Agarose gel analysis of 15-40-kb PCR amplimers

Accurate resolution of PCR products in the range of 15-40 kb may be obtained in agarose gels without pulsed field electrophoresis. A gel of 0.3% SeaKem Gold agarose cast on GelBond support film provides good resolution and sufficient get strength to reliably allow staining and photography. This paper describes a test system for Long PCR and demonstrates analysis of the PCR products on a gel run under standard low-voltage electrophoresis conditions.

Application of gels of 0.5 mm thickness to electrophoresis in the automated HPGE-1000 apparatus: improved resolution

Gel electrophoresis in commercial automated apparatus (HPGE-1000, LabIntelligence, Menlo Park, CA) is conventially conducted in gels of 3 mm thickness at about 15 V/cm. Since the intermittent scanning of the gel allows one to measure band width as a function of migration time, resolution may be evaluated quantitatively. Comparing the value of resolution between two proteins in electrophoresis on agarose gels of 0.5 and 3.0 mm thickness and at various field strengths, it was found that within the given Joule heat dissipation capacity of the apparatus, resolution between the proteins is improved when the gel thickness is reduced from 3.0 to 0.5 mm, which allows for an increase in field strength from 15 V/cm, conventional for that apparatus, to 45 V/cm.

Reproducibility of mobility in gel electrophoresis

The quantitative exploitation of gel electrophoresis to yield molecular and gel fiber properties rests on the assumption that mobility is characteristic of the macromolecule migrating as a band and is a physical constant for any system defined by pH, ionic strength and temperature. This assumption has not been tested intra-experimentally in previous literature. With the commercial introduction of automated gel electrophoresis apparatus, the collection of multiple mobility data during a single run without additional expense of labor has made it possible to test the assumption. As a start, we undertook that test for three proteins and their sodium dodecyl sulfate (SDS) derivatives, in agarose and polyacrylamide gel electrophoresis, various field strengths, continuous and discontinuous buffers, as well as intra- and interexperimentally. It was found that in agarose gel electrophoresis conducted in a single buffer, the standard deviation of mobility over a wide concentration range ranges intra-experimentally from 0.2 to 1.3% for two globular proteins and 1.4 to 5.3% for the same proteins derivatized with SDS. Interexperimentally, it was 3% in the single case tested to date. The standard deviation in polyacrylamide appears to be higher, varies in inverse relation to the mobility value, i.e. increases with gel concentration in the range of 11 to 19%T, and varies substantially between the two SDS-proteins investigated. Mobility in a discontinuous buffer system decreases continuously due to the decreasing leading phase/trailing phase ratio along the migration path. The decrease is sharpest in the "nonrestrictive" stacking gel.

New types of large-pore polyacrylamide-agarose mixed-bed matrices for DNA electrophoresis: pore size estimation from Ferguson plots of DNA fragments

The average pore size value of gels containing polyacrylamide, covalently linked to agarose, was found to be 30% higher than the value of a regular N,N'-methylenebisacrylamide (Bis) cross-linked gel of the same %T. By increasing the agarose concentration (10% of the total amount of polyacrylamide), gels containing low amounts of acrylamide (1.5-2%) are reproducibly obtained; their pore sizes are 130% larger than the pore sizes of a 4%T, 3.3%C polyacrylamide gel. In general, mixed-bed matrices were found to be more elastic and mechanically stronger than classical polyacrylamide gels since an agarose-induced gelation process takes place during their polymerization.

Methods and reagents. Agarose gel electrophoresis in your kitchen

Methods and reagents is a unique monthly column that highlights current discussions in the newsgroup bionet.molbio.methods-reagents, available on the Internet. This month's column describes how to make an electrophoresis system from common household items. For details on how to partake in the newsgroup, see the accompanying box.

