SEC: When Science Glows: DNA Analysis in AP Biology

This spring, AP Biology students learned how to do gel electrophoresis, a common biotechnology tool. DNA previously cut by enzymes is loaded into tiny wells on an agarose gel submerged in an electrically conductive solution. Agarose is a highly purified polysaccharide from red sea algae. DNA is highly negatively charged due to its many phosphate groups. When an electric current is applied through the solution and the gel, DNA fragments migrate towards the positive electrode and away from the negative electrode. Shorter pieces of DNA are less impeded by the agarose matrix and migrate faster. Larger fragments move slower. As the DNA migrates through the gel, the fragments of DNA separate into a ladder of DNA bands. In the past, high school labs used a blue dye that often resulted in poor visualization of the DNA bands. Ethidium bromide is used in research labs to visualize DNA bands, but ethidium bromide is a potent mutagen and is not suitable for use by high school students. With a new, safe fluorescent dye paired with the use of an orange filter, DNA bands can be visualized with the same clarity as if using ethidium bromide. The resulting banding pattern of the separated DNA fragments is very satisfying.