A monomethine cyanine dye Cyan 40 for two-photon-excited fluorescence detection of nucleic acids and their visualization in live cells

Monomethine cyanine dye 4-((1-methylbenzothiazolyliliden-2)methyl)-1,2,6-trimethylpyridinium perchlorate (Cyan 40) was investigated as a two-photon-excited fluorescence probe for nucleic acids (NA). Cyan 40 has been shown to demonstrate efficient two-photon-excited fluorescence in the presence of NA in vitro in contrast to solutions without NA. Two-photon confocal laser scanning microscopy (TPCLSM) and two-photon laser scanning microspectrofluorometry were used to check the possibility of using Cyan 40 as two-photon-excited fluorescence label for NA in living cells. Study of dye effect on viability of cells was also carried out. We ascertained that Cyan 40 is a cell-permeant dye, manifesting efficient two-photon-excited fluorescence when bound to NA in living cells, without any significant influence on viability of cells. TPCLSM images obtained from stained cells indicate preferential RNA staining by Cyan 40 compared with DNA.     

Interaction of cyanine dyes with nucleic acids: XXVI. Intercalation of the trimethine cyanine dye cyan 2 into double-stranded DNA: study by spectral luminescence methods

The interaction between double-stranded (ds) DNA and the cyanine dye Cyan 2 has been studied with spectral luminescence methods. Binding constant values have been determined by fluorescence titration and dye distribution in the two-phase system ethyl acetate-water (3.6 x 10(4) and 1.5 x 10(4) M(-1), respectively). Cyan 2 exhibits a small specificity for guanine-cytosine (GC) sequences in total DNA and synthetic polydeoxynucleotides poly(dA/dT) and poly(dGdC/dGdC). The DNA complexes with Cyan 2 are stable at high-ionic strength solution when NaCl is added. The dye molecule complexed with DNA is apparently shielded from the anionic quencher--iodide ion. The negative linear dichroism of the visible absorption band of aligned Cyan 2-DNA complexes indicates that the bound dye lies almost perpendicularly to the DNA helix axis. The linear dichroism of the absorption band at 260 nm suggests a considerable change in the DNA B-form. The results are consistent with an intercalative binding interaction between Cyan 2 and ds DNA.     

Spectral and fluorescent study of the interaction of anionic cyanine dyes with serum albumins

The noncovalent interaction of two anionic cyanine dyes with human and bovine serum albumins was studied by spectral and fluorescent methods. Upon the interaction with albumins, a growth of fluorescence and, in most cases, a long-wavelength shift of the dye absorption band are observed. For the meso-substituted cyanine dye 3,3′-di-(γ-sulfopropyl)-9-methylthiacarbocyanine betaine (K1), a mobile cis-trans equilibrium is observed: the dye in the free state occurs mainly as the cis-isomer, whereas in the complex with albumins the equilibrium is shifted toward the trans-isomer (this shift is greater for human albumin). Dye K1 is recommended as a spectral and fluorescent probe for serum albumins.     

Spectral study of the noncovalent interaction of thiacarbocyanine dyes with hyaluronic acid

The noncovalent interaction with hyaluronic acid (HA) of four cyanine dyes having similar structures, 3,3′,9-trimethylthiacarbocyanine (Cyan 2), 3,3′-dimethylthiacarbocyanine (Cyan 45), 3,3′-diethylthiacarbocyanine (DTC), and 3,3′-diethyl-9-methylthiacarbocyanine (DMTC), was studied using the absorption spectra. Dyes Cyan 2, Cyan 45, and DMTC were shown to form H-aggregates in the presence of HA, which is reflected in the appearance of a short-wavelength absorption band with a maximum at 440–450 nm. By the tendency to H-aggregation in the presence of HA, the dyes can be arranged in the series Cyan 2 > Cyan 45 > DMTC > DTC. The aggregation number for Cyan 2 was determined: n = 3. In buffer solutions pH 4.5, 7.0, and 9.1, the absorption spectra of H-aggregates of Cyan 2 have longer wavelengths (with maximums at 460–470 nm) than those in the absence of buffers. Cyan 2 is suggested as a spectral probe to detect HA in biological systems.     

Interactions of cyanine dyes with nucleic acids. XXIV. Aggregation of monomethine cyanine dyes in presence of DNA and its manifestation in absorption and fluorescence spectra.

