A comparison of rapid electrophoretic and chromatographic methods for the investigation of common histological dyes

Summary The compositions of fifty-nine common histological dyes, as well as duplicate samples of several dyes from different suppliers, have been studied by agar gel electrophoresis, agarose gel electrophoresis, paper electrophoresis, paper chromatography and thin layer chromatography. Tables are presented to show the number of components present in each dye as disclosed by the different methods; the cases where duplicate samples were available are summarised in a separate table.On the basis of effectiveness and convenience agar gel electrophoresis and thin layer chromatography were by far the best methods. The Chromatographic method was of slightly wider applicability but as electrophoretic methods gave information on dye charge, agar gel electrophoresis was the best single method.     

Seeing gel wells well

Indicator dyes have been incorporated in the stacking gel monomer used in acrylamide gels to render readily visible and delineate the sample wells. Some dyes, such as bromphenol blue, migrate during the electrophoresis, whereas others, such as the ortho-unsubstituted phenol red, become chemically bound to the polymerized gel. The method can be used for agarose gels.     

Agar Gel Electrophoresis: an Advantageous Technique for the Investigation of Certain Biological Stains

The agar gel method can be used to study direct dyes, for which paper can not be used because such dyes have a high affinity for the paper. A 1% gel made up with a buffer in the range of pH 9-4, of ionic strength 0.05, and spread on 8 × 10 cm lantern slides provides suitable conditions. Dyes to be tested are placed in 1.5 mm wells made in the agar and subjected to a current of 2.5 ma/cm width, at a potential of about 115 v. Separations, if any, occur in about 20 min. Mobility is affected by ionic strength; values above 0.05 may be less satisfactory by reducing mobility and allowing excessive diffusion of the dye. The method allows resolution of dyes whose molecular charges differ by only one unit. Photographic recording is sharp, since the gel is transparent. The method can be recommended as generally useful for studying both acid and direct dyes.     

Fluorography--limitations on its use for the quantitative detection of 3H- and 14C-labeled proteins in polyacrylamide gels

The suitability of fluorography for the detection of 3H- and 14C-labeled proteins on polyacrylamide gradient gels has been investigated. It was found that the absorbance of the fluorographic film image produced by a given level of radioactivity decreased as the acrylamide concentration in the gel increased. The use of Coomassie brilliant blue protein dyes to stain the gel prior to fluorography reduced the absorbance of the fluorographic image. It is concluded that quantitative fluorography can only be applied to unstained gels of a uniform acrylamide concentration.     

Cyanine dyes for the detection of double stranded DNA

Twenty three novel cyanine dyes have been applied as fluorescent stains for the detection of nucleic acids in agarose gel electrophoresis. Significant fluorescence enhancement of these dyes in the presence of double stranded DNA was observed. Five dyes offered superior sensitivity in the detection and quantification of DNA, over Ethidium Bromide, the most commonly used nucleic acid stain.     

Synthesis and spectroscopic characterisation of new ESIPT fluorescent protein probes.

Three new benzazole isothiocyanate fluorescent dyes, 2-(4'-isothiocyanate-2'-hydroxyphenyl)benzoxazole, 2-(4'-isothiocyanate-2'-hydroxyphenyl)benzothiazole and 2-(4'-isothiocyanate-2'-hydroxyphenyl)benzimidazole were synthesised, purified until optical purity grade and characterised by spectroscopic techniques. UV/VIS and steady-state fluorescence were also applied to characterise the photophysical behaviour of the dyes. These dyes exhibit an intense fluorescence emission with a large Stokes shift, inherent to the class of benzazoles which relax by the excited state intramolecular proton transfer (ESIPT) mechanism. The dyes were studied for labeling bovine serum albumin (BSA), resulting conjugates BSA-dye with a remarkable photostability under UV/VIS radiation in relation to classical protein labels. The resulting conjugates presented fluorescence in the blue-green region. Direct fluorescence detection of protein-labeled with those dyes after polyacrylamide gel electrophoresis indicates their potential use as fluorescent probes for proteins.     

