Improved procedure for the drying and storage of polyacrylamide slab gels.

An improved procedure for the drying and storage of polyacrylamide (PAA) slab gels of various sizes and acrylamide contents is presented. A PAA slab gel is preferentially fixed in methanol-acetic acid-glycerol-water (1.0:1.0:0.1:2.0) and then dried under low pressure in an adapted photoprint dryer between Cellophane and polyethylene foils at 75-80 degrees C for 50-90 min. Strong, transparent and flexible sheets are obtained that can be stored for extended periods. The potential of the procedure is exemplified following electrophoresis of both lipopolysaccharides and protein isolated from Coxiella burnetii bacterium.     

An expanding negative detection method for the visualization of DNA in polyacrylamide gels by eosin Y

A sensitive and easy technique has been developed for the negative detection of DNA following PAGE using eosin Y. After electrophoresis, gels are fixed and stained within 40 min to provide a detection limit of 0.1-0.2 ng of single DNA band, which appears as transparent and colorless under the opaque gel matrix background. The sensitivity of the new stain is fourfold better than zinc-imidazole negative and ethidium bromide stains. Furthermore, the newly developed staining method has been successfully applied to RNA visualization in polyacrylamide gels. In addition, the inclusion of inorganic salts in staining solution was also investigated, which has great effect on the staining efficiency.     

An improved silver stain for the visualization of lipopolysaccharides on polyacrylamide gels

A sensitive, brief, and user-friendly silver stain to meet the needs in high-efficiency detection of lipopolysaccharides (LPS) on polyacrylamide gels is described. In this study, the most commonly used formaldehyde-based LPS silver stain, which is potentially hazardous to the operator, is replaced by ascorbic acid (Vc) in alkaline sodium thiosulfate solution. It takes only about 35 min to complete all the protocol, with a detection limit of 4 ng of total LPS. The results indicate that this user-friendly method could be a good choice for LPS visualization on polyacrylamide gels.     

Alternative methods for fixing and staining gliadins in polyacrylamide gels.

Staining efficiencies of Coomassie Brilliant Blue G-250 (CBB G-250) and Coomassie Brilliant Blue R-250 (CBB R-250) in various media were studied in efforts to reduce or eliminate requirements for trichloroacetic acid (TCA). Stained gels were compared with gels stained with CBB R-250 in 12% TCA and evaluated for overall stain and background. Because of qualitative effects, stain intensities of low- and high-mobility gliadins were also evaluated. Results indicated gliadins are fixed under a wide range of conditions, permitting adjustment of conditions to provide optimum staining. CBB G-250 and R-250 in tap water fixed and stained most gliadins. Best results were obtained with CBB G-250 in 2% TCA, in 2% TCA containing 5% sodium sulfate, and in 2% and 5% phosphoric acid containing 5% sodium chloride or 5% sodium sulfate. Gels stained in these media were more easily observed during staining and more easily destained than gels stained in CBB R-250 in 12% TCA.     

Sensitive fluorescence detection of polyphosphate in polyacrylamide gels using 4',6-diamidino-2-phenylindol

PAGE is commonly used to identify and resolve inorganic polyphosphates (polyP). We now report highly sensitive and specific staining methods for polyP in polyacrylamide gels based on the fluorescent dye, 4',6-diamidino-2-phenylindol (DAPI). DAPI bound to polyP in gels fluoresced yellow while DAPI bound to nucleic acids or glycosaminoglycans fluoresced blue. Inclusion of EDTA prevented staining of glycosaminoglycans by DAPI. We also identified conditions under which DAPI that was bound to polyP (but not nucleic acids or other anionic polymers) rapidly photobleached. This allowed us to develop an even more sensitive and specific negative staining method that distinguishes polyP from nucleic acids and glycosaminoglycans. The lower LOD using DAPI negative staining was 4 pmol (0.3 ng) phosphate per band, compared to conventional toluidine blue staining with a lower LOD of 250 pmol per band.     

An explanation of the achromatic bands produced by peroxidase isozymes in polyacrylamide electrophoresis gels stained for malate dehydrogenase.

