A polyacrylamide gel is prepared with slots in it. The gel is formed by pouring a hot liquid polyacrylamide solution into a shallow box. The box should contain a comblike structure with teeth that point down into the solution. The polyacrylamide becomes a gel soon after it has been poured and the comb is removed to reveal rectangular holes.
The protein is treated with sodium dodecyl sulfate (SDS) in order to denature the subunits of a large protein so each one can be measured separately. The advantages to this are that the SDS gives the polypeptides a negative charge so they will migrate toward the negative end, or anode, of the gel. Secondly, the SDS makes sure all subunits will have the same charge and therefore will all migrate in the gel according to their molecular masses instead of charges.
A small amount of DNA or protein is placed in one of the rectangular holes at one end of the gel. An electric current is run through the gel at neutral pH. About 10 microliters of a DNA ladder as well as two controls are also loaded into the gel. The DNA ladder is used to allow measuring of how far the sample moved in the process of electrophoresis.
The machine is then turned on to 100 volts and let run for 30 minutes. After the samples have been electrophoresed for 30 minutes, the gel along with a tray are removed and placed in a staining tray for about three minutes. This is then followed by placing the gel in warm water for five minutes. The gel is now ready to be placed on the light box in order to observe the movement of the DNA fragments.
When viewing the gel under the light, some important things should be taken into consideration. A cell may be either heterozygous or homozygous for the gene depending on whether the copy is present or not present in both copies or in just one. The heterozygous result may appear as a single band because the segments of DNA that are amplified more efficiently appear darker in the gel. A dye is also added so each polypeptide can be seen both during and after electrophoresis.