Absorption, fluorescence emission and excitation spectra of benzothiazole cyanine dyes--thiazole orange (TO) and 7-methyl-6-(3-methyl-2,3-dihydro-1,3-benzothiazol-2-ylidenmethyl) [1,3] dioxolo [4',5':4,5] benzo [d] [1,3] thiazolium methylmethosulfate (Cyan 13)--were investigated over a wide concentration range. The dyes form aggregates with a 'sandwich'-like structure in water solution. At low dye to DNA concentrations ratios, Cyan 13 and TO monomers appear to interact with the DNA. On increasing the dye to DNA concentrations ratio, free dye molecules aggregate with the DNA-bound ones. The spectra of the free dye aggregates and the aggregates formed on the DNA, are characterized by an anomalously large (more than 100 nm) Stokes shift. This suggests, that the pi-electron systems of the aggregates undergo substantial changes in excited state, compared to those of the monomers. The formation of aggregates consisting of the free and DNA-bound dye molecules can be explained using the half-intercalation model of the interaction of the cyanine dye monomers with the DNA.     

Quantitative monitoring of His and Asp phosphorylation in a bacterial signaling system by using Phos‐tag Magenta/Cyan fluorescent dyes

In the bacterial signaling mechanisms known as two‐component systems (TCSs), signals are generally conveyed by means of a His–Asp phosphorelay. Each system consists of a histidine kinase (HK) and its cognate response regulator. Because of the labile nature of phosphorylated His and Asp residues, few approaches are available that permit a quantitative analysis of their phosphorylation status. Here, we show that the Phos‐tag dye technology is suitable for the fluorescent detection of His‐ and Asp‐phosphorylated proteins separated by SDS‐PAGE. The dynamics of the His–Asp phosphorelay of recombinant EnvZ‐OmpR, a TCS derived from Escherichia coli, were examined by SDS‐PAGE followed by simple rapid staining with Phos‐tag Magenta fluorescent dye. The technique permitted not only the quantitative monitoring of the autophosphorylation reactions of EnvZ and OmpR in the presence of adenosine triphosphate (ATP) or acetyl phosphate, respectively, but also that of the phosphotransfer reaction from EnvZ to OmpR, which occurs within 1 min in the presence of ATP. Furthermore, we demonstrate profiling of waldiomycin, an HK inhibitor, by using the Phos‐tag Cyan gel staining. We believe that the Phos‐tag dye technology provides a simple and convenient fluorometric approach for screening of HK inhibitors that have potential as new antimicrobial agents.     

Interaction of cyanine dyes with nucleic acids. XVIII. Formation of the carbocyanine dye J-aggregates in nucleic acid grooves.

Spectral properties of carbocyanine dye 3-methyl-2-[3-methyl-2-(3-methyl-2,3-dihydro-1,3-benzothiazole-2-iliden)-1- butenyl]-1,3-benzothiazole-3-il iodide (Cyan betaiPr) in water solution, as well as in the presence of different types of double stranded DNA have been studied. While in water solution of 'free' dye Cyan betaiPr stays mainly in monomeric form, in the presence of DNA the dye molecules form J-aggregates. The molecular structure of these J-aggregates causes the Davydov splitting of their absorption band, corresponding to the first electronic transition. A study of site-specificity showed that in the presence of poly (dA/dT) the majority of Cyan betaiPr molecules form J-aggregates, while in the presence of poly (dGC/dGC) dye molecules stay mainly in monomeric form and in presence of chicken erythrocytes DNA both J-aggregate and monomeric forms of dye are present. We suppose that Cyan betaiPr molecules aggregate in DNA groove, which serves as a template for J-aggregate forming. An increase of ionic strength of solution leads to the release of dye molecules from DNA grooves and prevents J-aggregates formation.     

Colorimetric and Fluorimetric DNA Detection with a Hydroxystyryl–Quinolizinium Photoacid and Its Application for Cell Imaging

The combination of styryl dye properties with the acidity and strong photoacidity of the 2,2′-[(1′′-hydroxy-4′′-methyl-(E)-2′′,6′′-phenylene)]-bisquinolizinium enables the detection of DNA by distinct absorption and emission color changes and the fluorimetric detection of DNA in cells with epifluorescence and confocal fluorescence microscopy.     

Chiral Selectivity in the Binding of [4]Helicene Derivatives to Double‐Stranded DNA

The interaction of a series of chiral cationic [4]helicene derivatives, which differ by their substituents, with double‐stranded DNA has been investigated by using a combination of spectroscopic techniques, including time‐resolved fluorescence, fluorescence anisotropy, and linear dichroism. Addition of DNA to helicene solutions results to a hypochromic shift of the visible absorption bands, an increase of fluorescence quantum yield and lifetime, a slowing down of fluorescence anisotropy decay, and a linear dichroism in flow‐oriented DNA, which unambiguously points to the binding of these dyes to DNA. Both helicene monomers and dimeric aggregates, which form at higher concentration, bind to DNA, the former most probably upon intercalation and the latter upon groove binding. The binding constant depends substantially on the dye substituents and is, in all cases, larger with the M than the P enantiomer, by factors ranging from 1.2 to 2.3, depending on the dye.     

