Density gradient electrophoresis of cells in a reversible gel

Density gradient electrophoresis permits the separation of cell types according to surface charge density with high resolution. Any source of flow compromises the resolving power of density gradient electrophoresis. Although procedures have been devised to successfully counteract electroosmotic and convective flows, the final collection of separands requires that they be pumped out of the electrophoresis column. Experiments were therefore designed to test the hypothesis that this flow could also be eliminated by trapping the separated bands in a gel, from which they could be collected by slicing the gel cylinder. Glutaraldehyde-fixed rat and rabbit erythrocytes were used as test particles in a phosphate-buffered isotonic Ficoll-sucrose density gradient in a 2.2 cm diameter, thermostated vertical glass column that could be opened at both ends. Two types of agarose were used as gel polymers: Electrophoresis grade agarose (J.T. Baker Chemical Co.) at final concentrations of 0.1 to 0.25% and SeaPrep ultralow gelling agarose (Marine Colloids Div., FMC Corp.) at a final concentration of 1.0%. Electrophoretic separability of the test particles and fluid stability were tested independently at 55 degrees C and 32 degrees C at which the two agaroses were, respectively, liquid. The experiments demonstrated that the higher temperatures required and the presence of agarose compromised neither the stability of the density gradient nor the migration properties of the cells, and cells can be separated in a sol at a temperature that is compatible with cell viability.

A novel instrument for separating large DNA molecules with pulsed homogeneous electric fields

A new instrument has been developed for the electrophoretic separation of large DNA molecules that can independently regulate the voltage of each of 24 electrodes and allow the magnitude, orientation, homogeneity, and duration of the electric field to be precisely controlled. Each parameter can be varied at any time during the electrophoretic process. Thus distinct sets of conditions can be combined to optimize the separation of various fragment sizes in a single run. Independent control of electrode voltage allows all of the fields to be generated with electrodes arranged in a closed contour, independent of a particular geometry. This device increases both the resolution in any size range and the speed of separation, especially for DNA molecules larger than 3 megabases.

A procedure for electro-elution of DNA from agarose gels

A simple device is described for efficient and reproducible electro-elution of DNA resolved in agarose gels. DNA (greater than 1 micrograms) is recovered with consistent yields of over 70% into preset elution volumes of 100 to 500 microliters.

Optimized conditions for pulsed field gel electrophoretic separations of DNA

Quantitative measurement of DNA migration in gel electrophoresis requires precisely controlled homogeneous electric fields. A new electrophoresis system has allowed us to explore several parameters governing DNA migration during homogeneous field pulsed field gel (PFG) electrophoresis. Migration was measured at different switch times, temperatures, agarose concentrations, and voltage gradients. Conditions which increase DNA velocities permit separation over a wider size range, but reduce resolution. We have also varied the angle between the alternating electric fields. Reorientation angles between 105 degrees and 165 degrees give equivalent resolution, despite significant differences in DNA velocity. Separation of DNA fragments from 50 to greater than 7000 kilobases (Kb) can easily be optimized for speed and resolution based on conditions we describe.

Pulsed homogeneous orthogonal field gel electrophoresis (PHOGE)

A versatile system (PHOGE) has been developed that allows resolution of molecules of DNA megabase pair size by the use of homogeneous, orthogonal, pulsed fields. The resulting electrophoretograms have characteristics that differ from those produced by other systems for pulsed field electrophoresis. Molecules in a two-fold range of sizes can be separated with maximum resolution, or a much larger range of sizes may be separated with lower resolution but with a linear relationship of mobility to size from 50 kb, or below, to at least 1 Mb. Straight lanes and large useable gel areas, characteristic of PHOGE, are also valuable for mapping procedures or for any other circumstance in which large numbers of samples of DNA are to be directly compared. Existing models cannot explain the results obtained, because a stage of the molecular reorientation appears to result in a rate of migration greater than that occurring by reptation. We suggest a mechanism that might account for the resolution observed and also suggest that the resolution achieved by existing OFAGE-type systems may be the result of the superimposition of PHOGE and FIGE separatory mechanisms. No maximum size of molecules that may be resolved by the PHOGE system has yet been determined.

Detection of turnip crinkle virus on agarose gel electropherograms at the nanogram load level

The previous conditions for the physical characterization of turnip crinkle virus (TCV) by quantitative agarose gel electrophoresis [1, 2] were limiting the method to the microgram load level and were therefore insufficiently sensitive to satisfy the need in many areas of virology for detection of viruses containing single-stranded RNA at the nanogram level. The present report remedies that defect by presenting a technique compatible with the nanogram load level of such viruses. The technique is based on a reduction of gel thickness and on the use of silver staining.

A computer program allows the separation of a wide range of chromosome sizes by pulsed field gel electrophoresis

The introduction of Pulsed Field Gel Electrophoresis techniques, which allow the separation of DNA molecules of molecular weights as high as chromosomes of lower eukaryotes, has given a powerful tool to geneticists. The resolution expected from these techniques is dependent on numerous parameters, among them pulse time and field strength. A given set of these parameters allows only a limited range of molecular weights to be resolved. To allow the separation of a broader molecular weight range on a single gel, we designed a computer program, driving a simple switching device, to take care of switching electrodes and power supplies in OFAGE migrations. This program has been designed to be used with any technique calling for periodic switching or inversion of the electric field, and/or variation of the electric field applied during electrophoresis. As an example, we show the results obtained with yeast genera in which chromosome sizes range from 260 to 9,000 kilobase pairs.

BBC microcomputer controlled field inversion gel electrophoresis

Agarose gel electrophoresis to separate DNA molecules is a widely used technique in molecular biology but there is an upper limit to the sizes that can be resolved. Pulsed field techniques have extended this limit but require expensive equipment. Here we describe a home-made control unit to interface conventional electrophoresis equipment to a BBC microcomputer for the purposes of field inversion gel electrophoresis.

