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PubMed1999

Recent developments in DNA sequencing by capillary and microdevice electrophoresis.

The present review covers papers published in the years 1997 and 1998 on DNA sequencing by capillary and microdevice electrophoresis. The article does not include other electrophoretic DNA applications such as analysis of oligonucleotides, genotyping, and mutational analysis. Capillary gel electrophoresis (CGE) is starting to become a viable competitor to slab gel electrophoresis for DNA sequencing. Commercially available multicapillary array sequencers are now entering sequencing facilities which to date have totally relied on traditional slab gel technology. CGE research on DNA sequencing therefore becomes increasingly concerned with the critical task of fine-tuning the operational parameters to create robust sequencing systems. Electrophoretic microdevices are being considered the next technological step in DNA sequencing by electrophoresis.

Coloring Agents↗

PubMed1999

When can the Ogston-Morris-Rodbard-Chrambach model be applied to gel electrophoresis?

The Ogston-Morris-Rodbard-Chrambach theory of gel electrophoresis is consistent with predictions from the volume averaging method with respect to the equivalence of the accessible volume fraction to the ratios of gel mobility to free solution mobility and the gel diffusion coefficient to free solution diffusion coefficient for the limiting case of small molecule electrophoresis with low electrical fields, low gel concentrations, and nonconductive gel fibers. When these conditions are not valid, more extensive calculations are required to determine the mobility and diffusion coefficient ratios as functions of the geometry and electrical field within the gel. The volume averaging theory shows that it is important to account for the electrical conductivity properties of the fibers that make up a gel electrophoresis medium, and this aspect is consistent with early theories of transport phenomena in gel electrophoresis.

Electrophoresis↗

PubMed2000

Capillary electrophoresis on microchip.

Capillary electrophoresis and related techniques on microchips have made great strides in recent years. This review concentrates on progress in capillary zone electrophoresis, but also covers other capillary techniques such as isoelectric focusing, isotachophoresis, free flow electrophoresis, and micellar electrokinetic chromatography. The material and technologies used to prepare microchips, microchip designs, channel geometries, sample manipulation and derivatization, detection, and applications of capillary electrophoresis to microchips are discussed. The progress in separation of nucleic acids and proteins is particularly emphasized.

Animals↗

PubMed2000

Analysis of galectin 1-mediated cell signaling by combined precipitation and electrophoresis techniques.

Galectin-1 (GAL1) is a beta-galactoside-binding protein that has been implicated in the regulation of viability of lymphoid cells. However, the signaling pathway governed by the binding of GAL1 to the cell membrane is not understood yet. As a first step toward the elucidation of GAL1-initiated signaling events, electrophoresis techniques such as sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), and two-dimensional electrophoresis (2-DE) were used together with precipitation techniques. This allowed us to identify the membrane receptor of GAL1, and to characterize the signal resulting from the binding of GAL1 to this receptor. Our results demonstrate that the tyrosine phosphatase CD45 is the receptor for GAL1, and that the src-type tyrosine kinase Lyn is a target for the effects of GAL1/CD45 interactions in B-cells. Furthermore, these results show the usefulness of combined precipitation and electrophoresis techniques to analyze phosphotyrosine-dependent mechanisms during the study of cell functions.

Blotting, Western↗

PubMed1995

Diagnosis of hepatocellular carcinoma by concanavalin A affinity electrophoresis of serum alpha-fetoprotein.

BACKGROUND: Concanavalin A (Con A) affinity electrophoresis of serum alpha-fetoprotein (AFP) can distinguish hepatocellular carcinoma (HCC) from other malignancies when the serum AFP concentration is elevated. However, Con A has not been able to distinguish HCC from benign chronic liver disease such as cirrhosis or chronic hepatitis. METHODS: The Con A affinity electrophoresis of serum AFP was analyzed in patients with a serum AFP concentration greater than 50 ng/mL by antibody affinity electrophoresis and Western blotting in an attempt to distinguish hepatocellular carcinoma from benign chronic liver disease. Before the assay, the serum AFP concentrations were adjusted between 100 ng/ml and 300 ng/ml by concentrating or diluting the samples. RESULTS: Of 180 patients with HCC, 44 (24%) had a single band and 91 (51%), 35 (19%), and 10 (6%) had 2, 3, and 4 bands, respectively. All 35 patients with chronic hepatitis had a single band. All but 1 of 72 patients with cirrhosis had a single band. Multiple AFP bands on Con A affinity electrophoresis appear to be diagnostic of HCC. This method has a sensitivity of 76%, a specificity of 99%, a positive predictive value of 99%, and a negative predictive value of 71% for detecting HCC. The number of AFP bands correlated with serum AFP concentration and tumor size in patients with HCC. CONCLUSIONS: This assay is useful for distinguishing HCC from benign chronic liver diseases.

