Quantitative comparison of long-wavelength Alexa Fluor dyes to Cy dyes: fluorescence of the dyes and their bioconjugates.

Amine-reactive N-hydroxysuccinimidyl esters of Alexa Fluor fluorescent dyes with principal absorption maxima at about 555 nm, 633 nm, 647 nm, 660 nm, 680 nm, 700 nm, and 750 nm were conjugated to antibodies and other selected proteins. These conjugates were compared with spectrally similar protein conjugates of the Cy3, Cy5, Cy5.5, Cy7, DY-630, DY-635, DY-680, and Atto 565 dyes. As N-hydroxysuccinimidyl ester dyes, the Alexa Fluor 555 dye was similar to the Cy3 dye, and the Alexa Fluor 647 dye was similar to the Cy5 dye with respect to absorption maxima, emission maxima, Stokes shifts, and extinction coefficients. However, both Alexa Fluor dyes were significantly more resistant to photobleaching than were their Cy dye counterparts. Absorption spectra of protein conjugates prepared from these dyes showed prominent blue-shifted shoulder peaks for conjugates of the Cy dyes but only minor shoulder peaks for conjugates of the Alexa Fluor dyes. The anomalous peaks, previously observed for protein conjugates of the Cy5 dye, are presumably due to the formation of dye aggregates. Absorption of light by the dye aggregates does not result in fluorescence, thereby diminishing the fluorescence of the conjugates. The Alexa Fluor 555 and the Alexa Fluor 647 dyes in protein conjugates exhibited significantly less of this self-quenching, and therefore the protein conjugates of Alexa Fluor dyes were significantly more fluorescent than those of the Cy dyes, especially at high degrees of labeling. The results from our flow cytometry, immunocytochemistry, and immunohistochemistry experiments demonstrate that protein-conjugated, long-wavelength Alexa Fluor dyes have advantages compared to the Cy dyes and other long-wavelength dyes in typical fluorescence-based cell labeling applications.     

Comparison of historic Grübler dyes with modern counterparts using thin layer chromatography.

The aniline dye industry was created in 1856 when William Perkin prepared the dye, mauve, from coal tar. Following that discovery, several dye manufacturing businesses were formed in Western Europe, most successfully in Germany. It was to these companies that early investigators turned to obtain these new dyes for the developing field of biology. In 1880, Dr. Georg Grübler started a company in Germany to supply the needs of biologists. Grübler dyes developed a reputation for excellence. In the study reported here, 29 samples of 12 Grübler dyes were compared to modern counterparts using thin layer chromatography. The dyes studied were basic fuchsine, acid fuchsine, safranine, pyronine, aniline blue, ponceau, gentian violet, methylene blue, orange G, malachite green, and Sudan III and IV. I found that these early Grübler dyes closely resembled modern day counterparts; however, the use of synonyms was confusing and some of the fat stains were mislabeled by modern criteria. The chromatograms of some dyes exhibited smearing, probably representing multiple closely related dye species. The study of old dyes provides interesting comparisons with modern counterparts as the center of dye manufacturing is moving from Europe and the United States to Asia.     

Dye-flow apparatus to measure the variation in axial xylem permeability over a stem cross-section

Abstract Equipment and methodology are described that allows the radial variation in axial xylem permeability (hydraulic conductivity) over a tree cross-section to be measured and the flow paths to be identified by the strictly controlled flow of dye through a specimen. The apparatus can be calibrated so that the point-to-point variation of absolute permeability over a xylem cross-section can be calculated from the dye-flow patterns, which otherwise show only relative variations in permeability. The effect of using different dyes and dye concentrations on the penetration time and the shape of the dye patterns was investigated. The penetration time through the wood of identical end-matched specimens is appreciably longer for fixing dyes than for non-fixing dyes, and for the fixing dyes it depends strongly on the dye concentration. However, the dye patterns of the end-matched specimens were indistinguishable with fixing and non-fixing dyes, and independent of dye concentration. The fixing dye toluidine blue at 0.25% to 0.5% (w/w) was found most suitable as it yields a clear permanent pattern.     

