium dyes showed monoexponential decays with ssDNA and dsDNA, but there was no discrimination between them. High dye-DNA ratios (e.g. 1:1) resulted in multiexponential decays for cyanine dyes, resulting from energy transfer or self-quenching deactivation. Shifts in both absorption and fluorescence maxima for both ssDNA and dsDNA DNA-cyanine dye complexes were small. Broadening of dye-ssDNA absorption and fluorescence bands for the cyanine dyes relative to dye-dsDNA bands was detected and attributed to higher degrees of rotational freedom in the former.     

New asymmetric monomethine cyanine dyes for nucleic-acid labelling: absorption and fluorescence spectral characteristics

Absorption spectra and fluorescence properties of a series of newly synthesized asymmetric monomethine cyanine dyes are studied. The dyes carry one or two positive charges. They are devoid of their own fluorescence in solution and become fluorescent upon binding to nucleic acids only. The fluorescence maxima of the new dyes are localized between 530 and 650 nm. The wavelength and intensity of fluorescence are dependent on molecular structure of the dye, type of nucleic acid and the concentration of both nucleic acid and salts. Some of the dyes are capable of distinguishing between single-stranded and double-stranded (ds) polynucleotides giving fluorescence maxima localized at different wavelengths. Detection threshold for dsDNA for most of the dyes is comparable to that of ethidium bromide. The sensitivity of the dye-dsDNA complexes to NaCl concentrations show that the new dyes interact with dsDNA by both intercalation and electrostatically.     

Key Structural Elements of Unsymmetrical Cyanine Dyes for Highly Sensitive Fluorescence Turn‐On DNA Probes

Unsymmetrical cyanine dyes, such as thiazole orange, are useful for the detection of nucleic acids with fluorescence because they dramatically enhance the fluorescence upon binding to nucleic acids. Herein, we synthesized a series of unsymmetrical cyanine dyes and evaluated their fluorescence properties. A systematic structure–property relationship study has revealed that the dialkylamino group at the 2‐position of quinoline in a series of unsymmetrical cyanine dyes plays a critical role in the fluorescence enhancement. Four newly designed unsymmetrical cyanine dyes showed negligible intrinsic fluorescence in the free state and strong fluorescence upon binding to double‐stranded DNA (dsDNA) with a quantum yield of 0.53 to 0.90, which is 2 to 3 times higher than previous unsymmetrical cyanine dyes. A detailed analysis of the fluorescence lifetime revealed that the dialkylamino group at the 2‐position of quinoline suppressed nonradiative decay in favor of increased fluorescence quantum yield. Moreover, these newly developed dyes were able to stain the nucleus specifically in fixed HeLa cells examined by using a confocal laser‐scanning microscope.     

A study of intramolecular H-complexes of novel bis(heptamethine cyanine) dyes

Near-infrared (NIR) bis(heptamethine cyanine) (BHmC) dyes containing a flexible polymethylene linker between the two cyanine subunits are a novel class of compounds with versatile spectroscopic properties. The first bis-cyanine of this type is BHmC-10 (with a decamethylene bridge) that has been reported by us recently [G. Patonay, J.S. Kim, R. Kodagahally, L. Strekowski, Appl. Spectrosc., in press]. As part of this work, additional bis-cyanines BHmC-4, BHmC-6, and BHmC-8 were synthesized and their spectral properties were evaluated for the dyes free in solution and in the presence of human serum albumin (HSA). These bis-cyanines undergo H-type aggregation, mainly H-type intramolecular complexation between the two cyanine subunits, when free in aqueous solution. This H-type interaction in phosphate buffer (pH 7.2) is characterized by hypsochromic (H) absorption at 700 nm, low extinction coefficient, and low fluorescence quantum yield. By contrast, an analogous monomeric cyanine exhibits strong fluorescence under similar conditions. Upon binding with HSA, the fluorescence of BHmC-6 changes negligibly, that for BHmC-8 shows a slight increase, and the fluorescence of BHmC-4 is greatly increased. It is suggested that BHmC-4 binds with HSA in the open form exclusively, while the H-type intramolecular interaction in BHmC-6 is mostly retained in the complex with HSA. Bis-cyanine BHmC-4 may be of significant bioanalytical utility due to its negligible fluorescence in aqueous solution and a strong increase in fluorescence upon binding with a protein.     

