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PubMed1993

Temperature-gradient gel electrophoresis for analysis and screening of thermostable proteases.

The thermal unfolding of microbial serine proteases was studied by temperature-gradient gel electrophoresis (TGGE). Conditions for a native polyacrylamide gel electrophoresis were established, and the temperature gradient was applied perpendicularly to the direction of electrophoretic migration. Mobility changes of the protease molecules were indicative for thermally induced conformational changes. The transition temperature was determined with good accuracy. The native and active protease conformation was detected by an activity assay in the temperature-gradient gel. As a consequence of the typical protease-autoproteolytic reaction at elevated temperatures, the unfolded protease conformation could not be detected for non-inhibited, active subtilisin. After inhibition by phenylmethylsulfonyl fluoride (PMSF) the complete structural transition could be followed by TGGE. This transition is "discontinuous", i.e. the thermal transition is either very slow, compared to the time of electrophoresis, or irreversible, as known for subtilisins from calorimetric data. Inhibition by the strong serine specific inhibitor diisopropyl fluorophosphate (DFP) led to two conformations at low temperature. One conformation is stabilized by 8 degrees C, the other by at least 20 degrees C as compared with PMSF inhibition. The influence of calcium ions on the subtilisin stability was investigated by a series of TGGE under different calcium concentrations. The strong calcium binding site is occupied even without added calcium, occupation of the weak binding site leads to a stabilization of 10 degrees C with a binding constant around 10(6) M-1. The subtilisin Carlsberg stability could also be investigated in unpurified bacterial culture supernatants. Thus, the method is suitable for screening of thermostable subtilisin mutants directly after expression in a bacterial host.(ABSTRACT TRUNCATED AT 250 WORDS)

Buffers↗

PubMed1993

The variance and the quantity 2Dt in capillary zone electrophoresis.

The variance is generally used as a measure of dispersion of zones in capillary zone electrophoresis (CZE). It is a quantitative measure of the separation power of a system and different causes of dispersion can be rated by their partial variances, which can be summed up to total variance. However, the additivity is only valid for independent dispersion sources, a fact that often seems to be ignored. The ubiquitous dispersion source diffusion is taken into consideration by the Einstein term 2Dt. Other sources of dispersion are, e.g., injection, detection, thermal gradients, adsorption, and hydrodynamic flow. For each of these sources various variance expressions have been derived. The origin of the term 2Dt and its relation to the variance is explained and the calculation of variance in general is discussed. The equivalence of the diffusion variance and the term 2Dt is verified with some simple initial forms of sample zone and the additivity of variances in ideal zone electrophoresis is demonstrated. The change of conductivity in zones results in asymmetrical zone forms which is an indication of nonideality of a system. It is shown that in such cases the term 2Dt is no longer valid and its use as an additive variance component leads to an erroneous total variance. Because in zone electrophoresis conductivity in a zone always changes more or less, the additivity of variances is never perfectly valid. However, in many cases the nonideality may be so small that the additivity in practice is still applicable.(ABSTRACT TRUNCATED AT 250 WORDS)

Capillary Action↗

PubMed1993

Control of electrohydrodynamic distortion of sample streams in continuous flow electrophoresis using oscillating fields.

Continuous flow electrophoresis is a method to separate ions contained in a sample continuously injected into a laminar flow of electrolyte as a cylindrical stream. Usually, the sample is more conductive than the electrolyte, and the charges created at the sample-electrolyte interface lead to electrohydrodynamic distortions which reduce the separation power of this technique. We demonstrate theoretically that the rate of electrohydrodynamic distortion of a cylindrical sample stream can be reduced to zero, by superimposing to the AC field responsible for the separation of a DC field transverse to it and to the flow direction, with an appropriate frequency, and an effective strength equal to that of the DC field. Using a continuous flow electrophoresis chamber, in which such a field is produced using capacitive electrodes, the major predictions of the theory are confirmed. In particular, it is shown that a sample stream more conductive than the carrying electrolyte, which was seriously deformed in the absence of a transverse AC field, recovers its cylindrical shape in presence of the field. The implications of this discovery for the separating power of continuous-flow electrophoresis are discussed.