Comparison of historic Grübler dyes with modern counterparts using thin layer chromatography

The aniline dye industry was created in 1856 when William Perkin prepared the dye, mauve, from coal tar. Following that discovery, several dye manufacturing businesses were formed in Western Europe, most successfully in Germany. It was to these companies that early investigators turned to obtain these new dyes for the developing field of biology. In 1880, Dr. Georg Grübler started a company in Germany to supply the needs of biologists. Grübler dyes developed a reputation for excellence. In the study reported here, 29 samples of 12 Grübler dyes were compared to modern counterparts using thin layer chromatography. The dyes studied were basic fuchsine, acid fuchsine, safranine, pyronine, aniline blue, ponceau, gentian violet, methylene blue, orange G, malachite green, and Sudan III and IV. I found that these early Grübler dyes closely resembled modern day counterparts; however, the use of synonyms was confusing and some of the fat stains were mislabeled by modern criteria. The chromatograms of some dyes exhibited smearing, probably representing multiple closely related dye species. The study of old dyes provides interesting comparisons with modern counterparts as the center of dye manufacturing is moving from Europe and the United States to Asia.     

One-bath trichrome staining: Investigation of a general mechanism based on a structure-staining correlation analysis

Summary Dye pairs of contrasting colours were selected from acid dyes of varied chemical characteristics. The 44 dye pairs were investigated in a one-bath trichrome staining system in which the dye-baths were strongly acid. Dye concentrations, concentration ratios and staining times were varied for each dye pair. Thirty dye pairs stained collagen fibres distinctly different colours to muscle cytoplasm, while 14 dye pairs gave muddy, non-selective staining. Comparison of dye structures showed that in selective pairs the larger dye always stained the collagen fibres, with cytoplasm being coloured by the smaller species. With 28/30 of the selective dye pairs the differences in anionic weights of the dyes was > 200. However, in dye pairs giving non-selective staining, the anionic weights of the members of 13/14 of the dye pairs differed by < 200. As no other structural feature correlated so clearly with selectivity, it was concluded that the selectivity of one-bath trichromes is diffusion-rate controlled, involving the interaction of differentially permeable tissue sites (collagen being more permeable than muscle cytoplasm) with dyes diffusing at different rates (large dyes slower than small). In keeping with this, lengthening staining times reduced staining selectivity. The rate control mechanism suggested a rational trouble-shooting guide for one-bath trichromes, encompassing such practical factors as dye concentration, embedding medium, fixative, dye-bath pH, section thickness and staining time.     

Laccase-mediator system in the decolorization of different types of recalcitrant dyes

Phloroglucinol, thymol, and violuric acid (VIO) were selected as laccase mediators after screening 14 different compounds with indigo carmine (indigoid dye) as a substrate. With the presence of these three mediators, a nearly complete decolorization (90-100%) was attained in 1 h. Thus, these three compounds were used as mediators for the decolorization of other four dyes. The results indicated that VIO was effective mediator in decolorization of Remazol brilliant blue R (RBBR, anthraquinoid dye) and Coomassie brilliant blue G-250 (CBB, triphenylmethane dyes), and Acid red (diazo dye). In presence of VIO, the four dyes described above attained 70% decolorization. Thymol was able to mediate decolorization of RBBR and Azure A (heterocyclic dye). Phloroglucinol has no mediating capability in decolorization of the four dyes analyzed. Mediator concentration, pH, and copper ion have an effect on the decolorization of the RBBR. Our data suggested that the decolorization capabilities of laccase/mediator system were related to the types of mediator, the dye structure and decolorization condition.     

