The Influence of Molecular Structure of Thiazine and Oxazine Dyes on Their Metachromatic Properties

In 29 thiazine and 12 oxazine dyes, greater metachromatic activity was found in thiazines than in their oxazine analogues. In the oxazine group only brilliant cresyl blue and the naphthophenoxazines showed marked mctachromasia. Metachromasia was not shown by members of the thiazine series with the following N-substituents: —NPr₂; —NEt₂; —NEtMe; —N(piperazino) and —N(morpholino). C-methyl substitution in positions 1 and 9 of the thiazine appeared to increase absorption in the beta peak relative to the alpha, even though the dye were nonmetachromatic; a peculiarity seen also in the naphthophenoxazines. Details of preparation, isolation and identification of the dyes are given.     

Absorption and fluorescence spectra of hypericin sodium salt in complexes with albumins

The spectra of absorption and fluorescence of hypericin sodium salt (Na-Hy) in organic solvents and in complexes with human serum albumin, bovine serum albumin, and lipoproteins of low and high density have been studied. It was shown that, as the proton donor properties of the solvent enhance, the absorption and fluorescence maxima shift toward the blue region, and as the proton-accepting properties increase, the maxima shift toward the red region. The absorption spectra of complexes of Na-Hy with bovine serum albumin significantly differ from those of complexes of this ligand with human serum albumin, which is evidenced by a lesser width of absorption bands and a lower value of the Stokes shift. The positions of the absorption and fluorescence maxima and the value of the Stokes shift for the complex of Na-Hy with human serum albumin increases when D₂O instead of common water is used as a solvent. It was concluded that H-bonds of hypericin play a significant role in the interaction with human serum albumin.     

Selective labeling of lipid droplets in aldehyde fixed cell monolayers by lipophilic fluorochromes

Abstract

We evaluated a number of lipophilic dyes and fluorochromes, including oxazone and thiazone derivatives of oxazine and thiazine dyes, scintillator agents, a carotenoid and a metal-porphyrin complex for visualization of lipid droplets within aldehyde fixed cultured HeLa and BGC-1 cells. Observation under ultraviolet, blue or green exciting light revealed selective fluorescence of lipid droplets, particularly after treatment with aqueous solutions of Nile blue and brilliant cresyl blue oxazones, toluidine blue thiazone, or propylene glycol solutions of canthaxanthin, ethyl-BAO, and ZnTPyP. Mounting in water was required to maintain the fluorescence of lipids; the use of glycerol, Mowiol or Vectashield was not adequate. The effect of dye structure on staining intensity was assessed with the aid of numerical structure parameters modeling lipophilicity (HI and log P), overall size (MW) and the size of the conjugated system (conjugated bond number; CBN). The best stains for lipid droplets were relatively lipophilic (HI > 4.0, log P > 5.0), of small size overall (MW < 370), with small conjugated systems (CBN < 24), and not significantly amphiphilic. The two hydrophobic-hydrophilic parameters (the classic log P and the hydrophobic index, HI; values calculated by molecular modeling software) were highly correlated; however, HI was a more suitable hydrophobicity index for the dyes studied here.     

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.     

Spectroscopic characterization of Coomassie blue and its binding to amyloid fibrils

Coomassie brilliant blue G-250 (CB) is the dye used frequently in the Bradford assay for protein concentration determination. In this study, we investigated how the solvent polarity and viscosity affect the CB absorption and fluorescence spectra and apply this understanding to investigate the binding of CB to lysozyme and insulin in the native and amyloid fibril states. Coomassie blue binds both to the native protein and to amyloid fibrils but gives distinctly different spectral responses. The absorption and fluorescence spectra of CB indicate that binding sites in the fibrils are less polar and hold the CB dye more rigidly than in the native forms. The spectral comparison of CB bound to the two different fibrils showed that the binding sites are different, and this was most likely due to differences in secondary structure as monitored by circular dichroism. Finally, linear dichroism was used to show that the fibril-bound CB is oriented preferentially parallel to the insulin amyloid fibril axis.     