Adult↗

PubMed2000

Higher resolution microplate array diagonal gel electrophoresis: application to a multiallelic minisatellite.

The 5' polymorphic region of the insulin (INS, MIM# 176730) gene contains a variable tandem repetition of 14-15 bp (a variable number of tandem repeats (VNTR) locus). After PCR amplification, we achieved precise sizing of class I alleles (range 641 to 843 bp) on 96-well open-face polyacrylamide microplate array diagonal gel electrophoresis (MADGE) gels, obtaining resolution of the 2% mobility difference which represents one tandem repeat. PCR products were run double-stranded, but no additional bands were generated except in the case of differences of three, two, and one repeat between alleles; none compromised allele identification, and in the latter case the heteroduplex was a useful confirmation signal. No end labelling of primers was required, as the sensitive Vistra Green intercalating dye for double strands was used for visualization of bands from diluted samples. Duracryl, a high mechanical-strength polyacrylamide derivative, proved to have good resolution properties for electrophoresis. A co-run ladder ensured precise binning without inter-lane variability. Simultaneous electrophoresis of gels in a thermostatically controlled tank allowed up to 1,000 samples to be run in 90 min. Gels were analyzed using a FluorImager 595 fluorescent scanning system, and alleles identified using a combination of Phoretix software for band migration measurement and Microsoft Excel to compute allele sizes. Unlike other systems for minisatellite allele sizing, throughput was not limited (in time or cost) by electrophoresis.

Alleles↗

PubMed2002

Membrane-mediated ultrafast restriction digestion and subsequent rapid gel microchip electrophoresis of DNA.

Ultrafast, membrane-mediated restriction digestion of DNA molecules followed by rapid gel microchip electrophoresis of the resulting fragments is described. Combination of restriction endonuclease digestion on small pore-size microfibrous membranes with sample loading and electrophoresis analysis in a multilane (up to 96) format resulted in very fast restriction digest based microscale DNA analysis. Complete digestion of several nanogram target DNA was accomplished on the microporous membrane at room temperature just in a few minutes with a single or a combination of various restriction enzymes, using only submicroliter quantities of samples and reagents. The reaction mixture containing membrane also served as sample loading device for the subsequent gel microchip electrophoresis based analysis. This work establishes methods for high-speed, high-throughput DNA analysis, featuring extremely low sample and reagent consumption, and fast restriction digestion in combination with sample loading and rapid gel microchip analysis of the resulting fragments. The entire restriction digestion, sample loading and electrophoresis analysis process required less than 20 min.

Bacteriophage phi X 174↗

PubMed2002

A simple mathematical model to aid quantification of electrophoresis gels by image analysis.

In many scientific disciplines, measurements are taken from films that have been exposed to energetic sources. Examples include radiographs where the source is an X-ray tube, autoradiography where the source is a radioactive isotope and electrophoresis gels where the source is an enhanced chemiluminescence reaction. In these situations it is of interest to quantify the darkening of the film and compute the strength of the source which in the cases of autoradiography and electrophoresis can be used to compute unknown concentrations of biochemicals. We developed a simple mathematical model of the darkening of films in radiography, autoradiography and electrophoresis bands disclosed by enhanced chemiluminescence, and present formulae to calculate the strength of the source from measurement of film blackening by image analysis. A simple model is used in two examples to predict blackening of film exposed to electromagnetic radiation. This blackening is measured by image analysis. Results show reasonable agreement between predictions of the model and blackening of film for the examples chosen. This model is proposed as an aid to quantification of electrophoresis gels.

Autoradiography↗

PubMed2002

Electrophoresis of cells and the biological relevance of surface charge.