When plant tissue extracts are electrophoresed on polyacrylamide gels and the gels are stained for malate dehydrogenase by the standard NAD-dependent dehydrogenase reaction, terminating in the formation of reduced Nitroblue Tetrazolium (NBT), achromatic bands, in addition to the expected chromatic bands, are observed. The achromatic bands are seen when the staining conditions favor a generalized background staining of the gel and have been shown, in a previous study, to be caused by peroxidase isozymes [1]. The present study examined the mechanism by which peroxidase produced the achromatic bands using horseradish peroxidase (HRP). The generalized background staining resulted from the phenazine methosulfate (PMS)-mediated reduction of NBT. This reduction was enhanced by H2O2 and suppressed by HRP. Peroxidase apparently catalyzes the peroxidative oxidation of reduced PMS, which suppresses the generalized reduction of NBT in gel regions containing peroxidase isozymes producing the achromatic bands. In contrast, however, HRP also appears to catalyze the peroxidative oxidation of reduced NAD, but this reaction increases the reduction of NBT. The results are discussed in the context of the mechanisms proposed by others for the PMS-mediated reduction of NBT and for the peroxidase-catalyzed NADH-dependent formation of H2O2. This peroxidase-catalyzed reaction has been proposed for the plant peroxidases involved in lignification.     

A two-step,single pot procedure for the synthesis of substituted dihydropyrazolo-pyrimidines

In this study, we report a two-step, one pot tandem microwave-assisted reaction of 3-formylchromones with aminopyrazoles followed by a tin-free radical addition. A library of alkyl substituted dihydropyrazolopyrimidines was prepared using this new process.     

Efficient one-pot, two-step, microwave-assisted procedure for the synthesis of polysubstituted 2-aminoimidazoles

A microwave-assisted, one-pot, two-step protocol was developed for the construction of polysubstituted 2-aminoimidazoles. This process involves the sequential formation of imidazo[1,2-a]pyrimidinium salts from readily available 2-aminopyrimidines and alpha-bromocarbonyl compounds, followed by opening of the pyrimidine ring with hydrazine. [reaction: see text]     

Efficient method for visualization and isolation of proteins resolved in polyacrylamide gels

Polyacrylamide gel electrophoresis is a popular method used to purify proteins for reconstitution experiments, amino acid composition and sequence determinations. In this report we describe methods that will be of general use in the isolation and characterization of proteins and the benefits of substituting boric acid for glycine in the electrophoresis tray buffers. We also describe how proteins resolved in a variety of gel systems (including those containing sodium dodecyl sulfate) may be rapidly visualized with 8-anilino-1-naphthalene sulfonic acid and efficiently transferred to a second gel for two-dimensional gel analysis, or isolated by electroelution for subsequent characterization.     

A two-step procedure for the preparation of mono-protected bis-N-heterocyclic alkyl ether systems

A two-step convenient sequence for the synthesis of previously inaccessible mono-Boc-protected bis-N-heterocyclic alkyl substituted ether derivatives 4 is described. Mitsunobu protocol was applied to the preparation of pyridinyl ether precursor 5. The reduction of the electron rich pyridinyl system 5 has been achieved catalytically using the combination of PtO₂-H₂SO₄ or PtO₂-pTsOH under a hydrogen atmosphere maintained by a gas balloon at ambient temperature.     

An enzymatic assay convenient for the control of aprotinin levels during proteinase inhibitor therapy

Conclusion Estimation of aprotinin in plasma with the described amidolytic assay can be achieved within 70–80min and is, therefore, convenient as a bedside-control of high dose proteinase inhibitor therapy. Moreover, an ELISA for aprotinin developed simultaneously (Müller-Esterl et al. this issue) allows the detection of up to 0.2KIU/ml within 4h and is suitable, therefore, for special purposes, e.g. retrospective studies and low dose inhibitor therapy.

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Ein enzymatischer Test zur Kontrolle der Aprotininspiegel bei der Proteinaseinhibitor-Therapie

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Research fellowship from Humboldt-Stiftung, Institute of Molecular Genetics, Prague, SSR     

The migration anomaly of DNA fragments in polyacrylamide gels allows the detection of small sequence-specific DNA structure variations

Curved DNA fragments have a reduced electrophoretic mobility in polyacrylamide gels. The retardation in gels is extremely sensitive to small structural variations which influence the DNA helix axis. This gel assay can also be used to detect very small structural variations in DNA sequences which are not curved: The noncurved sequences of interest can be combined with curved stretches in phase with the helix turn. Using such sequence constructions, even subtle influences on the DNA helix axis can be detected. Experiments of this kind allow the determination of a relative order of sequence-specific DNA twist and wedge angles.     