Thiazin Dyes in Supravital Staining of nerve Fibers

Supravital staining by thiazins of segments of small intestine and mesentery of young dogs was studied with reference to specificity for nervous tissue. Attempts to secure a purer form of methylene blue by alumina adsorption and alcohol elution of the commercial, medicinal dye yielded a product which appeared to be structurally different from the original dye. The treated dye had absorption maxima from 620 to 655 mμ in contrast with 665 for the untreated. Small nerve bundles were stained by the treated dye after 2 to 4 hours of immersion, but staining was always incomplete. Staining by untreated methylene blue was compared with that by the leucobase, thionol, methylene green, toluidine blue, new methylene blue and the azures. It was concluded that the specificity for nerve fibers resides mainly in the =N(CH₃)₂Cl radical, although some specificity appears to be effected by the methyl groups on the trivalent nitrogen, since azure A (dimethyl) and azure C (mono-methyl) stained weakly, but thionin did not. Methylene green showed some specificity but stained weakly. The leucobase was less active than the reoxidized dye obtained from it.     

A Selective Stain for Eosinophils Using Two Oxazine Dyes Applied Sequentially

A methanolic solution of the oxazine textile dye, C. I. basic blue 122, followed by an aqueous alkaline solution of the oxazine dye, C. I. basic blue 141, and a brief rinse in an acetate buffer at pH 3.45 produces intense black staining of eosinophil granules. This staining was selective for eosinophils while other types of peripheral blood leukocytes showed little if any staining under the same conditions. This staining procedure may be useful for detecting eosinophils in samples of blood, bone marrow, or urine when eosinophiluria results from interstitial nephritis.     

Mechanism of spectral changes of a carbocyanine dye with acidic polysaccharides and oligogalacturonides

Changes in the visible spectrum of a cationic carboeyanine dye in the presence of α (1–4) linked oligomers of d-galacturonic acid have been found to be dependent on the number of uronic acid residues in the molecule. Polygalacturonic acid caused a shift in the dye spectrum that was linearly proportional to the polymer concentration. Neither mono- nor digalacturonic acid had an effect on the dye spectrum. Tri- and tetragalacturonic acid caused spectral changes which were nonlinear with respect to oligomer concentration while penta- and hexagalacturonic acid showed concentration-dependent properties similar to polygalacturonic acid.The difference spectra with polygalacturonate and other acidic polysaccharides containing one anionic site per monosaccharide residue showed two absorption maxima in the region of 550 nm and 610 nm. All of the oligomers tested (containing 3 through 6 galacturonic acid residues) yielded only a single maxima for each in the region between 650 and 670 nm. This single maxima phenomenon was also observed with acidic polysaccharides having only one anionic site for every two monosaccharide residues (hyaluronic acid and chondroitin).     

A sensitive, viable-colony staining method using Nile red for direct screening of bacteria that accumulate polyhydroxyalkanoic acids and other lipid storage compounds

The oxazine dye Nile blue A and its fluorescent oxazone form, Nile red, were used to develop a simple and highly sensitive staining method to detect poly(3-hydroxybutyric acid) and other polyhydroxyalkanoic acids (PHAs) directly in growing bacterial colonies. In contrast to previously described methods, these dyes were directly included in the medium at concentrations of only 0.5 μg/ml, and growth of the cells occurred in the presence of the dyes. This allowed an estimation of the presence of PHAs in viable colonies at any time during the growth experiment and a powerful discrimination between PHA-negative and PHA-positive strains. The presence of Nile red or Nile blue A did not affect growth of the bacteria. This viable-colony staining method was in particular applicable to gram-negative bacteria such as Azotobacter vinelandii, Escherichia coli, Pseudomonas putida, and Ralstonia eutropha. It was less suitable for discriminating between PHA-negative and PHA-positive strains of gram-positive bacteria such as Bacillus megaterium or Rhodococcus ruber, but it could also be used to discriminate between wax-ester- and triacylglycerol-negative and -positive strains of Acinetobacter calcoaceticus or Rhodococcus opacus. The potential of this new method and its application to further investigations of PHA synthases and PHA biosynthesis pathways are discussed. Received: 12 August 1998 / Accepted: 11 November 1998     

