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.

The Horizontal Gel System Explained

In its simplest form, a horizontal gel apparatus consists of a box that is divided into two compartments by a platform in the middle. The gel is placed on this platform, and the 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 that 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.

NEXT TOPIC: Horizontal and Vertical Gel Systems - Vertical Tube Gels