Are picro-dye reactions for collagens quantitative? Chemical and histochemical considerations

Previous studies of picro-dye reactions demonstrated wide variations in the binding of different dyes. Picro-Sirius Red F3BA was recommended because it colors all collagens intensely and is suitable for polarization microscopy. Recent publications on quantitative uses of this stain were surprising. To obtain further information on the chemical mechanisms of dye binding by proteins, 94 sulfonated azo dyes were tested under the conditions of the picro-Sirius Red F3BA reaction. Reaction patterns varied widely, from failure to compete successfully with picrate ions for binding sites to strong coloration of all tissue structures. Only a few dyes stained collagen, reticulum fibers and basement membranes intensely and selectively. The reactivity of dyes was determined by their molecular configuration and the nature and position of substituents. Correlation with physico-chemical data showed that dye binding is due to non-ionic interactions, i.e. van der Waals and dispersion forces and hydrophobic bonding. Coulomb forces do not impart affinity - increasing sulfonation actually decreases dye uptake - but draw dyes within reach of non-ionic sites. Bound dyes form aggregates with additional dye ions; the aggregation number can range from 2 to many powers of 10. Clearly, dye binding by proteins is not stoichiometric.     

Chromatography of proteins on columns of polyvinylpolypyrrolidone using adsorbed textile dyes as affinity ligands

A simple and inexpensive chromatography system for proteins is introduced. When the amino derivatives of chlorotriazine dyes or other azo dyes were added to an aqueous slurry of the crosslinked polymer polyvinylpolypyrrolidone they were adsorbed, thus forming an immobilized dye chromatographic matrix. The association of the textile dyes with polyvinylpolypyrrolidone did not prevent them from acting as affinity ligands for proteins. Parameters such as ionic strength, dye concentration, and column size modulated the affinity effect exerted by the immobilized dyes. Lysozyme present in an egg white protein mixture bound to a column onto which the amino derivative of Procion Brown H-A was adsorbed and was eluted with a linear gradient of KCl. The resulting purification of the enzyme was 37-fold with 80% of the original activity being recovered. Free dye eluting with the lysozyme was removed on a column of polyvinylpolypyrrolidone equilibrated with 0.5 M KCl. After chromatography, the dye column was regenerated with 0.5 M NaOH and recharged with dye. The system presented here allows one to initially screen large numbers of potentially useful protein ligands to optimize a protein separation, followed by scaleup to a system size determined by the user.     

Developing azo and formazan dyes based on environmental considerations: Salmonella mutagenicity

In previous papers, the synthesis and chemical properties of iron-complexed azo and formazan dyes were reported. It was shown that in certain cases iron could be substituted for the traditionally used metals such as chromium and cobalt, without having an adverse effect on dye stability. While these results suggested that the iron analogs were potential replacements for the commercially used chromium and cobalt prototypes, characterization of potentially adverse environmental effects of the new dyes was deemed an essential step in their further development. The present paper provides results from using the Salmonella/mammalian microsome assay to determine the mutagenicity of some important commercial metal complexed dyes, their unmetallized forms, and the corresponding iron-complexed analogs. The study compared the mutagenic properties of six unmetallized azo dyes, six commercial cobalt- or chromium-complexed azo dyes, six iron-complexed azo dyes, six unmetallized formazan dyes, and six iron-complexed formazan dyes. The results of this study suggest that the mutagenicity of the unmetallized dye precursors plays a role in determining the mutagenicity of the iron-complexes. For the monoazo dye containing a nitro group, metal complex formation using iron or chromium decreased or removed mutagenicity in TA100; however, little reduction in mutagenicity was noted in TA98. For the formazan dye containing a nitro group, metal-complex formation using iron increased mutagenicity. Results varied for metal-complexes of azo and formazan dyes without nitro groups, but in general, the metal-complexed dyes based on mutagenic ligands were also mutagenic, while those dyes based on nonmutagenic ligands were nonmutagenic.     

Orientation and spectral properties of two stilbazolium merocyanine dyes in stretched and unstretched polyvinyl alcohol films

Spectral properties (anisotropy coefficients calculated for absorption, emission and fluorescence decay time) of two stilbazolium merocyanine dyes have been determined to evaluate the applicability of these dyes as sensitizers in photodynamic therapy. The dyes were embedded in an anisotropic polymer matrix. Analysis of the emission decay components measured in polarized light provides information on the interactions of the dye molecules with the polymer matrix being a model of an anisotropic biological system. Different values of the emission anisotropies obtained from various polarized components of fluorescence decays have shown that the orientations of the dye molecules influence their interactions with the polymer. This means that differently oriented dye molecules located in biological systems should exhibit different interactions with membranes. The chain length and type of side groups attached as well as the salt form of the dye molecule were shown to influence the dye-polymer interactions and should be taken into account before the application of merocyanine dyes in medicine. These dyes seem to be promising optical sensors with spectral properties, including the calculated anisotropy coefficients, sensitive to the molecular environment, useful to study orientation and interaction with neighbouring molecules in biological membranes.     