Buffers↗

PubMed1993

Agarose electrophoresis of DNA in discontinuous buffers, using a horizontal slab apparatus and a buffer system with improved properties.

Using a horizontal slab apparatus with a buffer in the reservoirs at the level of the gel ("sea-level electrophoresis"), the retrograde discontinuous buffer system reported by Wiltfang et al. for sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) of proteins was applied to DNA electrophoresis. This application yielded the advantages of an increased displacement rate of the moving boundary front and a decrease in the concentration of the counterion base in the resolving phase, which yielded reduced relative mobility values at equivalent gel concentrations and practicable low buffer concentrations. The change of relative mobilities (Rf) with a variation of field strength is decreased compared to that of the migration rate in the continuous Tris-boric-acid-EDTA (TBE) buffer and thus the robustness of the system is improved, as well as the efficiency of separation. The system of Wiltfang et al. has in common with previously described discontinuous DNA system, that it is able to stack DNA from dilute samples and is insensitive to sample components with lower net mobilities than DNA, such as acetate. However, the variance of Rf at constant current density in the discontinuous buffer system is not improved over that of the migration rate at constant field strength in the continuous TBE buffer.

Boric Acids↗

PubMed1993

Use of fluorogenic substrates to visualize trypsin and chymotrypsin inhibitors after electrophoresis.

Fluorogenic substrates were tested as a means of increasing both the sensitivity and the selectivity of trypsin and chymotrypsin inhibitor detection after electrophoretic separation. Out of six substrates applied to cellulose acetate membranes, N alpha-benzyloxycarbonyl-L-arginine-4-methylcoumarinyl-7-amide (Z-Arg-MCA) and benzyloxycarbonyl-glycyl-glycyl-L-arginine-4-trifluoromethylcoumariny l-7-amide (Z-Gly-Gly-Arg-TFMCA) were found to be suitable for trypsin, and L-alanyl-L-alanyl-L-phenylalanine-4-methylcoumarinyl-7-amide (Ala-Ala-Phe-MCA) was suitable for chymotrypsin. A procedure to detect trypsin and chymotrypsin inhibitors, and to discriminate between them, was developed. After electrophoresis, slab gels were first incubated with the enzyme (bovine trypsin, bovine chymotrypsin, or human duodenal juice) at 37 degrees C, and then covered with the respective substrate membrane and incubated at room temperature while being observed under UV light. Dark blue inhibitor bands on a light-blue-fluorescent background were obtained with Z-Arg-MCA/trypsin and Ala-Ala-Phe-MCA/chymotrypsin, whereas Z-Gly-Gly-Arg-TFMCA/trypsin resulted in dark inhibitor bands on a fluorescent green background. The "inhibitor overlay membrane technique" (IOM technique) was used after polyacrylamide gel isoelectric focusing with carrier ampholytes and immobilized pH gradients, pore-gradient polyacrylamide gel electrophoresis, and sodium dodecyl sulfate pore-gradient polyacrylamide gel electrophoresis.

Amino Acid Sequence↗

PubMed1993

Pulsed-field polyacrylamide gel electrophoresis: basic phenomena and applications.

Pulsed-field gel electrophoresis (PFGE) using polyacrylamide gels, termed pulsed-field polyacrylamide gel electrophoresis (PF-PAGE), had been developed for the effective separation of linear DNAs from circular ones [1]. The first generation PF-PAGE employed horizontal polyacrylamide gels run in a contour-clamped homogeneous electric field (CHEF) apparatus. The second generation system, using a vertical slab gel in a discontinuous buffer system and field inversion gel electrophoresis (FIGE), was found to be easier to handle and requires a much shorter time for separation than the previous one [2]. In this report, basic aspects of the second generation PF-PAGE, such as the effects of a discontinuous buffer system and field inversion on the DNA migration in polyacrylamide gels, were investigated. The results indicate that the periodic inversion of electric field can broaden the resolving capability of polyacrylamide gels, enabling DNAs that otherwise fail to enter polyacrylamide gels to be resolved in such systems. Successful and possible applications of PF-PAGE techniques are also discussed.

Base Sequence↗

PubMed1993

DNA electrophoresis in polymer solutions: Ogston sieving, reptation and constraint release.