ON THE NATURE OF THE DYE PENETRATING THE VACUOLE OF VALONIA FROM SOLUTIONS OF METHYLENE BLUE

When uninjured cells of Valonia are placed in methylene blue dissolved in sea water it is found, after 1 to 3 hours, that at pH 5.5 practically no dye penetrates, while at pH 9.5 more enters the vacuole. As the cells become injured more dye enters at pH 5.5, as well as at pH 9.5. No dye in reduced form is found in the sap of uninjured cells exposed from 1 to 3 hours to methylene blue in sea water at both pH values. When uninjured cells are placed in azure B solution, the rate of penetration of dye into the vacuole is found to increase with the rise in the pH value of the external dye solution. The partition coefficient of the dye between chloroform and sea water is higher at pH 9.5 than at pH 5.5 with both methylene blue and azure B. The color of the dye in chloroform absorbed from methylene blue or from azure B in sea water at pH 5.5 is blue, while it is reddish purple when absorbed from methylene blue and azure B at pH 9.5. Dry salt of methylene blue and azure B dissolved in chloroform appears blue. It is shown that chiefly azure B in form of free base is absorbed by chloroform from methylene blue or azure B dissolved in sea water at pH 9.5, but possibly a mixture of methylene blue and azure B in form of salt is absorbed from methylene blue at pH 5.5, and azure B in form of salt is absorbed from azure B in sea water at pH 5.5. Spectrophotometric analysis of the dye shows the following facts. 1. The dye which is absorbed by the cell wall from methylene blue solution is found to be chiefly methylene blue. 2. The dye which has penetrated from methylene blue solution into the vacuole of uninjured cells is found to be azure B or trimethyl thionine, a small amount of which may be present in a solution of methylene blue especially at a high pH value. 3. The dye which has penetrated from methylene blue solution into the vacuole of injured cells is either methylene blue or a mixture of methylene blue and azure B. 4. The dye which is absorbed by chloroform from methylene blue dissolved in sea water is also found to be azure B, when the pH value of the sea water is at 9.5, but it consists of azure B and to a less extent of methylene blue when the pH value is at 5.5. 5. Methylene blue employed for these experiments, when dissolved in sea water, in sap of Valonia, or in artificial sap, gives absorption maxima characteristic of methylene blue. Azure B found in the sap collected from the vacuole cannot be due to the transformation of methylene blue into this dye after methylene blue has penetrated into the vacuole from the external solution because no such transformation detectable by this method is found to take place within 3 hours after dissolving methylene blue in the sap of Valonia. These experiments indicate that the penetration of dye into the vacuole from methylene blue solution represents a diffusion of azure B in the form of free base. This result agrees with the theory that a basic dye penetrates the vacuole of living cells chiefly in the form of free base and only very slightly in the form of salt. But as soon as the cells are injured the methylene blue (in form of salt) enters the vacuole. It is suggested that these experiments do not show that methylene blue does not enter the protoplasm, but they point out the danger of basing any theoretical conclusion as to permeability on oxidation-reduction potential of living cells from experiments made or the penetration of dye from methylene blue solution into the vacuole, without determining the nature of the dye inside and outside the cell.     

Structure and dynamics of condensed DNA probed by 1,1'-(4,4,8,8-tetramethyl-4,8-diazaundecamethylene)bis[4-[[3- methylbenz-1,3-oxazol-2-yl]methylidine]-1,4-dihydroquinolinium] tetraiodide fluorescence

Information on the structure and dynamics of condensed forms of DNA is important in understanding both natural situations such as DNA packaging and artificial systems such as gene delivery complexes. We have established the fluorescence of bisintercalator 1,1'-(4,4,8,8-tetramethyl-4,8-diazaundecamethylene)bis[4-[[3-methylbenz-1,3-oxazol-2-yl]methylidine]-1,4-dihydroquinolinium] tetraiodide (YOYO-1) as a novel probe for DNA condensation. When the level of DNA-bound YOYO-1 is sufficiently large, condensation by either polyethylenimine (PEI) or the cationic detergent cetyltrimethylammonium bromide (CTAB) leads to electronic interaction among YOYO-1 molecules bound on the same DNA molecule. This interaction results in an excitonic blue shift of the absorption spectra of YOYO-1 and dramatic decrease in the fluorescence quantum yield. These observations constitute a signature of the condensation of DNA. We further examined the comparative properties of DNA condensed by PEI, CTAB, or Co(NH(3))(6)(3+) through the steady-state and dynamic fluorescence of YOYO-1. Condensation by either PEI or CTAB was associated with a blue shift in the absorption spectra of YOYO-1, although the magnitude of the shift was larger in the case of PEI when compared to that of CTAB. In contrast, condensation by Co(NH(3))(6)(3+) was not associated with a measurable shift in the absorption spectra. These results were interpreted as signifying the varying level of compactness of the DNA condensates. Quenching of fluorescence by acrylamide showed that condensation by all three agents led to an increase in the level of solvent exposure of the base pairs. Observation of the decay of fluorescence intensity and anisotropy of DNA-bound YOYO-1 showed that while condensation by either PEI or CTAB froze the segmental mobility of the helix, condensation by Co(NH(3))(6)(3+) enhanced the flexibility of DNA. The relevance of our findings to functions such as efficiency of gene delivery is discussed.     

