Artifacts in sodium dodecyl sulfate-polyacrylamide gel electrophoresis due to 2-mercaptoethanol

Mercaptoethanol, when present in the sample buffer during sodium dodecyl sulfate-polyacrylamide gel electrophoresis, is responsible for the appearance of two nonprotein bands (electrophoretic mobilities corresponding to 68 and 54 kdalton) stainable with silver and with Coomassie blue. After iodination in vitro of DNA preparations isolated by alkaline phenol extraction using chloramine-T procedure, part of the radioactive label is found in these bands, provided the reaction is terminated by mercaptoethanol, whereas only a diffuse background is present in this area if the reaction is stopped by sodium metabisulfite. Similar results are obtained with highly purified total cytoplasmic RNA. The results indicate that the appearance of the 68- and 54-kdalton bands is in artifact. The relevance of these results to the proteins tightly bound to DNA is discussed.     

Preparative electrophoresis on agarose submerged gels of two aggregating proteoglycan monomers from articular cartilage

Analytical electrophoresis on polyacrylamide-agarose gels of aggregating proteoglycan monomers from baboon articular cartilage produces two distinct bands, corresponding to two different aggregating monomer populations. A preparative electrophoresis procedure is described for isolating the two monomers. Proteoglycans were extracted from young baboon articular cartilage in 4 M guanidinium chloride containing proteolysis inhibitors and aggregated after hyaluronic acid addition. The aggregates were separated from non-aggregated proteoglycans by isopycnic centrifugation, followed by gel chromatography on Sepharose CL-2B. The monomers of the aggregates were obtained by isopycnic centrifugation under dissociative conditions. Two monomers were separated by preparative electrophoresis on 0.8 % agarose submerged gels. Approximately 60 % of the proteoglycans were recovered from the gel using a freeze-squeeze procedure. Aliquots of the separated monomers gave single bands when submitted to analytical polyacrylamide-agarose gel electrophoresis. Their migration and appearance were similar to that of the two bands present in the non separated preparation of monomers.     

Behavior of chymotrypsinogen during low pH gel electrophoresis is altered by persulfate

Chymotrypsinogen was observed to have two bands in a low-pH gel electrophoresis system, though the protein was pure by other criteria. Other proteins have also been reported to give artifacts under these conditions. Removal of persulfate from the gel by pre-electrophoresis or by substituting riboflavin eliminated the artifacts. The affected amino acid residue was identified as tryptophan by titration of persulfate-treated proteins with 2-hydroxy-5-nitrobenzyl bromide and by the spectral method of Edelhoch. Persulfate-treated chymotrypsinogen had the same mobility as the artifact, while oxidation of Met-192 with hydrogen peroxide produced a protein with a different mobility.     

Rapid and reliable dideoxy sequencing of double-stranded DNA

We report a simple and reliable protocol for nucleotide sequencing using the Sanger dideoxy technique on linearized double-stranded DNA molecules with specific oligonucleotide primers. The method is demonstrated for restriction fragments cloned into the plasmid vectors pSP64 and pSP65 using two vector-specific primers, the M 13 reverse primer and a new SP6 primer, flanking the multiple cloning site. Template DNA may be prepared by a rapid alkaline lysis procedure. Mild linearization conditions with the appropriate restriction endonuclease avoid the appearance of artifact bands.     

A reappraisal of the subunit molecular mass of chicken liver cytosol 5'-nucleotidase

The subunit molecular mass of chicken liver cytosol 5'-nucleotidase was earlier reported to be 51 kDa upon sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis (Naito, Y. and Tsushima, K. (1976) Biochim. Biophys. Acta 438, 159-168). By immunoblot analyses after SDS-gel electrophoresis, however, a fraction from the liver homogenized in the presence of leupeptin showed multiple bands with molecular masses around 57 kDa, and SDS-extracted proteins directly from the liver exhibited a single 70 kDa component. These results indicate that the 51 kDa peptide observed in the cytosol 5'-nucleotidase preparation might, in fact, be a proteolytic artifact.     