A novel method for specific visualisation of serum albumin in polyacrylamide gels by iodine staining.

Bovine serum, bovine serum albumins (delipidated or globulin free or Fraction V), rabbit serum, rabbit serum albumin, Atlantic salmon serum, purified Atlantic salmon serum albumin, human plasma alpha 2-macroglobulin, hemocyanin, trypsin inhibitor, bovine transferrin and bovine lactoferrin were examined by a novel method for specific visualisation of albumins. In native polyacrylamide gel electrophoresis the albumins were visualised by iodine staining as a transparent spot against a brown background whilst the other proteins could not be visualised. It is suggested that the brown background was due to penetration of the gel by iodine while the chemical binding of iodine by albumin produced a decolourisation reaction. This novel method provides a fast and simple approach to identifying serum albumin in polyacrylamide gels.     

Combined application of analytical high performance thin layer chromatography and electroblotting for the detection of anti-ganglioside antibodies in human sera.

Antibodies against gangliosides isolated from small tumour and nervous tissue specimens can be reliably detected in serum samples by the ganglioside electrotransfer technique without the need for previous purification steps. After separation by high performance thin layer chromatography gangliosides are transferred from silica gel plates to hydrophobic polyvinylidene difluoride membranes. These membranes are highly suitable for immunostaining. The use of a 15-slit device allows simultaneous testing of up to 15 serum samples. Samples of serum from 39 patients with clear-cell carcinoma of the kidney, mammary carcinoma, ovarian carcinoma and neurological disorders together with samples from healthy controls were tested for anti-ganglioside antibodies from various tissues.     

An image analysis suite for spot detection and spot matching in two-dimensional electrophoresis gels

We propose a suite of novel algorithms for image analysis of protein expression images obtained from 2-D electrophoresis. These algorithms are a segmentation algorithm for protein spot identification, and an algorithm for matching protein spots from two corresponding images for differential expression study. The proposed segmentation algorithm employs the watershed transformation, k-means analysis, and distance transform to locate the centroids and to extract the regions of the proteins spots. The proposed spot matching algorithm is an integration of the hierarchical-based and optimization-based methods. The hierarchical method is first used to find corresponding pairs of protein spots satisfying the local cross-correlation and overlapping constraints. The matching energy function based on local structure similarity, image similarity, and spatial constraints is then formulated and optimized. Our new algorithm suite has been extensively tested on synthetic and actual 2-D gel images from various biological experiments, and in quantitative comparisons with ImageMaster2D Platinum the proposed algorithms exhibit better spot detection and spot matching.     

An ESR study of polymer-Cu(II) complexes in poly(vinyl alcohol), polyacrylamide,and poly(vinyl pyrrolidone) films

Optical and ESR spectra of polymer-Cu(II) complexes in polymer films have been studied. The dependence on F₁ = [Cu²⁺]/[MU] and F₂ = [OH^?]/[Cu²⁺], where [MU] is the molar concentration of monomeric units of the polymer, has been obtained. Optical spectra and potentiometric titration curves in solution have also been studied. There exists a buffer region 0 ? F₂ ? 2. Optical spectra in films are slightly different from those in solutions. At least five different ESR signals, designated as A, B, C or D, and E, have been found in poly(vinyl alcohol)-Cu(II). These signals appear successively with increasing F₂. Assignments are proposed as follows. Signal A (F₂ ≈ 0), also found in poly(acrylamide)-Cu(II) and poly(vinyl pyrrolidone)-Cu(II), is due to a single Cu(II) coordinated with two water molecules and chelated with two oxygens or nitrogens attached to the polymer. A chain of Cu(II) ions singly and double bridged with OH^? ions is responsible for the B signal (F₂ ≈ 1). The C and D signals (F₂ ≈ 2) appear to be caused, respectively, by a dimeric Cu(II) complex singly or doubly bridged with OH^? ions. The E signal (F₂ ≈ 7) appears to be due to a monomeric Cu(II) complex, different from that responsible for the A signal.