Metachromatic staining and electron dense reaction of glycosaminoglycans by means of Cuprolinic Blue

Summary The cationic phthalocyanin-like dye Cuprolinic Blue, unlike phthalocyanin dyes such as Alcian Blue or Astra Blue, can definitely exhibit a clear metachromatic reaction with appropriate substrates, The application of Cuprolinic Blue to epoxy-embedded semithin sections revealed that mast cell cytoplasmic granules, goblet cell mucin and cartilage matrix stained in violet shades (metachromatic), whereas nuclear chromatin presented a bright blue coloration (orthochromatic). The metachromatic structures showed a high degree of contrast when ultrathin sections treated with Cuprolinic Blue were examined by electron microscopy.Cytophotometric measurements of stained components from the large intestine showed different absorption maxima: at 580 nm for mucin and at 640 nm for nuclei. The spectroscopical analysis revealed a clear-cut metachromatic shift when the dye was in the presence of chondroitin—4-sulphate. The addition of aluminium metal to Cuprolinic Blue solutions resulted in a striking spectral change; under such conditions the dye showed absorption maximum at 530 nm.     

Studies on Polychrome Methylene Blue I. Eosinates, their Spectra and Staining Capacity

The absorption spectra of eosinates of thiazin dyes in water exhibit absorption maxima at the same spectral locations as do the individual component dyes in aqueous solution.

Commercial samples of Wright's stain showing thiazin absorption maxima between 620 and 660 mμ generally give satisfactory blood stains. Nuclear staining is redder and cytoplasm grayer blue in 620-640 range, and consequently staining of malaria parasites is less satisfactory in that range. The best malaria stains show their thiazin absorption maxima usually between 650 and 660 mμ.

Successive batches of Wright's stain made by the same manufacturer, as well as experimental laboratory lots, may show wide variations in their thiazin absorption maxima and in their staining characteristics.     

Spectrofluorometric studies of the lipid probe, nile red

We found that the dye nile red, 9-diethylamino-5H-benzo[alpha]phenoxazine-5-one, can be applied as a fluorescent vital stain for the detection of intracellular lipid droplets by fluorescence microscopy and flow cytofluorometry (J. Cell. Biol. 1985. 100: 965-973). To understand the selectivity of the staining, we examined the fluorescence properties of nile red in the presence of organic solvents and model lipid systems. Nile red was found to be both very soluble and strongly fluorescent in organic solvents. The excitation and emission spectra of nile red shifted to shorter wavelengths with decreasing solvent polarity. However, the fluorescence of nile red was quenched in aqueous medium. Nile red was observed to fluoresce intensely in the presence of aqueous suspensions of phosphatidylcholine vesicles (excitation maximum: 549 nm; emission maximum: 628 nm). When neutral lipids such as triacylglycerols or cholesteryl esters were incorporated with phosphatidylcholine to form microemulsions, nile red fluorescence emission maxima shifted to shorter wavelengths. Serum lipoproteins also induced nile red fluorescence and produced spectral blue shifts. Nile red fluorescence was not observed in the presence of either immunoglobulin G or gelatin. These results demonstrate that nile red fluorescence accompanied by a spectral blue shift reflects the presence of nile red in a hydrophobic lipid environment and account for the selective detection of neutral lipid by the dye. Nile red thus serves as an excellent fluorescent lipid probe.     

New investigations on hematoxylin, hematein, and hematein-aluminium complexes. II. Hematein-aluminium complexes and hemalum staining.

The absorption spectra of hematein-aluminium solutions have been recorded at various concentrations and pH values; the solutions were prepared using analytically pure hematein and potassium alum as aluminium source. In aqueous solution, four different hematein-aluminium complexes could be distinguished by absorption spectroscopy. In weakly acidic media we observed the violet 1:1 and 1:2 complexes HmAl (VII) and HmAl2(3) (VIII), and in strongly acidic solution the red 1:1 complex HmAl2 (IX). Whereas, in weakly alkaline solution the blue 1:1 complex HmAl0 (X) was detected. By change of the pH value the complexes were mutual interconverted. The dye complexes were characterized by their absorption spectra and molar extinction coefficients. We have stained HeLa cells with the complex solutions under different experimental conditions. In all cases the nuclear staining was intense whereas the staining of the cytoplasm was weak. The microspectra of the stained nuclei were recorded and compared with the absorption spectra of the complexes in solution. Thus it was possible to identify the bound dye species. After staining in acidic media, the cells were red to red-violet depending on the reaction conditions. The three cationic dye species VII, VIII, and IX were bound in varying amounts. After blueing in weakly acidic media or in water, only the violet dye complex VII was detected whereas, after blueing in weakly alkaline media, only the blue complex X has been observed. Enzymatic digestion experiments have shown that the dye complexes in the nuclei were bound to DNA while those in the cytoplasm and nucleoli were bound to RNA. The binding between the dye complexes and the nucleic acids is discussed.     