The electrophoresis of long polyelectrolytes is considered theoretically, with special attention to duplex DNA. We first discuss quantitative approaches to determine unambiguously the entanglement properties of polymer solutions. Following an idea proposed by Grossman and Soane, we then assume that the "mesh" size of the solution plays the role of a dynamic "pore size" in order to apply theories for gel electrophoresis. In the framework of the Ogston model, we predict that duplex DNA up to 1 kb or more should be separable in dilute (i.e. nonentangled) solutions of high molecular weight polymers. In an entangled solution, and for DNA larger than the pore size, we use a recently developed fluctuation-reptation model to predict the range of sizes in which separation should be possible as a function of electric field E and pore size zeta b. For zeta b larger than the Kuhn length of DNA, we predict a separation up to a size N*scaling as E-1 zeta b-1. For zeta b smaller than the Kuhn length, two different regimes are expected. For small electric fields (typically of the order of 10 V/cm), N*should be proportional to E-1 zeta b-3/2, whereas for high electric fields such as encountered in capillary electrophoresis, we expect that N*is proportional to E-2/5 zeta b-12/5. These predictions are qualitatively different from earlier ones. Finally, we demonstrate that the finite lifetime of the "pores" in an entangled solution (as opposed to a gel) may lead to a new migration mechanism by constraint release, which is not size-dependent.(ABSTRACT TRUNCATED AT 250 WORDS)

Chemical Phenomena↗

PubMedDate not supplied

A new type of pH- and detergent-stable coating for elimination of electroendosmosis and adsorption in (capillary) electrophoresis.

We describe a method to coat fused silica, quartz, or glass electrophoresis tubes with hydrophilic polymers, such as methyl cellulose or dextran, in order to eliminate electroendosmosis and adsorption of solutes onto the tube wall. The coating was not split off upon exposure to a 5% solution of sodium dodecyl sulfate (SDS) at pH around 12 during a period of sixteen days or to 0.5 M HCl (pH 0.3) during 10 days. The high stability of the coating, which is attached to the silica surface via Si-O-Si-C bonds, permits electrophoresis experiments at extreme (besides neutral) pH values and allows short washes of the electrophoresis tubes between the runs with 0.05 M sodium hydroxide (pH 12.7) containing 5% SDS, and with 1 M HCl. These washing solutions release efficiently those solutes which have a tendency to adsorb onto the coating, which is a prerequisite for reproducible runs. The quality of the coating was strongly affected by the surface structure of the commercial fused silica tubing, which may vary from batch to batch. Attempts to standardize the surface structure of any tubing by treatments with NaOH and HCl to obtain a coating, the quality of which is independent of the original surface structure, were not successful. Therefore, it may be necessary to modify certain details of the coating procedure for each new batch of tubing to obtain optimum stability. Alternative coating procedures are therefore described, one of which is of general applicability (see last paragraph in Section 4).

Adsorption↗

PubMedDate not supplied

Application of high-performance capillary electrophoresis to the analysis of H1 histones.

High-performance capillary electrophoresis for the separation of rat testis H1 histone variants and their phosphorylated modifications is described. The influence of buffer pH, hydroxypropylmethyl cellulose, and buffer concentration has been investigated. Under optimized conditions (500 mM phosphate buffer, pH 2, 0.03% hydroxypropylmethyl cellulose) using an uncoated capillary, eight H1 histone subfractions, including two H1(0) histones and H1t and their phosphorylated modifications, are resolved. Application of capillary electrophoresis to the separation of H1 histones provides an important new alternative to high-performance liquid chromatography (HPLC) and traditional gel electrophoresis.

Buffers↗

PubMed1994

Quantitative analysis of hyaluronan in vitreous humor using capillary electrophoresis.

Capillary electrophoresis was used for the separation and quantitative analysis of the glycosaminoglycan hyaluronan in human and bovine vitreous with detection by UV absorbance at 200 nm. Calibration was carried out using standards made up from known concentrations of hyaluronan of umbilical cord origin. The purity of the standard was examined by 1H NMR (nuclear magnetic resonance). Concentrations as low as 25 micrograms/mL could be detected by capillary electrophoresis. Confirmation that the signal was due to hyaluronan was obtained by depolymerization of the native mucopolysaccharide by hyaluronidase. This resulted in loss of the hyaluronan peak and appearance of several new peaks corresponding to the oligomeric fragments which had shorter migration times. Capillary electrophoresis is a reproducible and sensitive technique for the quantification and characterisation of hyaluronan in vitreous samples.