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.     

光谱法研究噻菁染料与血清蛋白的相互作用

本文通过吸收和荧光光谱法研究了一种噻菁染料与人血清蛋白及牛血清蛋白的相互作用。吸收光谱数据表明,与血清蛋白结合后,噻菁染料单体的吸收峰发生红移,同时强度也有很大变化;还通过吸收光谱计算确定了噻菁染料与血清蛋白的结合位点数（ n ）。与人血清蛋白或牛血清蛋白结合后,噻菁染料的荧光量子产率增加。分析噻菁染料的荧光强度随溶液中血清蛋白浓度的变化得到了二者反应的表观结合常数（ K _a）和自由能变化（ ΔG ）。根据表观结合常数（ K _a）可以判断,人血清蛋白比牛血清蛋白与噻菁染料的结合更强。     

Molecular Recognition and Visual Detection of G‐Quadruplexes by a Dicarbocyanine Dye

The interactions of a dicarbocyanine dye 3,3′‐diethylthiadicarbocyanine, DiSC₂(5) , with DNA G‐quadruplexes were studied by means of a combination of various spectroscopic techniques. Aggregation of excess dye as a result of its positive charge is promoted by the presence of the polyanionic quadruplex structure. Specific high‐affinity binding to the parallel quadruplex of the MYC promoter sequence involves stacking of DiSC₂(5) on the external G‐tetrads; the 5′‐terminal tetrad is the favored binding site. Significant energy transfer between DNA and the dye in the UV spectral region is observed upon DiSC₂(5) binding. The transfer efficiency strongly depends on the DNA secondary structure as well as on the G‐quadruplex topology. These photophysical features enable the selective detection of DNA quadruplexes through sensitized DiSC₂(5) fluorescence in the visible region.     

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.     

Interaction of cyanine dyes with nucleic acids. XXV. Influence of affinity-modifying groups in the structure of benzothiazol-4-[2,6-dimethylpyridinium] dyes on the spectral properties of the dyes in the presence of nucleic acids.

Novel monomethine pyridinium cyanine dyes of similar structure and containing 'affinity-modifying' groups of different chemical nature were studied by spectral-luminescent methods as possible fluorescent probes for the nucleic acids detection. It was shown that the nature of the functional groups in the dye linker influences the fluorescent properties of the dye-nucleic acids complexes. Incorporation of a hydroxyl group into the linker structure leads to a significant increase in the fluorescence intensity of the dye--double-stranded DNA complexes relative to the parent dye Cyan 40.     

Recognition-mediated contrasting fluorescence behaviour of 4′,6-diamidino-2-phenylindole (DAPI): probing the pKa of p-sulfonatocalix[4/6]arenes

Abstract

The interaction between a biologically important dye, 4′,6-diamidino-2-phenylindole (DAPI) and a macrocyclic host, p-sulfonatocalix[6]arene (SCX6) has been investigated using ground-state absorption, steady-state as well as time-resolved fluorescence measurements at two preset pH conditions: 2.5 and 6. Acknowledging the complexation with SCX6 at both the pHs with strong binding, DAPI shows spectral shifts in the absorption and emission spectra; however, strikingly, the fluorescence intensity behaviour is seen contrastingly opposite. At lower pH (~2.5), DAPI displays six-fold intensity, whereas drastic quenching in the fluorescence intensity is recorded at pH 6. Detailed spectroscopic analysis revealed that the SCX6 with phenolate ion stabilised at the lower rim, prevailing at pH 6, efficiently quench the excited state of DAPI, presumably through an electron transfer process, whereas at pH 2.5, the undissociated phenolic groups extend the dye a favourable encapsulation to prevent the excited-state protonation process resulting in remarkable enhancement in the fluorescence. This interesting host–guided fluorescence response with pH is worth as fluorescence on-off switch at lower pH conditions as well as the DAPI system offers a good optical probe for the easy determination of the pK_a of p-sulfonatocalixarenes by visible fluorescence measurements.     