Optical properties of Alexa 488 and Cy5 immobilized on a glass surface

The absorption and emission spectra were measured for Cy5 and Alexa 488 fluorophores confined on a glass surface. The data were obtained using fluorometry and spectroscopic ellipsometry. Red shifts of the surface-immobilized fluorophore absorption spectra relative to the fluorophore spectra in aqueous solution were observed using both methods. We interpret these red shifts in terms of a change in the polarizability and polarity of the effective solvent. A formula is given that can be used to estimate expected shifts in absorption and emission maxima for surface-immobilized fluorophores. Spectroscopic ellipsometry measurements provide identification of the fluorophores confined on a glass surface. These results suggest that the design of microarray detection systems should be based on the optical properties of fluorophores attached to the surface and not on the optical properties of fluorophores in solution.     

The toluidine blue-membrane filter method: absorption spectra of toluidine blue stained bacterial cells and the relationship between absorbance and dry mass of bacteria

Propan-2-ol did not leach dye from toluidine blue stained bacteria on membrane filters but ethanol did. The absorption spectra of toluidine blue stained cells of two Gram-positive and two Gram-negative organisms differed with the latter organisms exhibiting metachromasia. The results suggest that toluidine blue stains the cell envelope. Linear regression equations were derived for each of four organisms, Streptococcus cremoris, Lactobacillus bulgaricus, Pseudomonas fluorescens and Escherichia coli, relating absorbance at the peak of the absorption spectra and the mass of cells on the filters. With these equations it should be possible to determine mass of cells with an error between 3% and 7.5% depending on the organism. Since the regression equations are similar, the amount of toluidine blue retained per milligram of cells may be constant under standard conditions, irrespective of species.     

The mode of action of antifungal agents. Effect of horse erythrocyte membranes on amphotericin B]

The Tris-HCl solution of the heptaen antibiotic, amphotericin B, gives a very important circular dichroism exhibiting a disymetric couplet. The absorption is affected by a blue shift of the maxima. The addition of erythrocyte membranes reduces the couplet and increases the small negative peaks to positive values at 422 and 399 nm. As a time function the evolution of spectra is hyperbol like. Such transformations are more important than those obtained with molecular cholesterol. These striking modifications of the C. D. spectra are correlated with conformational changes of the aggregative form of the antibiotic.     

Spectroscopic and molecular docking investigation of polynucleotides and DNA binding affinity to Nile blue dye

We used UV-vis absorption spectroscopy, fluorescence spectrophotometry and molecular docking calculations to investigate intermolecular interaction between the cationic dye, Nile blue (NB), and synthetic polynucleotides, poly(A-T), poly(G-C) and calf thymus DNA (Ct-DNA) at physiological pH. Strong hypsochromic absorbance and fluorescence quenching were observed that showed strong binding of NB to these polynucleotides and DNA. The binding affinity values derived from maximum absorption of the spectra of NB bound to various polynucleotides and Ct-DNA concentrations suggests that NB exhibits greater binding affinity to poly(G-C) than to poly(A-T). The thermodynamic parameters suggested that hydrogen bonds and van der Waals forces might play a major role in the binding of NB to DNA. The molecular docking results suggested that NB was an intercalator of the stacked base pairs of Ct-DNA.     

The Toluidine Blue-Membrane Filter Method: Absorption Spectra of Toluidine Blue Stained Bacterial Cells and the Relationship Between Absorbance and Dry Mass of Bacteria

Propan-2-ol did not leach dye from toluidine blue stained bacteria on membrane filters but ethanol did. The absorption spectra of toluidine blue stained cells of two Gram-positive and two Gram-negative organisms differed with the latter organisms exhibiting metachromasia. The results suggest that toluidine blue stains the cell envelope. Linear regression equations were derived for each of four organisms, Streptococcus cremoris, Lactobacillus bulgaricus, Pseudomonas fluorescens and Escherichia coli, relating absorbance at the peak of the absorption spectra and the mass of cells on the filters. With these equations it should be possible to determine mass of cells with an error between 3% and 7.5% depending on the organism. Since the regression equations are similar, the amount of toluidine blue retained per milligram of cells may be constant under standard conditions, irrespective of species.