Recent developments in electrophoresis of cells are reviewed. Problems and progress in automation and miniaturization of analytical electrophoresis instruments as well as in the interpretation of experimentally determined electrophoretic mobility (EPM) data are summarized: In recent times, the EPM determination techniques not only became more reliable and faster, but also more knowledge could be gained about the cell surface electrical properties, the structure of the glycocalyx as well as its influence on the cell peripheral regions and microenvironment by applying cell electrophoresis. In addition, ways are shown to solve discrepancies between physical requirements of a preparative cell electrophoresis procedure and the quantities of ions, which have to be dissolved in cell suspension media. As the modern machines allow the purification of untagged cells suspended in more cell friendly and physiological media, they are likely to be valuable tools in several useful practical applications in clinical transplantation, gene therapy and treatment of disease states.

Animals↗

PubMed2002

Multistage electrophoresis II: treatment of a kinetic separation as a pseudoequilibrium process.

An electrophoresis device is described which separates cells, particles, proteins and other separands by collecting samples having decreasing electrophoretic mobility in a train of inverted cavities while an electric field is applied between the inverted cavities and a sample cuvette containing a mixture of cells, particles, proteins or other separands. A circular plate is provided for the inverted cavities, and this circular plate is rotated to collect fractions. The system utilizes an innovative purification method that combines free electrophoresis and multistage extraction in an instrument capable of separating living cells, particles, and proteins in useful quantities at high concentrations. Most multistage processes are based on equilibrium separations, but electrophoresis is a kinetic separation; therefore, a pseudoequilibrium paradigm was developed for use in optimizing separation parameters including number of stages and electrophoresis time per stage. This paradigm allows the application of McCabe-Thiele type analysis, and it was calculated, for example, that two separands differing by 20% in electrophoretic mobility can be purified to 95% purity with acceptable yield in about seven stages. Laboratory experiments demonstrated a 95% purification in four stages of a separand originally present at 4% when electrophoretic mobilities differed by 80%.

Anions↗

PubMed2002

Characterization of the early stages of programmed cell death in maize root cells by using comet assay and the combination of cell electrophoresis with annexin binding.

An emerging topic in plant biology is whether plant cells display similar elements of programmed cell death (PCD) as animal cells do. We have studied cell death in maize roots exposed to cold stress by using fluorescence microscopy, terminal deoxynucleotidyl transferase (TdT)-mediated dUTP nick end labeling (TUNEL), DNA gel electrophoresis, single cell gel electrophoresis (SCGE), cell electrophoresis, and annexin binding techniques. The results showed that cell death in maize root cells triggered by cold stress was accompanied by a subset of features characteristic of animal PCD such as nuclear condensation and fragmentation, and oligonucleosomal DNA fragmentation. In addition to DNA laddering and TUNEL positivity, a "comet" pattern indicative of DNA breakage appeared as short as after one day of treatment. The maize root cell PCD process was also accompanied by an increase in negative surface charge of the dying cells due to exposure of phosphatiolylserine (PS) from inner to outer membrane. After annexin binding, however, the enhanced electrophoretic mobility (EPM) of the dying cells decreased nearly to normal values. This result suggests that the combination between cell electrophoresis and annexin binding provides a quantitative method for monitoring PS exposure during plant PCD.

Annexins↗

PubMed2002

Evalution of capillary electrophoresis-frontal analysis for the study of low molecular weight drug-human serum albumin interactions.

Capillary electrophoresis frontal analysis was applied to 12 low molecular weight compounds including 8 drug substances displaying a range of different properties with respect to binding affinity, binding location, structure, lipophilicity, charge at physiological pH, and electrophoretic mobility. It was found that capillary electrophoresis frontal analysis can be used as a general method to study and quantify drug-human serum albumin interactions. The binding parameters obtained were consistent with literature values. Dextran was in some cases added to the run buffer to improve separation of the drug and human serum albumin plateau peaks. Results indicate that mobility differences between free and complexed human serum albumin give rise to only minor errors. Capillary electrophoresis frontal analysis was also found applicable to the study of human serum albumin drug displacement reactions. Low sensitivity of the UV-detection system was found to be the major limitation of capillary electrophoresis frontal analysis. The method is simple, and minimal effort has to be put into method development, which makes it well suited for screening in early drug development.

Binding, Competitive↗

PubMed2002

Protein fingerprinting of Saccharomyces isolates with therapeutic relevance using one- and two-dimensional electrophoresis.