Recovery of functional DNA inserts by electroendosmotic elution during gel electrophoresis

In contrast to all previous preparative electrophoresis apparatus which used a pump, electroendosmotic elution uses bound electrical charges at the end of the separating gel to generate a buffer flow. The electroendosmotic flow increased with increasing currents and decreasing buffer concentrations: its exact characteristics for the built apparatus were determined. The electroendosmotic device was able to separate two DNA fragments differing in size by only 5% with a recovery over 95%. As demonstrated in practical examples of recovery and uses of DNA inserts, up to 10 micrograms of DNA per band can be loaded at a time. The recovered DNA can be used directly for nick-translation, ligation... without further treatment. The performances of the method are expected to improve still further if the charge density and pores of the electroendosmotic medium can be "made-to-order" to provide a better flow profile of the eluting buffer.

An improved voltage measurement device for gel electrophoresis in tube apparatus

A device for the measurement of voltage across tube gels was designed and constructed which allows one to measure voltage during electrophoresis without any manipulation of the gel electrophoresis apparatus or gel tube and with the elimination of a source of inaccuracy in previous such devices.

RNA fingerprinting using a small horizontal agarose gel electrophoresis apparatus

The electrophoresis step in the RNA fingerprinting procedure has been modified by replacing the large and expensive electrophoresis tank with a horizontal agarose gel electrophoresis box, a common piece of laboratory equipment. Two RNA molecules (67 and 298 nucleotides long) transcribed in vitro from a truncated human beta-globin gene have been fingerprinted and analyzed by the modified technique. The resolution of the oligonucleotides in this procedure is comparable to that seen using the tank and is sufficient to separate relatively large oligonucleotides with similar base composition.

High resolution preparative gel electrophoresis of DNA fragments and plasmid DNA using a continuous elution apparatus

An apparatus designed for preparative gel electrophoretic separation of proteins (M. A. Hediger, (1984) Anal. Biochem. 142, 445-454) has been used successfully for separating DNA restriction fragments. The apparatus displayed yields and resolutions that are higher than those obtainable with commercially available devices. The amounts of DNA applied to the column range from a few micrograms to milligram quantities. Restriction DNA fragments very similar in size were isolated in pure form with the apparatus. After ethanol precipitation, these fragments were successfully used for restriction enzyme cleavages, ligation, or chemical sequencing. Furthermore the apparatus provides a convenient method for the large-scale isolation of plasmid DNA. The method requires only 4 h of electrophoresis and therefore greatly reduces the preparation time compared with the conventional equilibrium centrifugation method which requires centrifugation times of up to 60 h. In contrast to the centrifugation method, contaminants such as RNA, proteins, and chromosomal DNA are efficiently removed by this technique.

Rapid and quantitative recovery of DNA fragments from gels by displacement electrophoresis (isotachophoresis)

The use of displacement electrophoresis (synonymous to isotachophoresis, steady-state stacking, and moving boundary electrophoresis) for recovery of DNA fragments from agarose and polyacrylamide gels is described. Complete recovery of DNA molecules ranging from oligonucleotides to 20 000-basepairs-long fragments was achieved. The DNA is recovered in a small volume (0.1-0.3 ml) and can be used directly in enzyme-mediated cleavage and ligation reactions. The recovered DNA contained no inhibitory contaminants as revealed by ligation or restriction enzyme cleavage.

Blot hybridisation analysis of genomic DNA

Restriction endonuclease analysis of specific gene sequences is proving to be a valuable technique for characterisation and diagnosis of inherited disorders. This paper describes detailed protocols for isolation, restriction, and blot hybridisation of genomic DNA. Problems and alternatives in the procedure are discussed and a troubleshooting guide has been provided to help rectify faults.

Computer-based image analysis of one-dimensional electrophoretic gels used for the separation of DNA restriction fragments

A stand-alone, interactive computer system has been developed that automates the analysis of ethidium bromide-stained agarose and acrylamide gels on which DNA restriction fragments have been separated by size. High-resolution digital images of the gels are obtained using a camera that contains a one-dimensional, 2048-pixel photodiode array that is mechanically translated through 2048 discrete steps in a direction perpendicular to the gel lanes. An automatic band-detection algorithm is used to establish the positions of the gel bands. A color-video graphics system, on which both the gel image and a variety of operator-controlled overlays are displayed, allows the operator to visualize and interact with critical stages of the analysis. The principal interactive steps involve defining the regions of the image that are to be analyzed and editing the results of the band-detection process. The system produces a machine-readable output file that contains the positions, intensities, and descriptive classifications of all the bands, as well as documentary information about the experiment. This file is normally further processed on a larger computer to obtain fragment-size assignments.

Philothermal and chemotactic locomotion of leukocytes. Method and results

A newly developed technique for quantitating the locomotion of polymorphonuclear leukocyte (PMN) populations in temperature gradients has revealed that PMNs accumulate toward higher temperatures. The experiments yield measurements of the numbers of cells that adhere to glass and migrate from a cell suspension through a liquid/gel meniscus into a glass/agarose interface, and of their spatial distribution at subsequent time intervals. Cell locomotion was investigated as a function of the magnitude, sign, and temporal variation of the temperature gradient, the cell concentration in the source suspension, and the presence or absence of chemoattractant gradients. It was found (1) that a temperature gradient stimulates crossing of the meniscus toward higher temperatures, (2) that only a portion of the cells reverses direction of locomotion in response to reversal of the temperature gradient after the cells have traversed the meniscus, and (3) that the distribution of cells in the migration space depends on cell concentration, suggesting that the dynamics of PMN locomotion depend on cell-cell interactions.