Biodegradation of bioaccessible textile azo dyes by Phanerochaete chrysosporium

Azo dyes are important chemical pollutants of industrial origin. Textile azo dyes with bioaccessible groups for lignin degrading fungi, such as 2-methoxyphenol (guaiacol) and 2,6-dimethoxyphenol (syringol), were synthesised using different aminobenzoic and aminosulphonic acids as diazo components. The inocula of the best biodegradation assays were obtained from a pre-growth medium (PAM), containing one of the synthesised dyes. The results of the dye biodegradation assays were evaluated every 7 days, by the decrease of the absorbance at the maximum wavelength of the dye, by the decrease of the sucrose concentration in the culture medium and by the increase of the biomass during the 28 days of assay. It was observed that the extent of dye biodegradation depended on the sucrose concentration, on the degraded dye structure and, on the dye present in the PAM medium.     

Biodegradation of bioaccessible textile azo dyes by Phanerochaete chrysosporium

Azo dyes are important chemical pollutants of industrial origin. Textile azo dyes with bioaccessible groups for lignin degrading fungi, such as 2-methoxyphenol (guaiacol) and 2,6-dimethoxyphenol (syringol), were synthesised using different aminobenzoic and aminosulphonic acids as diazo components. The inocula of the best biodegradation assays were obtained from a pre-growth medium (PAM), containing one of the synthesised dyes. The results of the dye biodegradation assays were evaluated every 7 days, by the decrease of the absorbance at the maximum wavelength of the dye, by the decrease of the sucrose concentration in the culture medium and by the increase of the biomass during the 28 days of assay. It was observed that the extent of dye biodegradation depended on the sucrose concentration, on the degraded dye structure and, on the dye present in the PAM medium.     

花生壳粉生物吸附水溶液中阴离子染料的研究

An untried,low cost, locally available biosorbent for its anionic dye removal capacity from aqueous solution was investigated. Powder prepared from peanut hull had been used for hiosorption of three anionic dyes, amaranth (Am), sunset yellow (SY) and fast green FCF (FG). The effects of various experimental parameters (e.g.initial pH and dye concentration, sorbent dosage, particle size, ion strength, contact time etc.) were examined and optimal experimental conditions were decided. At initial pH 2.0, three dyes studied could be removed effectively.When the dye concentration was 50 mg" L-1 the percentages of dyes sorbed was 95.5 % in Am, 91.3 % in SY and 94.98 % in FG, respectively. The ratios of dyes sorbed had neared maximum values in all three dyes whensorbent dose of 5.0 g·L^-1 and the sorbent particle size in 80—100 mesh was used. The increasing the ion strength of solution caused the decrease in biosorption percentages of dyes. The equilibrium values arrived at about 36 hour for all three dyes. The isothermal data of biosorption followed the Langmuir and Freundlich models. The biosorption processes conformed the pseudo-first-order rate kinetics. The results indicated that powdered peanut hull was an attractive candidate for removing anionic dyes from dye wastewater.     

Are picro-dye reactions for collagens quantitative?