Novel Cyanine Dyes: Synthesis,Characterization and Photosensitization‐Structure Correlation

Novel furo, thieno and pyrrolo[2,3‐b]pyrazole cyanine dyes were synthesized. The structure‐photosensitization properties correlation of the dyes were examined in 95% ethanol solution by absorption spectroscopy. The chemical structure of the starting biheterocyclic compounds and their derived cyanine dyes were confirmed by elemental analysis, IR and ¹H NMR spectroscopy.     

Synthesis and fluorescence characteristics of novel asymmetric cyanine dyes for DNA detection

Sixteen new asymmetric monomethine cyanine dyes have been synthesized and their spectral characteristics and interaction with double stranded DNA have been investigated. The dyes absorb in the region 453–519 nm and have molar absorptivities in the range 37.900–93.100 l M^?1 cm^?1. The dyes do not have intrinsic fluorescence, but in the presence of dsDNA they exhibited a significant enhancement in fluorescence. The most pronounced increase was found for D9, D10, D12 and D16 allowing the recommendation of these dyes as the most sensitive DNA markers. Thermodynamic analysis of cyanine–DNA complexation was carried out using the McGhee & von Hippel non-cooperative excluded site model, and binding parameters have been derived. A hypothesis describing the DNA–dye binding mode has been proposed.     

High efficiency photocurrent generation by two-dimensional mixed J-aggregates of cyanine dyes

Two-dimensional mixed J-aggregates of structurally and spectrally analogous anionic cyanine dyes, coadsorbed on a self-assembled monolayer of aminoalkanethiolate on Au(111), generated a high-efficiency (20-30% quantum efficiency) cathodic photocurrent and a significant photovoltaic effect in reversible Fe2+/Fe3+ redox solution.     

Short-wavelength fluorescence caused by sequential two-photon excitation of some cyanine dyes: Effect of solvent viscosity on the quantum yields

Short-wavelength (SW) fluorescence of some cyanine dyes caused by sequential two-photon excitation was studied. The fluorescence quantum yield of the SW fluorescence shows a significant dependence on the solvent viscosity, but only a small dependence on temperature. This reveals the dynamic character of the emitting state: much lower intramolecular barrier and larger solute-solvent viscous drag compared to the S₁ state in the molecular conformational change which is important as a radiationless decay channel.     

Cyanine dyes as protectors of K562 cells from photosensitized cell damage

Several cyanine dyes were found to protect K562 leukemia cells against toxicity mediated by cis-di(4-sulfonatophenyl)diphenylporphine (TPPS2) and light. Most cyanine dyes derived from dimethylindole were better photoprotectors than cyanine dyes with other structures. This correlated with the fact that cyanine dyes derived from dimethylindole were predominately monomeric at millimolar concentrations within K562 cells, while other cyanine dyes formed aggregates. For cyanine dyes that are derived from dimethylindole and have absorption band wavelengths greater than 700 nm, fluorescence-energy transfer from TPPS2 to the cyanine dye was the most important mechanism for photoprotection. There was no spectroscopic evidence for complex formation between the cyanine dyes and TPPS2. The dimethylindole derivative, 1,1',3,3,3',3'-hexamethylindodicarbocyanine, was an excellent photoprotector, but a poor quencher of TPPS2 fluorescence and a relatively poor singlet-oxygen quencher. This cyanine dye may act by quenching excited triplet TPPS2. Singlet-oxygen quenching may contribute to the photoprotection provided by cyanine dyes not derived from dimethylindole. Differences in the subcellular distribution of the various cyanine dyes studied may have contributed to the different apparent mechanisms of photoprotection.     