Commercial automated gel electrophoresis apparatus: application to DNA, band dispersion, nonlinear Ferguson curves, and isolation

Recently available commercial automated gel electrophoresis apparatus with intermittent scanning of fluorescently labeled gel patterns (the HPGE-1000 apparatus of LabIntelligence, Menlo Park CA) was tested with regard to (i) its applicability to DNA in its native conformation, (ii) its ability to recognize the correct number of components, (iii) its capability to evaluate the width and shape of bands detected during electrophoresis, (iv) its ability to yield nonlinear Ferguson plots in a labor-saving fashion, and (v) its preparative potential. Ethidium homodimer (EtD) DNA (bp) ratios were systematically varied and the mobility of DNA fragments labeled at each ratio was measured in order to find a ratio which provided an unaltered mobility and presumably therefore an unaltered conformation of the fragment. That ratio was found to be 1/40 EtD/DNA (bp) or less. With such weak labeling of DNA, a representative fragment of 527 bp length requires a minimum load of 200 ng and a 2 micrograms load for a full-scale peak height. Using the baseline automatically selected by the software of the apparatus, the band areas of the 17 components of a DNA digest were consistently evaluated by the software, as evidenced by the proportionality between DNA length and area. The areas of the separated bands of DNA fragments of 1857 and 121 bp length were found to be constant with time of electrophoresis. The dispersion coefficient was found to decrease with agarose concentration in electrophoresis at 1 V/cm; however, at higher field strength, the band width of the 1857 bp fragment was surprisingly found to increase with gel concentration, presumably due to stretching.(ABSTRACT TRUNCATED AT 250 WORDS)

Nonlinear "Ferguson curves" by two runs of the commercial automated HPGE-1000 gel electrophoresis apparatus with intermittent scanning of fluorescence

The exploitation of gel electrophoretic migration distance to gain information of molecular and gel fiber properties depends on the functions relating mobility with gel concentration. To the degree that these are nonlinear, the definition of those functions by past methods has been excessively laborious or, in application of gel concentration gradients, based on a number of assumptions. The recent commercial introduction of gel electrophoresis apparatus capable of intermittent scanning of the pattern promised to solve these problems. The present study shows that such apparatus allows for a precise definition of a nonlinear "Ferguson curve" (mobility vs. gel concentration) in two experiments, using different gel concentrations in the eight channels of the HPGE-1000 apparatus and 5-29 scans in each during the course of an electrophoretic run. Simultaneously, these Ferguson curves are obtained for five components of a DNA ladder ranging in DNA length from 121 to 1857 bp.

Electrophoresis for genotyping: microtiter array diagonal gel electrophoresis on horizontal polyacrylamide gels, hydrolink, or agarose

Electrophoresis of DNA has been performed traditionally in either an agarose or acrylamide gel matrix. Considerable effort has been directed to improved quality agaroses capable of high resolution, but for small fragments, such as those from polymerase chain reaction (PCR) and post-PCR digests, acrylamide still offers the highest resolution. Although agarose gels can easily be prepared in an open-faced format to gain the conveniences of horizontal electrophoresis, acrylamide does not polymerize in the presence of air and the usual configurations for gel preparation lead to electrophoresis in the vertical dimension. We describe here a very simple device and method to prepare and manipulate horizontal polyacrylamide gels (H-PAGE). In addition, the open-faced horizontal arrangement enables loading of arrays of wells. Since many procedures are undertaken in standard 96-well microtiter plates, we have also designed a device which preserves the exact configuration of the 8 x 12 array and enables electrophoresis in tracks following a 71.6 degrees diagonal between wells (MADGE, microtiter array diagonal gel electrophoresis), using either acrylamide or agarose. This eliminates almost all of the staff time taken in setup, loading, and recordkeeping and offers high resolution for genotyping pattern recognition. The nature and size of the gels allow direct stacking of gels in one tank, so that a tank used typically to analyze 30-60 samples can readily be used to analyze 1000-2000 samples. The gels would also enable robotic loading. Electrophoresis allows analysis of size and charge, parameters inaccessible to liquid-phase methods: thus, genotyping size patterns, variable length repeats, and haplotypes is possible, as well as adaptability to typing of point variations using protocols which create a difference detectable by electrophoresis.

One-hour downward capillary blotting of RNA at neutral pH

This report describes a setup for the downward capillary blotting of RNA with the use of 10 x SSC as a transfer solution. The setup is composed of a stack of blotting papers, hybridization membrane, and agarose gel. Two layers of blotting paper connect the stack with two reservoirs containing transfer solution. Using this setup, blotting of RNA fragments (< 7.5 kb) can be completed in 1 h. If necessary, the blotting time can be expanded from 1 to 18 h without decrease in hybridization efficiency of RNA.