Summary Previous studies of picro-dye reactions demonstrated wide variations in the binding of different dyes. Picro-Sirius Red F3BA was recommended because it colors all collagens intensely and is suitable for polarization microscopy. Recent publications on quantitative uses of this stain were surprising. To obtain further information on the chemical mechanisms of dye binding by proteins, 94 sulfonated azo dyes were tested under the conditions of the picro-Sirius Red F3BA reaction.Reaction patterns varied widely, from failure to compete successfully with picrate ions for binding sites to strong coloration of all tissue structures. Only a few dyes stained collagen, reticulum fibers and basement membranes intensely and selectively.The reactivity of dyes was determined by their molecular configuration and the nature and position of substituents. Correlation with physico-chemical data showed that dye binding is due to non-ionic interactions, i.e. van der Waals and dispersion forces and hydrophobic bonding. Coulomb forces do not impart affinity-increasing sulfonation actually decreases dye uptake — but draw dyes within reach of non-ionic sites. Bound dyes form aggregates with additional dye ions; the aggregation number can range from 2 to many powers of 10. Clearly, dye binding by proteins is not stoichiometric.Dedicated to Professor Dr. T.H. Schiebler on the occasion of his 65th birthday     

Decolorization of basic, direct and reactive dyes by pre-treated narrow-leaved cattail (Typha angustifolia Linn.)

The efficiency of basic, direct and reactive dye removal from water by narrow-leaved cattail (NLC) powder treated with distilled water (DW-NLC), 37% formaldehyde+0.2 N sulfuric acid (FH-NLC), or 0.1 N sodium hydroxide (NaOH-NLC) at various pH levels (3, 5, 7, and 9) was tested. Desorption of the adsorbed dyes was also investigated. The type of NLC treatment and pH of the dye solution had little effect on removal of basic dyes, and efficiencies ranged from 97% to 99% over the range of pH used. Over a wide range of pH levels, all types of treated cattail powder had negative charges and probably attracted the basic dyes possessing positive charges. Efficiency of removal by the three NLC treatments ranged from 37% to 42% for direct dyes and from 22% to 54% for direct dyes at pH 7. The pH of the dye solution had substantial effects on the efficiency of removal in direct and reactive dyes. Dye removal was highest at pH 3, with 99% for a direct dye (Sirius Red Violet RL) and 96% for a reactive dye (Basilen Red M-5B). There was mutual attraction between negatively charged direct dye molecules and positively charged molecules on the surface of the FH-treated cattail. In tests of desorption of dyes from cattail in distilled water, the desorption percentage for FH-NLC after adsorbing basic, direct and reactive dyes was 6%, 10% and 35%, respectively, which indicated a chemisorption mechanism for basic and direct dyes and some physiosorption for reactive dyes.     

Redox-mediated decolorization of synthetic dyes by fungal laccases

Laccases from the lignin-degrading basidiomycetes Trametes versicolor, Polyporus pinisitus and the ascomycete Myceliophthora thermophila were found to decolorize synthetic dyes to different extents. Differences were attributed to the specific catalytic properties of the individual enzymes and to the structure of the dyes. Due to their higher oxidative capacities, the laccases from the two basidiomycetes decolorized dyes more efficiently than that of the ascomycete. The azo dye Direct Red 28, the indigoid Acid Blue 74 and anthraquinonic dyes were directly enzymatically decolorized within 16 h. The addition of 2 mM of the redox-mediator 1-hydroxybenzotriazole further improved and facilitated the decolorization of all nine dyes investigated. Laccases decolorized dyes both individually and in complex mixtures in the presence of bentonite or immobilized in alginate beads. Our data suggest that laccase/mediator systems are effective biocatalysts for the treatment of effluents from textile, dye or printing industries.     

Optimization of staining conditions for microalgae with three lipophilic dyes to reduce precipitation and fluorescence variability

When the fluorescence signal of a dye is being quantified, the staining protocol is an important factor in ensuring accuracy and reproducibility. Increasingly, lipophilic dyes are being used to quantify cellular lipids in microalgae. However, there is little discussion about the sensitivity of these dyes to staining conditions. To address this, microalgae were stained with either the lipophilic dyes often used for lipid quantification (Nile Red and BODIPY) or a lipophilic dye commonly used to stain neuronal cell membranes (DiO), and fluorescence was measured using flow cytometry. The concentration of the cells being stained was found not to affect the fluorescence. Conversely, the concentration of dye significantly affected the fluorescence intensity from either insufficient saturation of the cellular lipids or formation of dye precipitate. Precipitates of all three dyes were detected as events by flow cytometry and fluoresced at a similar intensity as the chlorophyll in the microalgae. Prevention of precipitate formation is, therefore, critical to ensure accurate fluorescence measurement with these dyes. It was also observed that the presence of organic solvents, such as acetone and dimethyl sulfoxide (DMSO), were not required to increase penetration of the dyes into cells and that the presence of these solvents resulted in increased cellular debris. Thus, staining conditions affected the fluorescence of all three lipophilic dyes, but Nile Red was found to have a stable fluorescence intensity that was unaffected by the broadest range of conditions and could be correlated to cellular lipid content.     