In therapeutic products and preparations Saccharomyces cerevisiae is used because of its nutritive properties. Moreover, so called Saccharomyces boulardii yeasts are used in the prevention and treatment of several types of diarrhea. Taxonomically however, S. boulardii is not accepted as a distinct species. The protein fingerprint obtained after sodium dodecyl sulfate-polyacrylamide gel electrophoresis was identical for all isolates and therefore confirmed the designation of S. boulardii to the species S. cerevisiae. In contrast, using native polyacrylamide gel electrophoresis, 12 different protein fingerprints were detected, and allowed grouping of the product isolates. The spot patterns obtained by two-dimensional electrophoresis revealed a large degree of resemblance, however, small qualitative expression differences could be detected as well. Firstly, a spot having an isoelectric point of approximately 6 and 30 kDa could not be detected in S. boulardii yeasts. Secondly, nine different formations of spots occurred in the region around 16 kDa and pH 6. Therefore, on the one hand, it could be demonstrated that all of the product isolates belong to the same species, and on the other hand, it was possible to extensively subdivide the strains. In particular, two-dimensional electrophoresis allowed clustering of so called S. boulardii strains within the species S. cerevisiae.

Electrophoresis, Gel, Two-Dimensional↗

PubMed2002

Structure analysis of lipoglycans and lipoglycan-derived carbohydrates by capillary electrophoresis and mass spectrometry.

Lipoglycans (lipopolysaccharides, lipoarabinomannans and glycolipids) are unique components of the cell membrane of all cells and the envelope of many bacteria. They play important roles in determining cell-environment interactions, which, however, are only partly understood due to incomplete description of their structural components, lipids and glycans. Capillary electrophoresis is an analytical technique of high separation efficiency and minimum sample requirements and has successfully been used for the analysis of several molecules of biological importance: proteins, nucleic acids and glycoconjugates. In the last years, a few applications of capillary electrophoresis to the analysis of lipoglycans have been reported. Analysis of lipoglycans involves the study of two parameters: intact molecules and carbohydrate parts. The conjunction of capillary electrophoresis and mass spectroscopy not only enhances the detection sensitivity, but also provides structural information on these structurally complex molecules. The interest in the field is rising and the results from the exact determination on the lipoglycan structure are expected to improve our understanding of the molecular mechanism of lipoglycan binding to proteins and cells of host organisms as well as their relationship to the virulence and pathogenesis of bacteria. In this report, an overview of the capillary electrophoresis methods used to analyze and characterize the intact lipoglycans as well as their carbohydrate parts is presented.

Carbohydrate Conformation↗

PubMed2002

Capillary electrophoresis for the analysis of glycosaminoglycans and glycosaminoglycan-derived oligosaccharides.

Glycosaminoglycans are a family of polydisperse, highly sulfated complex mixtures of linear polysaccharides that are involved in many life processes. Defining the structure of glycosaminoglycans is an important factor in elucidating their structure-activity relationship. Capillary electrophoresis has emerged as a highly promising technique consuming an extremely small amount of sample and capable of rapid, high-resolution separation, characterization and quantitation of analytes. Numerous capillary electrophoresis methods for analysis of intact glycosaminoglycans and glycosaminoglycan-derived oligosaccharides have been developed. These methods allow for both qualitative and quantitative analysis with a high level of sensitivity. This review is concerned with separation methods of capillary electrophoresis, detection methods and applications to several aspects of research into glycosaminoglycans and glycosaminoglycan-derived oligosaccharides. The importance of capillary electrophoresis in biological and pharmaceutical samples in glycobiology and carbohydrate biochemistry and its possible applications in disease diagnosis and monitoring chemical synthesis are described.

Carbohydrate Conformation↗

PubMed1988

Two-dimensional electrophoresis as a tool for structural and genetic studies of seed proteins from Poaceae and Fagaceae.