Purification of muscle enzymes by pseudoaffinity chromatography

A method based on pseudoaffinity chromatography has been developed for the separation of lactate dehydrogenase (LDH), pyruvate kinase (PK) and aldolase from rabbit muscle extract using cross-linked guar (CLG) and cross-linked pectin (CLP) as the matrices, and dyes as the ligands. Screening of several dyes revealed that dyes No. 1014 and No. 1015, immobilized on CLG and CLP displayed a higher affinity for LDH and PK. Aldolase was not retained on any of the dye columns. It was observed that 1014-CLP and 1014-CLG columns retained 90% and 55% LDH activities, respectively, whereas 1015-CLP and 1015-CLG retained 83% LDH and 72% PK. A coupled-column system comprising 1014-CLP and 1015-CLP or 1014-CLG and 1015-CLG could separate LDH, PK, and aldolase from a mixture of these enzymes, as well as from rabbit muscle extract. Enzymes were found to be homogeneous on polyacrylamide gel electrophoresis. The method has been found to be simple and economical.     

The improved method in agarose gel electrophoresis of nucleic acid

In most molecular experiments, nucleic acids are subjected to agarose gel electrophoresis to determine the size of the molecule. The addition of a nucleic acid dye allows the nucleic acid to be detected under the UV image system after running the gel, so the nucleic acid dye is an integral part of the electrophoresis experiment. But when considering the mutagenicity and toxicity of nucleic acid dyes, one must be careful to insure the proper disposal of experimental waste. In this article, a new usage of nucleic acid dye in agarose gel electrophoresis is described where the nucleic acid dyes were added to the loading buffer and nucleic acid marker buffer. The results show that this method has advantages as: a smaller amount of dye can be used, there is less time in contact with the dye, and its operation is easier and reduces toxicity damage. Also the bands showed a much clearer image, having a lower background value. The improved method shows better results with lower toxicity and is superior to the traditional method.     

Direct structural analysis of modified RNA by fluorescent in-line probing

Chemical probing is a common method for the structural characterization of RNA. Typically, RNA is radioactively end-labelled, subjected to probing conditions, and the cleavage fragment pattern is analysed by gel electrophoresis. In recent years, many chemical modifications, like fluorophores, were introduced into RNA, but methods are lacking that detect the influence of the modification on the RNA structure with single-nucleotide resolution. Here, we first demonstrate that a 5'-terminal (32)P label can be replaced by a dye label for in-line probing of riboswitch RNAs. Next, we show that small, highly structured FRET-labelled Diels-Alderase ribozymes can be directly probed, using the internal or terminal FRET dyes as reporters. The probing patterns indeed reveal whether or not the attachment of the dyes influences the structure. The existence of two dye labels in typical FRET constructs is found to be beneficial, as 'duplexing' allows observation of the complete RNA on a single gel. Structural information can be derived from the probing gels by deconvolution of the superimposed band patterns. Finally, we use fluorescent in-line probing to experimentally validate the structural consequences of photocaging, unambiguously demonstrating the intentional destruction of selected elements of secondary or tertiary structure.     

Methods for the estimation of the number and quality of animal cells immobilized in carbohydrate gels.

Rapid and reliable methods for the determination of survival, proliferation, and metabolic activity of immobilized cells in gels are described. The first method is based on an MTT assay that measures qualitatively and quantitatively the metabolic activity of the cells. The second method determines cell number by measuring the amount of DNA available for Feulgen staining. In the third method, two fluorescent dyes are used to differentially stain viable and dead cells. The fourth method involves the use of glutaraldehyde to protect the cells when melting the gel to facilitate hemocytometric count. The presented techniques should help to test the efficiency of the immobilization procedures and to monitor the growth and survival of immobilized cells.     

A versatile apparatus for polyacrylamide and agarose gel electrophoresis in Plexiglas slab gel molds

A simple vertical slab gel electrophoresis apparatus for analytical, preparative, and two-dimensional electrophoresis is described. The use of permanently sealed Plexiglas acrylic plastic slab gel molds which need to be sealed only at the bottom during gel formation, rather than the glass plate sandwich used in most previous designs, virtually eliminates leakage during gel formation and, in addition, permits the continuous monitoring with ultraviolet light of proteins and nucleic acids labeled with fluorescent dyes during electrophoresis. Results obtainable with this apparatus are equivalent to those achieved in other apparati which are more expensive to fabricate or purchase.     