Study of dye decolorization in an immobilized laccase enzyme-reactor using online spectroscopy

Decolorization of textile dyes by a laccase from Trametes modesta immobilized on gamma-aluminum oxide pellets was studied. An enzyme reactor was equipped with various UV/Vis spectroscopic sensors allowing the continuous online monitoring of the decolorization reactions. Decolorization of the dye solutions was followed via an immersion transmission probe. Adsorption processes were observed using diffuse reflectance measurements of the solid carrier material. Generally, immobilization of the laccase does not seem to sterically affect dye decolorization. A range of commercial textile dyes was screened for decolorization and it was found that the application of this enzymatic remediation system is not limited to a certain structural group of dyes. Anthrachinonic dyes (Lanaset Blue 2R, Terasil Pink 2GLA), some azo dyes, Indigo Carmine, and the triphenylmethane dye Crystal Violet were efficiently decolorized. However, the laccase displayed pronounced substrate specificities when a range of structurally related model azodyes was subjected to the biotransformation. Azodyes containing hydroxy groups in ortho or para position relative to the azo bond were preferentially oxidized. The reactor performance was studied more closely using Indigo Carmine.     

Effect of chemical structures of acridine and triphenylmethane dyes on the induced optical activity of DNA-dye complexes

Fifteen symmetrically substituted acridine dyes, all of which are interrelated by their chemical structures, each belonging to a C_2v symmetry, and three triphenylmethane dyes with amino or dimethylamino substituents are utilized to study necessary conditions for the appearance of extrinsic Cotton effects upon their binding to native and heat-denatured deoxyribonucleic acid (DNA). Three different kinds of the DNA–dye complexes, i.e., (1) dye added to native DNA, (2) heat-denatured DNA–dye complex, and (3) dye added to preheated DNA, were examined for each dye at a fixed P/D value of about 4. Optical activity was always observed for the compelexes of type (1) in each absorption band of the dyes in the visible and near-ultraviolet region. Two exceptions are 9-acetamido- and 9-hydroxyacridine, both being nonionic in aqueous solution at a pH range of 6. Acridinium chloride was unable to exhibit any definite extrinsic Cotton effect for complexes (2) and (3). Thus, the monocationic form of a dye due to the protonation or quaternization of the ring nitrogen in acridines or exonuclear amino nitrogen in triphenylmethane dyes is concluded to be an essential factor for extrinsic Cotton effect to appear. Changes in the absorption spectra upon complex formation are also related to the structure of dyes. Hypochromism and bathochromism are associated with the induced optical activity in all cases in the presence of native and denatured DNA.     

Dextrin and salt as impurities of histological dyes

Summary The dextrin and salt contents of 18 common histological dyes (usually obtained from more than one supplier) were estimated by solvent extraction of dye from the commercial sample with organic solvents such as ethanol, iso-propanol and methanol. The procedure is also suitable for preparing large quantities of dextrin and salt-free dyes. The dye contents of the commercial dye samples varied widely:many commercial dyes were pure but nearly half the samples contained less than 75% dye. The solvent insoluble residues from 10 commercial pyronin and rhodamine dyes were studied in more detail. Tests for dextrin and for NH ₄ ⁺ , Cl^– and SO ₄ ^2– ions were applied and the dextrin:salt ratio determined by combustion. Only 3 of the residues contained appreciable amounts of salt. Certain samples contained organic materials other than dextrin.