Characterization of a Saponaria officinalis seed ribosome-inactivating protein: immunoreactivity and sequence homologies

A ribosome inactivating protein from Saponaria officinalis, SO-6, was purified and the N-terminus sequenced. The sequence shows extensive homology with Pokeweed antiviral protein, Pokeweed antiviral protein II, Pokeweed antiviral seed protein and dodecandrin. SDS gel electrophoresis in the Laemmli system revealed two bands of similar intensities with a smear between them, probably an artifact due to the high pI of the protein. Use of a harsher denaturing gel system resulted in one band in electrophoresis. Immune antisera was raised in rabbits against this protein and it cross reacted with other proteins (SO-5, SO-8 and SO-9) from seeds of Saponaria officinalis, but not with gelonin, Momordica charantia inhibitor and dianthin 32.     

Resolution of microsomal membranes into fractions differing in polypeptide composition

Microsomes from rat liver, prepared by gel filtration, were subjected to centrifugation in a continuous sucrose density gradient containing a low concentration of deoxycholate. The membranes were subfractionated into five bands differing in appearance and equilibrium density. Each band, when analysed by sodium dodecyl sulphate polyacrylamide gel electrophoresis, displayed a characteristic population of membrane proteins.     

An artifact band frequently associated with variable number of tandem repeat marker at phenylalanine hydroxylase gene: application in carrier detection and prenatal diagnosis of phenylketonuria

The variable number of tandem repeat (VNTR) marker located at the 3′-end of the phenylalanine hydroxylase (PAH) gene, PAHVNTR marker, is commonly used in carrier detection and prenatal diagnosis of the PKU disease. During the molecular diagnosis of the disease, an artifact band associated with the PAHVTNR marker was frequently observed. Analysis of genotyping data from nine trios families indicated that in heterozygote individuals, the observed stutter (artifact) bands at PAHVNTR marker were minor bands with one repeat sequence shorter than the upper main bands. More investigations using sequencing revealed that the artifact band was associated with VNTRs including seven or higher core repeats. In statistical analysis, 75% of the studied heterozygote individuals represented PCR artifact band. The presence of the artifact band associated with PAHVNTR marker highlights a serious alarm risk of possible technical misdiagnosis in the application of the PAHVNTR marker in carrier detection and prenatal diagnosis of the PKU disease.     

Ox liver butyryl-coenzyme A synthetase--a subunit enzyme?

Butyryl-CoA synthetase extracted from untreated or freeze-dried liver mitochondria consisted of two fractions of Mr 40,000 and 46,000 as determined by gel permeation chromatography, the higher value being confirmed by sedimentation equilibrium. A red pigment having the characteristic of haem was associated with the enzyme. This appeared to be an artifact of isolation. A number of active bands were obtained on polyacrylamide gel electrophoresis and isoelectric focusing, and on treatment with sodium dodecylsulphate or 6 M guanidine hydrochloride both dissociation and aggregation of the enzyme fractions occurred. As no evidence of protease contamination or proteolytic action could be detected, it is suggested that the active enzymes contain more than one polypeptide chain.     

Pattern of Protein Synthesis in Monkey Cells Infected by Simian Virus 40

After infection of several permanent monkey cell lines by simian virus 40 (SV40), four additional protein bands can be detected by simple sodium dodecyl sulfate-polyacrylamide gel electrophoresis of whole-cell extracts. These bands appear only after the onset of viral deoxyribonucleic acid (DNA) synthesis, and inhibitors of DNA synthesis prevent their appearance. Three of them correspond to three previously identified capsid components, VP1, VP2, and VP3. The fourth protein band, which does not correspond to a previously identified virion component, is induced by SV40 infection of CV-1 and BSC-1 cultures but not by infection of MA-134 cultures.     

Bullous pemphigoid antigen. II. Isolation from the urine of a patient.

This report concerns the isolation of bullous pemphigoid antigen from the nondialyzable urinary components of a patient with the disease. The isolation was accomplished by ion exchange chromatography and gel filtration. Pemphigoid antigen was found to be a basic glycoprotein that on SDS gel electrophoresis showed two major bands, one in the 18,000 m. w. region and the second with a m. w. of 74,000. Between these two bands, two additional bands appeared; one of 35,000 daltons and the other of 68,000 daltons. The 18,000 m. w. band was eluted from the gel and rerun on SDS gels. These gels showed the 18,000 m.w. band and also the appearance of the 35,000 and 74,000 m.w. bands. This finding indicates that urinary pemphigoid antigen may exist both as a single monomeric form and in polymeric aggregates.     