Improved sampling and analytical method for airborne carbon disulfide measurement in the workplace

Summary An improved sampling and analytical method for airborne carbon disulfide (CS₂) both in the laboratory and in a rayon viscose manufacturing plant is described. A tube-type diffusive sampler (ATD) packed with solid Spherocarb was used for airborne CS₂ collection. The ATD was then thermally desorbed and analyzed by (GC-MS). A standard curve range of 0.69 to 103.4 μg was established with correlation coefficient (r)>0.998. Desorption efficiency was 100% mean recovery 97.8% and coefficient of variation<10%. The limit of detection (LOD) was 0.21 μg and limit of quantitation (LOQ) 0.69 μg. Temperature and humidity effects were not significant. There was no influence from tube direction to exposure gas stream. The uptake rate was stable over an 8h period. Even after 90 repeated usages, the uptake rate still remained quite stable. ATD samples were stable at <4°C for at least 2 weeks. Field validation data showed a strong linear correlation (r>0.97) between the proposed method and the current method for fixed-point samples. The proposed method can provide a specific, sensitive, convenient, and reliable tool for assessment of occupational exposure to CS₂. Using this method to assess CS₂ exposures gives findings comparable to those of the traditional method with respect to accuracy, precision, and effects of environmental interference.     

Inhibition of peroxyoxalate chemiluminescence by intercalation of fluorescent acceptors between DNA bases

We have examined the ability of different fluorescent DNA dyes to become chemically excited by the peroxyoxalate chemiluminescent reaction. The intercalating dyes ethidium bromide and propidium iodide, and the bis-intercalating dyes ethidium homodimer-1, benzoxazolium-4-pyridinium dimer-1 and benzoxazolium-4-quinolinium dimer-1, exhibit an intense chemiluminescence when they are excited by the bis(2,4,6-trichlorophenyl)oxalate (TCPO)-H2O2 reaction in the absence of DNA. However, the chemiluminescence of these dyes is very low when they are bound to double-stranded DNA (dsDNA). In contrast, the minor groove-binding dye Hoechst 33258 excited by the TCPO-H2O2 reaction shows approximately the same chemiluminescence intensity when it is free in solution or complexed with dsDNA. Structural alterations or partial dissociation of dsDNA-bis-intercalating dye complexes produced by the addition of acetone, NaCl, MgCl2 or the cationic surfactant cetyltrimethylammonium bromide increases the chemiluminescence intensity. A moderate chemiluminescence intensity is observed when bis-intercalating dyes are complexed with single-stranded DNA. Our results indicate that the energy from the intermediates produced in the peroxyoxalate chemiluminescent reaction cannot be efficiently transferred to fluorescent dyes complexed with DNA; chemiexcitation is almost completely inhibited when dyes are buried in the dsDNA structure by intercalation between the base pairs.     

The electronic structure of the bases of cyanine dyes and the barriers of their conformational transformations

The equilibrium geometry and electronic transitions of cyanine dyes and their bases and also the barriers to rotation of the terminal groups in the ground and excited states were calculated in the AM1 approximation. It was found that in contrast to the cyanine dyes the bases are closer in electronic structure to conjugated systems of the polyene type. The calculated barriers to rotation are significantly higher in the bases than in the dyes. Institute of Organic Chemistry, National Academy of Sciences of Ukraine, 5 Murmanskaya ul., Kiev 253094, Ukraine. Translated from Teoreticheskaya i éksperimental'naya Khimiya, Vol. 35, No. 4, pp. 222–226, July–August, 1999.     

Supra-Cyanines: Ultrabright Cyanine-Based Fluorescent Supramolecular Materials in Solution and in the Solid State

Fluorescent materials with high brightness play a crucial role in the advancement of various technologies such as bioimaging, photonics, and OLEDs. While significant efforts are dedicated to designing new organic dyes with improved performance, enhancing the brightness of existing dyes holds equal importance. In this study, we present a simple supramolecular strategy to develop ultrabright cyanine-based fluorescent materials by addressing long-standing challenges associated with cyanine dyes, including undesired cis-trans photoisomerization and aggregation-caused quenching. Supra-cyanines are obtained by incorporating cyanine moieties in a cyclic peptide-based supramolecular scaffold, and exhibit high fluorescence quantum yields (up to 50 %) in both solution and in the solid state. These findings offer a versatile approach for constructing highly emissive cyanine-based supramolecular materials.     