Animals↗

PubMedDate not supplied

The use of a hollow fiber membrane module in sample conditioning prior to electrophoresis.

A new method to continuously change the buffer conditions in samples prior to electrophoresis by counter-current dialysis has been developed using a hollow fiber membrane module (VariPerm M, bitop, Witten). It is demonstrated that the collected fractions of a column eluate after hydrophobic interaction chromatography cannot be analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) due to the high content of ammonium sulfate. In contrast, when the hollow fiber membrane module is used for on-line desalting of the eluate during chromatography, it is possible to detect distinct bands on SDS-gels even after sample concentration by evaporation. Moreover, adding polyethyleneglycol 20,000 to the counter-current dialysis buffer the hollow fiber membrane module is suitable for combined on-line sample desalting and sample concentration of living organisms during free flow electrophoresis (FFE): a culture of Nitrosomonas eutropha which could not significantly be detected by FFE without conditioning was successfully analyzed when concentrated and desalted on-line during sample application.

Ammonium Sulfate↗

PubMed1994

Capillary electrophoresis separation of oligosaccharides: I. Effect of operational variables.

The influence of operating variables on the separation of labeled oligosaccharide molecules in capillary electrophoresis with polymer networks is presented. In this study, an equation was derived that relates the effects of electrophoresis variables such as field strength, temperature, molecular weight and gel concentration to the migration velocity. As a model system, 8-aminonaphthalene-1,3,6-trisulfonate ANTS-labeled wheat starch digest was examined to show the validity of the equation. As an illustration of the high resolving power achievable with capillary electrophoresis, oligosaccharide molecules up to the degree of polymerization of 25 were separated with the very high efficiency of N > 10(6) and efficiency generation rate of 3500 plates/m/s for maltose. Separation based on the size of the oligosaccharides was not obtained with either entangled or unentangled polymer solutions.

Electric Conductivity↗

PubMed1994

Separation of long DNA fragments by capillary gel electrophoresis with laser-induced fluorescence detection.

Long DNA fragments were separated by capillary gel electrophoresis with laser-induced fluorescence detection, and two approaches to obtaining high-resolution separation of DNA fragments were examined. One method achieved high resolution at the expense of detection time, while the other achieved both high resolution and fast detection. The former approach used a 300 cm long capillary with a gel concentration of 4% T and an electric field strength of 70 V/cm. The resolution limit in this electrophoresis was 800 bases with a resolution value of 0.5 for adjacent peaks. Under these conditions, the measurement time was 44 h. The latter approach used a 200 cm long capillary with a gel concentration of 3% T and an electric field strength of 170 V/cm. The resolution limit in this electrophoresis was 680 bases with a resolution value of 0.5 for adjacent peaks, and the measurement time was only 10 h. With both approaches, fragments with less than 600 bases were efficiently separated. The resolution values for adjacent peaks with less than 500 bases are greater than 1.0, and those for peaks with less than 100 bases are greater than 2.7. These approaches thus improve the accuracy of the base sequence determination.

DNA↗

PubMed1994

Effect of operational variables on the separation of proteins by capillary sodium dodecyl sulfate-gel electrophoresis.

Capillary sodium dodecyl sulfate (SDS)-gel electrophoresis, for fast and high-resolution separations of protein molecules based on their molecular masses was investigated, employing a polymeric sieving network of polyethylene oxide (PEO). A standard mixture of five proteins ranging from 14.2-66.0 kDa in molecular mass was used to evaluate the sieving matrix. A general migration velocity equation was derived for capillary SDS-gel electrophoresis of proteins and supported by the experimental data. This equation gives a better understanding of SDS-protein separations via capillary gel electrophoresis. Results are presented regarding the effects of different operational variables such as gel concentration, electric field strength, molecular mass, and temperature on the electrophoretic migration properties of the different size protein molecules.

Electromagnetic Fields↗

PubMed1994

Native electrophoresis to monitor chemical modifications of human interleukin-3.