Spectroscopic Properties of Fluorescein and Rhodamine Dyes Attached to DNA

We report the spectroscopic properties of fluorescein, x-rhodamine, tetramethyl-rhodamine, attached to single strand, duplex DNA, and to the digestion products by DNAse I. The properties reported include: molar absorptivity, quantum yield, absorbance and fluorescence spectra, fluorescence lifetime, intrinsic lifetime (τ⁰), static quenching (S) and the Förster critical distances (R₀) between fluorescein and x-rhodamine or tetramethyl-rhodamine (acceptors). These spectroscopic properties depend strongly on the local dye environment. Fluorescein was studied: (1) attached to biotin (BF), (2) BF bound to avidin; and attached to two positions in DNA. X-rhodamine and tetramethyl-rhodamine were studied as free dyes and attached at the 5′-end of DNA. We propose a general method to determine the molar absorptivity and τ⁰ of a dye attached to DNA based on the reaction of a biotinylated and dye-labeled oligomer with standardized avidin. The molar absorptivity of a second dye attached to a DNA duplex can be obtained by comparing spectra of doubly and singly labeled sequences. S, arising from dye–DNA interactions can then be determined. R₀ for free and attached dyes showed differences from 1.1 to 4.2 Å. We present evidence for the direct interaction of dyes attached to the termini of various single-stranded DNA sequences.     

Spectroscopic Investigations on the Interaction of Crystal Violet with Nonionic Micelles of Brij and Igepal Surfactants in Aqueous Media

The behavior of the triphenylmethane dye crystal violet in aqueous solutions containing polyoxyethylene nonionic surfactants was investigated using absorption and fluorescence spectroscopic techniques. The interactions of the dye were examined in micellar media in order to prevent dye aggregation and to ensure maximum dye and surfactant interaction. The relative fluorescence enhancements and the binding constants of the dye to the surfactant micelles were determined. The micropolarities of the micellar environment sensed by the pyrene probe were estimated from the I ₁/I ₃ intensity ratios of the fluorescence spectra of pyrene. The fluorescence quenching of pyrene by hexadecylpyridinium chloride was investigated in aqueous surfactant mixtures at a fixed concentration of surfactant in order to determine the aggregation numbers. Attempts were made to correlate the binding constants obtained in this investigation to various micellar parameters.     

Preparation and Characterization of Uniform Near IR Polystyrene Nanoparticles

Biomaterials for in vivo fluorescence imaging are required to be biocompatible, nontoxic, photostable and highly fluorescent. Fluorescence must be in the near infrared (NIR) region of the electromagnetic spectrum to avoid absorption and autofluorescence of endogenous tissues. NIR fluorescent polystyrene nanoparticles may be considered ideal biomaterials for in vivo imaging applications. These NIR nanoparticles were prepared by a swelling process of polystyrene template nanoparticles with a hydrophobic NIR dye dissolved in a water‐miscible swelling solvent, a method developed for preparation of nonbiodegradable nanoparticles, for NIR fluorescent bioimaging applications. This method overcomes common problems that occur with dye entrapment during nanoparticle formation such as loss of fluorescence and size polydispersity. Fluorescence intensity of the nanoparticles was found to be size dependent, and was optimized for differently sized nanoparticles. The resulting NIR nanoparticles were also found to be more fluorescent and highly photostable compared to the free dye in solution, showing their potential as biomaterials for in vivo fluorescence imaging.     

Verification and Biophysical Characterization of a New Three‐Color Förster Resonance‐Energy‐Transfer (FRET) System in DNA

We report on a new three‐color FRET system consisting of three fluorescent dyes, i.e., of a carbostyril (=quinolin‐2(1H)‐one)‐derived donor D, a (bathophenanthroline)ruthenium complex as a relay chromophore A₁, and a Cy dye as A₂ (FRET=Förster resonance‐energy‐transfer) (cf. Fig. 1). With their widely matching spectroscopic properties (cf. Fig. 2), the combination of these dyes yielded excellent FRET efficiencies. Furthermore, fluorescence lifetime measurements revealed that the long fluorescence lifetime of the Ru complex was transferred to the Cy dye offering the possibility to measure the whole system in a time‐resolved mode. The FRET system was established on double‐stranded DNA (cf. Fig. 3) but it should also be generally applicable to other biomolecules.     

联二噻吩稠合的近红外BODIPY染料的合成与光谱性质

以叠氮乙酸乙酯和联二噻吩甲醛为原料,合成了联二噻吩并吡咯单体,之后在酸催化下与4-N,N-二甲基氨基苯甲醛缩合并与三氟化硼配位,得到一个新型的BODIPY染料SY。采用¹H NMR、质谱以及元素分析对其结构进行了表征。化合物SY在二氯甲烷中的最大吸收和发射波长分别为654和689 nm;采用荧光光谱滴定方法研究了它对pH值的响应,酸性条件下N,N-二甲基苯氨基团发生质子化,抑制了光诱导电子转移对BODIPY母体的荧光淬灭,其溶液的荧光显著增强,染料SY可以作为近红外的pH值荧光探针。