DNA is separated by placing the molecules on a gel made from very purified seaweed called agarose. The gel is then dropped in a saline-filled tank through which electricity is conducted. Next, blue-dyed DNA samples are pipetted into the gel. The blue dye allows the DNA to be tracked. When electricity is applied to the tank, the DNA molecules snake through the solution at various speeds and are easily separated.
Proteins are separated based on their charge: whether they are positive or negative. In this case, the electrophoresis gel is placed in a column with electrodes at each end. The upper portion is negative or cathode and the lower part is positive or anode. The gels separate into a Running Gel and a Stacking Gel. Pass a current through the gels and watch the proteins migrate either to the cathode or anode half of the system, depending on their charge.
You can use electrophoresis either with column or slab gels. Column gels allow molecules to move straight down and are less likely to move sideways through the medium. This makes for easier resolution of the bands of molecules. With slab gels, however, a two-dimensional analysis is possible and several samples can be run at the same time. Slab gels are more economical and are, therefore, used more frequently.
Electrophoresis gels are usually made from agarose, which is a purified form of powdered seaweed extract. Boil some water and pour in the agarose powder. It will dissolve in the boiling water and become polymerized after it cools down. This means that the sugars in the solution link together and become a matrix that is jelly-like in consistency. The more agarose you use, the firmer the gel.