Structure of extracellular hemoglobin from the brine shrimp Artemia salina.

1. Hemoglobin from the brine shrimp Artemia salina, purified by ultracentrifugation and preparative gel electrophoresis in non-denaturing medium, gave in sodium dodecyl sulfate-polyacrylamide gel electrophoresis a single band corresponding to a polypeptide chain with Mr 150,000. 2. Crosslinking by glutardialdehyde resulted in the appearance of a band corresponding to a molecular mass twice that of a polypeptide chain. 3. Limited trypsinolysis gave eight proteolytic bands corresponding to submultiples 8/9-1/9 of a polypeptide chain. 4. We conclude that a molecule of Artemia hemoglobin is composed of two single polypeptide chain subunits and that each subunit consists of nine structural units roughly equal in size.     

High molecular weight forms of the insulin receptor

The insulin receptor of liver, adipose, and placental plasma membranes was photoaffinity labeled with radioiodinated N epsilon B29-(monoazidobenzoyl)insulin. Three specifically labeled bands of 450, 360, and 260 kilodaltons (kDa) were identified in each tissue by polyacrylamide gel electrophoresis of the membranes solubilized in sodium dodecyl sulfate (SDS). The 360- and 260-kDa bands corresponded to partially reduced forms of the 450-kDa band. The distribution of radioactivity between the three insulin receptor bands was dependent on the tissue, the purity of the receptor preparation, and the conditions of solubilization in SDS. The 360- and 260-kDa bands became more prominent in each tissue with an increasing time of solubilization in SDS. However, with a short solubilization time in SDS, the 450-, 360-, and 260-kDa bands of the receptor were distributed approximately in a ratio of 85:15:0 in all three tissues. Inclusion of sulfhydryl alkylating reagents during solubilization in SDS altered this ratio to about 95:5:0. We conclude that the 450-kDa band represents the predominant form of the photolabeled insulin receptor and that the 260-kDa and probably the 360-kDa form as well were generated during the experimental manipulations preceding identification of the receptor. However, the appearance of the 360- and 260-kDa bands was not due to reductant present in SDS or buffer solutions and could not be accounted for by proteolytic degradation of the receptor. Furthermore, purification of the receptor over 2000-fold did not prevent the appearance of the 360- and 260-kDa bands.(ABSTRACT TRUNCATED AT 250 WORDS)     

Optimization of the DGGE band identification method

Denaturant gradient gel electrophoresis (DGGE) enables insight into the diversity of the studied microbial communities on the basis of separation of PCR amplification products according to their nucleotide sequence composition. However, the success of the method is accompanied by the inherent appearance of various sequence artifacts that bias the impression of community structure by generating additional bands representing no virtual microbes. PCR-DGGE artifacts require optimization of the method when aiming at the phylogenetic identification of the selected DGGE bands. The aim of our study was to develop a procedure which will increase the reliability of the identification. Samples of rumen fluid were used for the optimization since they contain a complex microbial community that supports the generation of artifactual bands. An optimized procedure following band excision and elution of microbial DNA is proposed including nuclease treatment, selection of DNA polymerase with proofreading activity, and cloning prior to sequencing and identification analysis.     

Soluble proteins and hydrolases during crown-gall induction in the tomato,Lycopersicon esculentum

Synopsis Soluble proteins isolated from tissues of the tomatoLycopersicon esculentum, after inoculation withAgrobacterium tumefaciens to induce tumours, have been examined by gel electrophoresis and cytochemically. Changes that occur include the suppression of host enzymes, the appearance of bacterial enzymes in the host tissues and the appearance of new enzyme bands in the affected cells. These changes are detectable within 6 hr of infection and prior to evident morphological changes, and may be explained as derepression and repression of host genes, or the expression of released bacterial genes in the host cells.     