Native electrophoresis on the Pharmacia PhastSystem using a new buffer system is used to monitor chemical modifications of human interleukin-3. The method is faster, more gentle and more convenient than amino acid analysis. Micrograms of protein suffice in contrast with milligrams required in spectrophotometric methods. As compared to generally used native electrophoresis, the combination of a changed conductivity, lower pH and the low density matrix results in a much better separation and detection of both the reaction products containing a high charge and the reaction products containing a low charge. This enables monitoring of extensive modifications as well as mild modifications. Our method also provides indications for denaturation of the protein. It has proven to be highly reproducible for at least 10 different modification reactions. Information can be obtained about the presence of the various distinct forms of the modified molecule, for instance leading to the average number of groups on the molecule. It also detects modifications not detectable with generally used native electrophoresis.

Circular Dichroism↗

PubMed1995

Protein concentration by precipitation with pyrogallol red prior to electrophoresis.

The pyrogallol red protein assay (Clinical Chemistry 1986, 32, 1551-1554) is based upon formation of a blue protein-dye complex in the presence of molybdate under acidic conditions. However, centrifugation of the assay mixture results in loss of color yield and precipitation of the protein-dye complex which can be recovered and resolubilized to achieve protein concentration prior to sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The method has been evaluated relative to trichloroacetic acid (TCA) precipitation for recovery and electrophoresis of commercial protein and peptide molecular weight markers. Precipitation with pyrogallol red-molybdate (PRM) gives better and more uniform recovery of both proteins and peptides as compared to TCA. The lower limit of PRM precipitation is similar to TCA and corresponds to 1 microgram protein per mL assay mixture. This is equivalent to 100 microL of 10 micrograms/mL protein using the standard protein assay or 1 microgram/mL protein using a modified assay incorporating a fivefold concentrate of the dye reagent. Application of the method is demonstrated by concentration of urinary proteins. The method is simple and economic and useful for conserving trace amounts of precious sample as it allows recovery of protein for electrophoresis following protein assay.

Chemical Precipitation↗

PubMed1995

Differentiation of scombroid fish species (tunas, bonitos and mackerels) by isoelectric focusing, titration curve analysis and native polyacrylamide gel electrophoresis of sarcoplasmic proteins.

Differentiation of scombroid fishes was possible by electrophoresis of sarcoplasmic proteins using either isoelectric focusing (IEF), titration curve analysis, or native polyacrylamide gel electrophoresis (PAGE). By IEF with Phast-Gels 3-9 species specific patterns, characterized by a few bands in the cathodal part of the gels, were obtained. This type of gel was also used for titration curve analysis. Here, too, the closely related species Thunnus thynnus and T. albacares gave different protein patterns. Native PAGE, native cathodal electrophoresis in Clean Gel 10% with buffer pH 5.5, proved to be a fast and simple method for differentiation of scombroid fishes. As most of the prominent sarcoplasmic proteins of these species have pIs in the neutral or alkaline pH range, they are positively charged at pH 5.5 and move to the cathode.

Animals↗

PubMed1995

Application of dual internal standards for precise sizing of polymerase chain reaction products using capillary electrophoresis.

Capillary electrophoresis (CE) is an analytical technique which provides rapid, high resolution analysis of amplified DNA fragments produced by the polymerase chain reaction (PCR). In this study, two internal standards are used as size markers to bracket und precisely size PCR products. The technique is applied to typing PCR products from the short tandem repeat locus HUMTH01. HUMTH01 consists of five to seven major alleles in the size range of 179-203 bp, with each allele four bp apart. Using this genetic marker, a population containing 97 individuals was examined with both polyacrylamide gel electrophoresis and CE. Identical genotypes were obtained with both techniques demonstrating the reliability of CE in DNA typing applications. The DNA analysis took place in sets of 10 with a calibration of the CE being performed between each set of samples. For the 97 samples examined, the pooled standard deviation was 0.3 bp. The observed genotype frequencies determined from the sample set did not deviate significantly from Hardy-Weinberg expectations. From these CE results, we conclude that HUMTH01 PCR products can be accurately and precisely sized by capillary electrophoresis using the method described.

Base Sequence↗