In gel electrophoresis, DNA fragments move through a porous matrix made of agarose, a gelatin-like substance purified from seaweed. The agarose is melted like Jell-O® and then poured into a plastic tray to harden into a slab called a gel. A plastic comb inserted at one end while the gel is hardening forms wells where DNA samples can be placed. The DNA is mixed with a loading buffer that contains glycerol—this makes it heavier than water, so it will sink to the bottom of the well. The gel is then covered with a buffer solution that can carry electric current, and electrodes are placed at each end of the gel and connected to a power supply. Because DNA is negatively charged (each nucleotide has a negatively charged phosphate attached to it), it will move toward the positive electrode. Larger molecules move through the agarose more slowly, while smaller ones can slip through the pores faster.
As the DNA migrates, the different fragments will form bands; each band is composed of many identical copies of a particular-size piece of DNA (you can’t do gel electrophoresis with one DNA molecule: you need millions or billions of identical molecules). The last step is to make the DNA bands visible, using a fluorescent molecule that inserts between the bases in the DNA helix. We use a commercial loading buffer called EZ-Vision which includes the fluorescent molecule, so the gel is already stained when it’s done running. Another method is to soak the gel in ethidium bromide after running it. Either way, the bands can be seen using ultraviolet light and photographed to make a permanent record.