gel electrophoresis

Picture a crowd of runners of different sizes pushing through a dense thicket toward a finish line. The small, nimble runners slip through quickly; the big bulky ones snag and lag behind. Run them all for the same time and they spread out by size. Gel electrophoresis does exactly this to molecules, using electricity as the push and a jelly-like gel as the thicket.

DNA and RNA carry a uniform negative charge along their backbone, so in an electric field they all move toward the positive electrode. You load your sample into wells at one end of a slab of gel — agarose for DNA, a finer polyacrylamide for small fragments or proteins — and switch on the current. The gel is a microscopic mesh, so short fragments thread through quickly and travel far, while long fragments are held up and stay near the start. After running, every fragment of the same length has migrated the same distance, forming a sharp band. Staining the DNA (with a dye that glows under UV light) reveals a ladder of bands, and comparing them to a known size standard tells you each fragment's length. Proteins, which have no uniform charge, are first coated with the detergent SDS to give them a uniform negative charge so they too separate purely by size (SDS-PAGE).

Gel electrophoresis is the everyday workhorse of the molecular biology lab — the way you actually see DNA, check that a restriction digest cut as planned, confirm a PCR worked, purify a fragment by cutting its band out of the gel, or estimate the size of a gene or protein. It is also the separation step underneath the blotting methods: Southern, Northern, and Western blots all begin by running molecules out on a gel.