Determining a significant change in protein expression with DeCyder during a pair-wise comparison using two-dimensional difference gel electrophoresis

Two-dimensional difference gel electrophoresis (DIGE) is a tool for measuring changes in protein expression between samples involving pre-electrophoretic labeling with cyanine dyes. Here we assess a common method to analyze DIGE data using the DeCyder software system. Experimental error was studied by a series of same sample comparisons. Aliquots of sample were labeled with N-hydroxyl succinimidyl ester-derivatives of Cy2, Cy3, and Cy5 dyes and run together on one gel. This allowed assessment of how experimental error influenced differential expression analysis. Bias in the log volume ratios was observed, which could be explained by differences in dye background. Further complications are caused by significant gel-to-gel variation in the spot volume ratio distributions. Using DeCyder alone results in an inability to define ratio thresholds for 90 or 95% confidence. An alternative normalization method was thus applied which resulted in improved data distribution and allowed greater sensitivity in analysis. When combined with a standardizing function, this allowed gel-independent thresholds for 90% confidence. The new approach, detailed here, represents a method to greatly improve the success of DIGE data analysis.     

ProteomIQ blue, a potent post-stain for the visualization and subsequent mass spectrometry based identification of fluorescent stained proteins on 2D-gels

Manual spot excision for protein identification from fluorescent stained two-dimensional (2-D) gels is hard to accomplish. Here, we explore the use of ProteomIQ Blue as a post-stain method for the visualization of fluorescent stained/labeled proteins. We show that ProteomIQ Blue post-staining is almost as sensitive as staining with SYPRO Ruby or cyanine dyes alone. More than 90% of the protein spots that are stained with the fluorescent stains are still detectable with ProteomIQ Blue. In protein identification by mass spectrometry, ProteomIQ Blue post-stained spots provide high sensitivity and high protein sequence coverage of the peptide mass maps in both MALDI-TOF-MS and ESI-MS/MS analyses. In conclusion, post-staining of fluorescent stained gels with ProteomIQ Blue provides a facile and a powerful method to achieve quantitative protein analysis as well as protein identification in the same semianalytical gel without requiring sophisticated/expensive robotic equipment.     

Fluorescent two-dimensional difference gel electrophoresis unveils the potential of gel-based proteomics

Comparing different proteomes by classical two-dimensional electrophoresis is challenging and often complicated by substantial gel-to-gel variation. Separating two or more protein samples labelled with different fluorescent dyes in one single gel, as in two-dimensional difference gel electrophoresis, reduces this variability considerably. Recent technological innovations, specifically the introduction of a pooled internal standard, even further improve the quantification accuracy and statistical confidence of this method. In addition, decreasing the sample complexity by one of several protein or organelle fractionation procedures increases the number of spots investigated by this protein differential display methodology.     

The fluorescent dyes TO-PRO-3 and TOTO-3 iodide allow detection of microbial cells in soil samples without interference from background fluorescence

Visualization of microorganisms in soils and sediments using fluorescent dyes is a common method in microbial ecology studies, but is often hampered by strong nonspecific background fluorescence that can mask genuine cellular signals. The cyanine nucleic acid binding dyes TO-PRO-3 and TOTO-3 iodide enabled a clear detection of microbial cells in a mineral soil, while nonspecific background was greatly reduced compared with commonly used dyes. When used as counterstains for fluorescence in situ hybridization (FISH), both cyanine dyes allowed identification of microbial cells despite strong background from nonspecifically bound probes. TO-PRO-3 and TOTO-3 are easy to use and represent superior alternatives for detecting microorganisms in soil environments.     

Identification of Fusarium graminearum in cereal samples by DNA Detection Test Strips

AIMS: Development of a fast, sensitive and easy to handle method for the detection of Fusarium graminearum contamination in cereal samples by PCR. METHODS AND RESULTS: DNA Detection Test Strips were used for PCR-product detection and the method was compared to agarose gel electrophoresis. A minimum of 0.26 ng of purified target DNA was detectable with the Test Strip Detection limit in less contaminated samples was slightly lower when gel electrophoresis was used for amplicon detection. In highly contaminated samples, detection limits of both methods were similar. CONCLUSIONS: Detection of PCR products was performed in 20 min without the need of special technical equipment or hazardous fluorescent DNA dyes. SIGNIFICANCE AND IMPACT OF THE STUDY: The new method described is useful for the screening of cereals in industrial quality control.     