Capabilities and potentialities of transverse pore gradient gel electrophoresis

Transverse pore gradient gel electrophoresis is important as a tool for obtaining nonlinear Ferguson plots [log(mobility) vs. gel concentration], e.g. in application to DNA in polyacrylamide gels or to agarose gels, with the purpose of evaluating molecular properties (size, conformation, malleability) and gel fiber properties (fiber radius and length per unit volume). To date, it is capable of (i) yielding gel patterns ("Ferguson curves") of migration distance vs. predicted % T-range of the pore gradient, assuming its linearity; (ii) yielding information regarding molecular conformation from the intersection of Ferguson curves of unknowns (e.g. bent DNA) with those of standards; (iii) acquisition of Ferguson curves by computer, using prototype instrumentation; (iv) mathematical manipulation of acquired Ferguson curves to yielding Ferguson plots, providing that mobility in free solution has been assessed by capillary zone electrophoresis. The potentialities of the method remain unfulfilled to date due to (i) the unavailability, with a single exception, of an accurate and precise way to produce pore gradients of known shape; (ii) unavailability of a routinely applicable analysis for % T; (iii) unavailability of optimized, user-friendly and foolproof instrumentation for computer acquisition of Ferguson curves, including the present inapplicability of a commercially available electrophoresis apparatus with intermittent optical detection to transverse pore gradient gels; and (iv) unresolved problems in the statistical evaluation of Ferguson curves.

Separation of large DNA molecules with high voltage pulsed field gel electrophoresis

We have developed two high voltage (3 kV and 10 kV) high speed pulsed field gel electrophoresis systems for the separation of DNA as large as 460 kbp. These systems enable us to combine the rapid speed of high voltages and the separation power of pulsed field electrophoresis to achieve high resolution and short run durations. We found that large DNA fragments can be separated at voltage gradients much higher than commonly used. Yeast chromosomes as large as 460 kbp can be separated in 4 h at 20 V/cm and 1-50 kbp DNA can be rapidly separated in 30 min at 55 V/cm. This is 25 times faster in mobility for the separation of relatively small DNA fragments (< 50 kbp). We have also found an inverse relationship between the voltage applied and the size separation limit at that particular voltage gradient (55 V/cm limits the separation to 50 kbp while 20 V/cm can separate up to 460 kbp). Depending on the size range, DNA can be separated 8- to 25-fold faster and with better resolution than existing electrophoretic systems.

Analysis of an origin of DNA amplification in Sciara coprophila by a novel three-dimensional gel method

The replication origin region for DNA amplification in Sciara coprophila DNA puff II/9A was analyzed with a novel three-dimensional (3D) gel method. Our 3D gel method involves running a neutral/neutral 2D gel and then cutting out vertical gel slices from the area containing replication intermediates, rotating these slices 90 degrees to form the third dimension, and running an alkaline gel for each of the slices. Therefore, replication intermediates are separated into forks and bubbles and then are resolved into parental and nascent strands. We used this technique to determine the size of forks and bubbles and to confirm the location of the major initiation region previously mapped by 2D gels to a 1-kb region. Furthermore, our 3D gel analyses suggest that only one initiation event in the origin region occurs on a single DNA molecule and that the fork arc in the composite fork-plus-bubble pattern in neutral/neutral 2D gels does not result from broken bubbles.

Voltage gradient electrophoresis of nucleic acids on agarose gels

A very simple method is described which allows the separation of DNA molecules in a wide molecular weight range (from 0.6 to about 30 kb) in the same electrophoresis agarose gel. This is based on the achievement of a voltage gradient through a simple device consisting of a Plexiglas plate placed slantwise with respect to the gel surface plane, submerged in the electrophoretic running buffer. Further applications of our system are also described.

Agarose gel electrophoresis system for the separation of antibiotics used in animal agriculture

A novel electrophoresis system using agarose gel has been developed for the separation and as an aid in the classification of antibiotics. This system utilizes Nunc cell factory disposable tissue culture dishes, which serve as bioassay dish and cooling chamber for agarose gel, in a custom designed electrophoresis unit. Tris(hydroxymethyl) methylamine-succinate buffer at pH 6.0 and 8.0 are employed as the electrolyte for electrophoresis. Bioautography was used as the indicator of mobility. Any agar diffusion assay can be modified to use this system. A suggested name for this system is Nunc cell factory agarose gel electrophoresis (NUAGE). Selected antibiotics, representative of the aminoglycoside, beta-lactam, macrolide, moenocinol, peptide, polyene, polyether, quinone and tetracycline classes, were separated with this system.

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.