Electrophoresis is used to separate pieces of DNA that vary in length. DNA is essentially sifted through a thin slab of "gel", similar in consistency to over-hardened jello. The gel can be made of different materials - agarose or acrylamide - depending on the size of the DNA fragments to be separated. Liquid gel is poured into a mold leaving small slits or wells in one end where DNA samples (suspended in a buffer and dye) are placed once the gel solidifies (Figure 4-A). This illustration shows loading of a DNA sample in lanes 1 & 2, and DNA already run through the gel in lanes 3 & 4. In reality, all lanes are run together with a control sample in one lane (lane 5) containing a "ladder" of DNA fragments of known size to help estimate the sample size.

Once the DNA is loaded, the gel is immersed in a buffer solution and placed under a continuous electrical current. The DNA molecule has an overall negative electrical charge due to its chemical structure, so it is attracted to the positive end of the gel and slowly moves through the gel matrix (4-A). Typically, gels are run for several hours. After the run, DNA trapped in the gel can be visualized using the chemical ethidium bromide, which integrates into the grooves of DNA, and fluoresces under ultraviolet light. DNA may appear as a smear down each lane (4 -B, lane 1), or in the case of a PCR sample, as a discrete heavy band since most of the DNA is of one length (4-B, lane 3).