Gel electrophoresis equipment consists of a casting tray, casting combs, gel box, power supply, agarose gel and UV light box. The casting tray and gel box are made from either Plexiglas or Teflon, both of which are non-conductive materials. When an electric current is passed from the power supply through a buffer contained in the gel box, the current does not transfer from the gel box into the researcher. The casting tray and combs are used to create the gel. Casting trays come in various sizes, as do the combs. A small gel may be used to run five or six samples while a large gel may run up to 20 samples. The researcher will use the UV light box in combination with a luminescent dye to read the results of an electrophoresis experiment.
The gel used in electrophoresis is made from a heated solution of agarose and buffer that is then poured into a casting tray with casting combs at one end. Once cool, the agarose polymerizes, becoming a porous gel similar to Jello only heavier and sturdier. After the researcher places the gel in the gel box and covers it with buffer, the DNA samples are mixed with a luminescent dye known as ethidium bromide and a thickener. The thickener allows the sample to sink to the bottom of the well instead of floating off into the solution. The concentration of agarose, in solution, dictates the size of DNA fragments that can move through the gel and how quickly. Most laboratories use a 0.8 percent agarose gel capable of separating DNA fragments of 500 to 20,000 base pairs. The casting comb creates small wells in one end of the gel.
DNA is a negatively charged molecule. When the power supply is attached to the gel box, the negative electrode is placed at the same end as the DNA sample, while the positive electrode is placed at the opposite end of the gel box. As the current flows through the buffer solution, the DNA sample is attracted to the positive current. The longer the current runs through the buffer, the further the DNA sample with move through the gel. If a sample contains two or more fragment sizes, longer run times will show greater separation between the two bands.
In order to read the results, the gel is placed on a UV light box. The UV light causes the ethidium bromide attached to the DNA fragments to glow as a linear band. The brighter and thicker the band, the more DNA contained in the sample. When the DNA sample is loaded with a standard containing several known fragment sizes, the scientist can estimate the approximate size of the DNA fragment. If the scientist is attempting to separate a particular fragment size from a mixed sample, he can excise the gel around the band and extract the DNA later.