菁染料分子中取代基效应的交替现象

本文利用同系线性规律对菁染料的取代基效应进行了研究.提出菁染料的取代基效应与通常的取代基效应不同,在菁染料分子中取代基效应存在较大的交替现象;根据取代基团的内部结构及其所在位置的关系,推导出一套经验公式,并对菁染料的电子吸收光谱进行了定量计算.本文定量地预测了由苯并硫氮茂环、萘并琉氮茂环和苯并硒氮茂环等组成的菁染料及其衍生物(共一百多个化合物)的电子吸收光谱峰值,与实验值相比,峰值偏离在±5nm内的约占70%左右,在±5-±10nm的约占25%,大于±10nm的约占5%.     

Solubilization of Cationic Hemicyanine Dyesin Anionic Surfactant Micelles: A Partitioning Study

Summary.  Cationic hemicyanine dyes of the 1-methyl-4-(4-(di-n-alkylamino)-styryl) pyridinium betain type (alkyl group=methyl to butyl) have been investigated by differential spectroscopy in order to ascertain their solubilization in aqueous micellar solution of sodium dodecylbenzene sulfonate (SDBS). The differential absorption spectra were recorded as a function of surfactant concentration at 25.0°C. Thermodynamic parameters were calculated from partition coefficient data. The results show that cationic hemicyanine dyes are solubilized at the micellar surface, indicating an electrostatic interaction between dyes and surfactant micelles. Received October 15, 1999. Accepted February 14, 2000     

Capillary electrophoresis of double-stranded DNA fragments using a new fluorescence intercalating dye EvaGreen

EvaGreen is a new DNA intercalating dye successfully used in quantitative real-time PCR. In the present work, we firstly apply EvaGreen to the analysis of dsDNA by CE with LIF detection. Comparisons of EvaGreen dye with the commonly used dyes SYBR Green I and SYBR Gold were preformed in dsDNA analysis by CE. The linear range of dsDNA using EvaGreen was slightly wider than that using SYBR Gold and SYBR Green I, and the detection limits of dsDNA were not significantly different for the three dyes. Good separations of dsDNA fragments were obtained using the three dyes. Reproducibility of migration time and the peak area of dsDNA fragments with EvaGreen were better than those for SYBR Green I and SYBR Gold. The RSD values were 0.24-0.27% for migration time and 3.45-7.59% for peak area within the same day, 1.35-1.63% for migration time and 6.72-12.05% for peak area for three days. Our data demonstrated that EvaGreen is well suited for the dsDNA analysis by CE with LIF detection.     

水分散体系中AgBr比表面的测定及晶体习性的确定

The surface area and crystal hibit of an AgBr dispersion were determined by a in situ method. In this method, the difference of the absorption spectra of an cationic cyanine dye Ⅰ in adsorption and solution state was used for the measurement of AgBr surface area. It was 17.1 m~2/g AgBr. And the crystal habit was determined hased upon the absorption spectra of an other two cyanine dyes (Ⅱ and Ⅲ) in adsorption state. It showed a cubic crystal.     

Quadruplex-to-duplex transition of G-rich oligonucleotides probed by cationic water-soluble conjugated polyelectrolytes

G-quartet DNA converts to duplex form in the presence of its complementary strand. This conformational change can be detected in real time by a homogeneous assay method based on the signal amplification of conjugated polyelectrolytes and the specific interaction of intercalating dyes with double-stranded DNA (dsDNA). The probe solution contains a cationic, conjugated polymer (CCP), G-quadruplex labeled with a fluorescein at the 5'-terminus (G-quadruplex-Fl), and ethidium bromide (EB). The addition of a complementary target results in the transition from G-quadruplex to duplex (dsDNA-Fl) and EB intercalation within the duplex structure. Excitation of the CCP leads to energy transfer from CCP to dsDNA-Fl (FRET-1) and then energy transfer from dsDNA-Fl to EB (FRET-2). Increasing the number of mismatched bases discourages dsDNA formation, which is detected in the assay.     

母核结构对三碳菁染料光氧化过程的影响

本文研究三种不同母核结构的三碳菁染料在乙醇溶剂中的光氧化反应,实验中采用了近红外区光谱能量分布平稳的光源,得出了母核结构对染料的光氧化稳定的影响,其影响次序:叮恶唑>硒唑>噻唑。同时本文还利用β值的测定,算出染料光氧化过程中敏化产生的单重态氧的浓度以及二者反应的速率常数。