A gel electrophoresis apparatus must allow the researcher to maintain a uniform electric field across the gel, provide cooling to prevent thermal artifacts, and allow access to the gel for sample loading and monitoring the run. Two types of apparatus are in common use: vertical and horizontal. Vertical gel systems are further subdivided into slab gels and tube gels. In general, agarose gels are run in the horizontal format, while acrylamide gels are run vertically.

In its simplest form, a horizontal gel apparatus consists of a box which is divided into two compartments by a platform in the middle. The gel is placed on this platform, and buffer is added until the gel is fully submerged. Electrodes in each compartment supply the electric field. The resulting current flows through both the gel and the buffer over the gel, so the thickness of these must be controlled for fully reproducible results. Cooling is provided by the buffer which surrounds the gel, and this buffer is often recirculated to prevent the development of a pH gradient and also to aid in temperature control. Access to the gel is through the overlaying buffer. Samples are loaded through this buffer layer, and the apparatus has a clear lid to allow the run to be monitored.

One major limitation of the horizontal apparatus is that, since the two compartments are connected by a layer of buffer, it is not possible to use discontinuous buffer systems. Another limitation is that the gels are cast in trays which are not covered. Because atmospheric oxygen has full access to the upper surface of the gel, acrylamide will not polymerize in this system. Horizontal systems are primarily used to run agarose gels which are run in continuous buffer systems and are not affected by O2. For agarose gels, the simplicity and ease of use of the horizontal system make this system the best choice.

Horizontal gels are cast in trays which have removable ends. The ends are installed (often the ends are simply adhesive tape), and the molten agarose solution is poured into the tray. A comb is inserted so that the teeth penetrate the gel to within 1-2mm of the bottom of the tray. The overall gel thickness is generally 0.5-1cm. The gel is allowed to cool, the comb is removed, and the gel is mounted in the apparatus (See Complete Protocol).

A typical vertical apparatus used for sequencing is shown in the figure below. This system shows the components common to all vertical slab systems. The gel is cast between two glass plates, separated by spacers, typically <2mm thick. The gel is mounted in the system so that the top is in contact with the negative electrode chamber, and the bottom is in contact with the positive electrode chamber. Unlike the horizontal system, the only connection between the buffer chambers is through the gel. This allows precise and reproducible control of the voltage gradient. Because of the high resistance of the thin gel, the apparatus must have provisions for cooling. In the system shown, the front of the gel cassette is exposed to the air, while the back of the gel is held against a metal plate which dissipates heat rapidly. In some systems, the upper buffer chamber extends almost to the bottom of the gel, and the upper buffer is used for cooling. The relatively small amount of current carried through the gel means that buffer recirculation is generally not required.

The figure below shows a standard "mini" gel apparatus. Such gels, generally 10cm x 10cm or smaller, have become the standard for many applications, because of their ease of preparation and handling, and short run times. As with the "full size" system, the gels are cast between glass plates, but in the mini-gel system, the cassettes are mounted onto a "U" shaped frame, so that the cassettes themselves form the sides of the negative electrode chamber. This assembly is placed in a tank of buffer which contains the positive electrode. This means that the gels are effectively submerged in buffer during the run, providing optimal cooling.

In general, vertical slab gels are loaded through the top, under a layer of buffer. The gels are monitored during the run through the front glass plate. The fact that the body of the gel in these systems cannot be accessed until the end of the run can be an inconvenience. Some sample recovery techniques used on horizontal gels are not available for vertical gels. However, the resolution and reproducibility of vertical polyacrylamide gels more than compensate for this.

Vertical gels are cast in a cassette made up of two glass plates separated by spacers which run along the sides of the plates. The bottom of the cassette is sealed by some temporary means (tape, agarose, or a gasket). The gel monomer solution is treated to initiate polymerization, and poured into the cassette. A comb is inserted into the top of the cassette to form the sample wells, and the gel is allowed sufficient time to polymerize. After polymerization, the bottom of the gel is unsealed, and the cassette is mounted in the apparatus.

Tube gels were used frequently in the development of gel electrophoresis. Although they are still used for some applications (most notably for isoelectric focusing as part of 2D electrophoresis), tube gels have been superseded by slab gels for most applications. Tube gels are cast (as the name implies) in glass tubes of 1-3mm diameter. The gels are run in a box which is divided into two chambers horizontally. The horizontal partition has gasketed mounting holes for the tube gels. The upper and lower chambers are filled with buffer, and current applied. The principle limitation of this system is that only one sample can be loaded per gel. Slab gels, which can accommodate up to 96 samples on a single gel, are the method of choice in most cases.

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