The application of two-dimensional electrophoretic procedures to structural and genetic studies of seed proteins from Poaceae (including the cultivated cereals) and Fagaceae is described. The following related problems have been considered: covalent and non-covalent association of protein subunits in multiple oligomeric structures; chromosomal locations of genes encoding seed proteins; quantitation of gene products in relation to gene expression and regulation; purification of protein components to study their homology relationships and in vitro activities; evolutionary and phylogenetic relationships; identification of genetic stocks. Isoelectric focusing, pore-gradient electrophoresis, electrophoresis at different pH's, are among the separation procedures used in the first dimension, whereas sodium dodecyl sulfate-polyacrylamide gel electrophoresis and starch-gel electrophoresis at acid pH have been the preferred second-dimensional methods. Dissociating conditions (sodium dodecyl sulfate, Nonidet P-40, or urea) and reducing conditions (2-mercaptoethanol) have been used when required.

Aneuploidy↗

PubMedDate not supplied

Temperature-gradient gel electrophoresis of nucleic acids: analysis of conformational transitions, sequence variations, and protein-nucleic acid interactions.

Temperature-gradient gel electrophoresis (TGGE) is applied to analyze conformational transitions and sequence variations of nucleic acids and protein-nucleic acid interactions. A linear and highly reproducible temperature-gradient is established perpendicular or parallel to the direction of the electrophoresis. The instrument consists of an electrically insulated metal plate, which is heated at one edge and cooled at the other edge by two thermostating baths and is used as an ancillary device for commercial horizontal gel electrophoresis instruments. Biopolymers are separated in TGGE according to size, shape and thermal stability of their conformational transitions. If the temperature-gradient is established perpendicular to the electrophoresis, monomolecular conformational transitions of nucleic acids show up as continuous transition curves; strand-separation leads to discontinuous transitions. In the studies on viroid RNA it was shown that natural circular viroid RNA undergoes one highly cooperative transition detected by TGGE as a drastic retardation in mobility. Oligomeric replication intermediates of viroids exhibit coexisting structures which could not be detected by any other technique. Double-stranded satellite RNA from cucumber mosaic virus is a mixture of sequence variants, all of which have the identical length of 335 nucleotides. In TGGE six different strains were resolved. Sequence variants of viroids were analyzed by hybridizing viroid RNA to (-)strand viroid RNA transcripts from viroid cDNA clones. Sequence variations lead to mismatches in the double strands and thereby to a shift of the transition curve to lower temperature. Mutations in plasmids, particularly in cloned inserts, were detected by mixing plasmids of two different clones, linearizing, denaturing, renaturing, and searching for shifts in the transition curves, which are generated by mismatch-formation during the renaturation of (+)- and (-)strands from different clones. Examples are given for different viroid clones and HIV-clones from one and the same patient. In another example, clones with point mutations from site-directed mutagenesis are analyzed and selected by TGGE. TGGE is also applied to study the effect of amino acid exchanges in the Tet repressor from E. coli on the thermal stability of the repressor and on the mode of binding of the repressor to the operator DNA. The results are discussed under the aspect that TGGE may be applied as routine analytical laboratory procedure.

Base Sequence↗

PubMedDate not supplied

The use of denaturing gradient gel electrophoresis to screen for DNA sequence polymorphisms in the human factor VIII gene.

We describe the use of denaturing gradient gel electrophoresis to screen for DNA sequence polymorphisms in the human factor VIII gene. DNA fragments that differ in sequence by only a single base pair can be separated on denaturing gradient gels due to changes in their melting behavior. Previous studies have demonstrated the use of denaturing gradient gels to detect sequence changes in human genomic DNA, including mutations in the beta globin gene and polymorphisms on chromosome 20. We have begun to use denaturing gradient gels to look for polymorphisms within the human factor VIII gene. The DNA sequences of seven cloned fragments from introns in the human factor VIII gene were determined and used to predict a melting map for each fragment. The melting behavior of each cloned fragment was evaluated by electrophoresis into denaturing gradient gels. Appropriate fragments were then used as radioactive probes for hybridization to human DNA samples that had been digested with restriction enzymes. Heteroduplexes formed between the probe and genomic DNA samples were electrophoresed into denaturing gradient gels. The final positions of heteroduplex bands were determined by autoradiography. We describe a general approach for using denaturing gradient gel electrophoresis to find DNA polymorphisms, with particular emphasis on the predictive value of DNA sequence data. We compare the efficiency of polymorphism detection by denaturing gradient gel electrophoresis with detection by restriction fragment length polymorphism (RFLP) analysis. The factor VIII gene appears to have a low level of DNA sequence polymorphism.(ABSTRACT TRUNCATED AT 250 WORDS)

Base Sequence↗