Electrophoresis and electrofocusing of rhodopsin solubilized by triton X-100]

Detergent-rhodopsin micells (component I) were separated from other fast and slow migrating protein components under electrophoresis of triton X-100 solubilized bovine rod outer segments (ROS). Treatment of ROS by alum caused a complete disappearance of non-rhodopsin proteins and the appearance of slow migrating band (component II). Preliminary bleaching of dark extracts did not affect the migration rate of the component I. The addition of urea to solubilizing mixture caused the increase of component I content and the diffusity components I and II bands. The rate of electrophoretic migration and the content of components I and II sharply decreased together with the appearance of fast migrating pink-brown band after the addition of 2-mercaptoethanol. The extracts from alum-treated ROS were separated into 15-20 protein bands under acrylamide gel isoelectric focusing. Such protein heterogeneity probably depended on the ability of triton X-100 to form micells with different isoelectric points during the interaction with ampholines in the electric field. These micells, having different isoelectric points, are shown to contain one and the same protein--opsin.     

Physico-chemical and kinetic properties of hexokinase isoenzymes from human normal and tumor tissues]

Individual hexokinase isoenzymes (isoHK) are isolated from normal and malignant human stomach mucosa. IsoHK from tumour tissue are found to have KM for glucose 10 times as low as isoHK from normal tissue. Molecular weights of individual isoHK from normal and tumour tissues are similar (at the range of 112,000-125,000). The treatment of protein preparation with 8M urea in the presence of 1% sodium docecyl sulphate resulted in the appearance of a single band with molecular weight of 58,000-60,000 for all the isoHK under polyacrylamide gel electrophoresis. Intensive bands with molecular weight of 60,000 and 96,000 and a number of minor bands were observed under polyacrylamide gel disc elect-ophoresis in the absence of urea. 2-Mercaptoethanol did not affect the results of disc electrophoresis. It is concluded that the molecule of human hexokinase consists of two subunits with molecular weight of 60,000.     

Molecular weight determinations of proteins by polyacrylamide gel electrophoresis with sodium dodecyl sulfate in just the sample solution

This report describes a simple modification of the procedure for SDS polyacrylamide gel electrophoresis by using SDS in the sample solution and eliminating its use in the gel and the electrode compartments. The results obtained were comparable to those with SDS in the entire system. The log molecular weight-relative mobility plots for a variety of proteins, the reproducibility and the appearance of the bands such as their intentisy and sharpness were very similar. Therefore SDS in the entire system is not necessary to determine the molecular weight of a protein.     

Photoinduced cell killing and crosslinking of fluorescein conjugated concanavalin A to cell surface proteins

Bleaching of fluorescein conjugated concanavalin A (F-Con A) labelled plasma membranes with 488 nm laser light leads to some broadening and a loss of protein bands and the appearance of high molecular weight material as shown by sodium dodecylsulfate polyacrylamide gel electrophoresis, indicating membrane protein crosslinking. The F-Con A is found throughout the high molecular weight regions linked to other proteins in large aggregates. Irradiation of whole cells labelled with F-Con A leads to cell death. These effects are dependent upon total light exposure and F-Con A concentration.     

Artifactual staining of proteins on polyacrylamide gels by nitrobluetetrazolium chloride and phenazine methosulfate

Different purified proteins were shown to give purple formazan bands corresponding to the protein stain following electrophoresis on polyacrylamide gels, in the presence of nitrobluetetrazolium (NBT) and phenazine methosulfate (PMS). Both PMS and NBT are needed for formazan production which has a favorable pH at 8.5. Sulfhydryl blockers in the incubation medium inhibited this color development to different extents. While proteins with free SH groups like bovine serum albumin, ovalbumin, and urease showed this pyridine nucleotide independent artifact, nonthiol proteins, viz., bovine pancreatic ribonuclease A, and riboflavin-binding protein from chicken egg white failed to do so. The nonenzymatic formazan formation observed with different proteins could also be shown in an in vitro assay system. It is clear that the “nothing dehydrogenase” phenomenon observed in several cases may be due to the thiol group-mediated artifactual staining of proteins.