The use of a new reactive dye for quantitation of prestained proteins on polyacrylamide gels.

An evaluation of a number of commercial reactive textile dyes with regard to suitability for staining of proteins prior to polyacrylamide gel electrophoresis showed that a blue dye containing a difluorochloropyrimidyl group gave excellent quantitation. The sensitivity was as good as with other dyes suggested for the same purpose. Reaction conditions have been optimized to reach completion in 3 hr at 40°C. A simple device for slicing gels is described. The main errors responsible for experimental scatter are briefly discussed.     

Alginate gel biochip for real-time monitoring of intracellular processes in bacterial and yeast cells

A method was developed for producing cell biochips on the basis of calcium alginate. Cell immobilization in microvolumes of nontoxic alginate gel under mild conditions extended the range of testable micro-organisms. The possibility of studying the intracellular processes with alginate gel biochips was demonstrated in model experiments with Escherichia coli, Bordetella bronchiseptica, and Saccharomyces cerevisiae. Cell biochips proved to be suitable for simultaneous monitoring of nucleic acid and protein syntheses with two fluorescent dyes. The effect of chloramphenicol on nucleic acid synthesis was studied with five bacterial strains. Inducible synthesis of the green fluorescence protein (EGFP) in E. coli cells was monitored with the use of biochips. The level of EGFP synthesis correlated with the inductor concentration in the medium.Translated from Molekulyarnaya Biologiya, Vol. 39, No. 1, 2005, pp. 96–102.Original Russian Text Copyright © 2005 by Fesenko, Nasedkina, Chudinov, Prokopenko, Yurasov, Zasedatelev.     

The Azure Dyes their Purification and Physicochemical properties. II. Purification of Azure B

A method is described for the purification of the dye azure B in quantities sufficient for biological staining experiments on a larger scale. The method is based on the use of column chromatography. Two columns are employed. In column A with silica gel as adsorbent the azure B fraction is isolated from a suitable substrate ('technical' azure B gained by a modification of Bernthsen's synthesis of methylene blue, or plychrome methylene blue) using an acetate-formate mixture as eluent. In column B, on an Amberlite polyineric adsorbent (XAD-2) the acetate-formate anions are exchanged for chloride. Regeneration of both columns is possible: KMnO₄, Na₂S₂O₄ and water are run through column A, 5% NaOH, methanol and water through column B. Purification of azure B on economic terms is thus attained. The opinion is expressed that this method is also applicable to the purification of other cationic dyes.     

Use of polynucleotide/polyacrylamide-gel electrophoresis as a sensitive technique for the detection and comparison of ribonuclease activities.

A technique is described in which the incorporation of a polynucleotide substrate into the matrix of a polyacrylamide gel allows the use of electrophoresis for the detection of polycationic ribonuclease activity rather than simply the presence of protein. Because use is made of the catalytic properties of ribonucleases, polynucleotide/polyacrylamide-gel electrophoresis is apparoximately 10(5) times more sensitive for the detection of these enzymes than conventional gel electrophoresis with the use of protein-staining dyes. Initial studies showed that the poor migration, in the gels, of highly charged polycationic ribonucleases in the presence of negatively charged synthetic polynucleotides could be overcome by high concentrations of spermine. The positively charged polyamine, by neutralizing the polyanionic polynucleotide, enabled these basic enzymes to migrate considerable distances in the gel. Electrophoresis of the RNAases under conditions of low pH, and incubation of the gel at neutral pH followed by staining for polynucleotide, resulted in coloured gels containing clear bands that define regions of enzyme activity. Alterations in spermine concentration or substrate identity caused changes in the positions of these bands, suggesting a dynamic interaction among the enzyme, polyamine and polynucleotide. Because of the advantages, in terms of selectivity and sensitivity of polynucleotide/polyacrylamide-gel electrophoresis, this technique was used to demonstrate the nuclease homogenity of three purified bovine muscle enzymes, and to compare these enzymes with each other, as well as with bovine pancreatic ribonuclease A.