Scientists sort DNA by size using a slab of jelly made from seaweed
One of molecular biology's workhorse tools is basically a race through jelly. Load DNA into a slab of gel, switch on an electric field, and fragments crawl toward the positive end, with small pieces slipping through the pores faster than big ones. The gel most often used for DNA, agarose, is extracted from seaweed.
Gel electrophoresis separates large biological molecules such as DNA, RNA and proteins by size and charge. DNA carries a negative charge, so an electric field pulls it through a porous matrix. Shorter strands travel farther in a given time, an effect called sieving, and the fragments settle into distinct bands. Running a ladder of molecules of known size in a neighbouring lane lets researchers estimate the size of unknown fragments, since the distance travelled is roughly inversely proportional to the logarithm of molecular size.
The gel does two jobs: it suppresses the churning currents that heat from the electric field would otherwise create, and it holds the separated bands in place so they can be stained afterward. The technique often follows DNA copying by the polymerase chain reaction and can prepare samples for sequencing, cloning or other analyses.
Two materials dominate. Agarose, made of long uncharged sugar chains, sets physically as it cools, forms large irregular pores and is easy to cast and handle; it separates DNA from about 50 to 20,000 base pairs and is run horizontally, submerged in buffer. Most recipes use between 0.7 and 2 percent agarose, and 1 percent gels are common. Polyacrylamide forms through a chemical reaction, has uniform pores and resolves tiny DNA pieces of 5 to 500 base pairs as well as proteins, and it runs vertically. Its raw ingredient, acrylamide, is a potent neurotoxin that needs careful handling.
The method has limits. The current heats the gel, which can melt, and long runs can exhaust the buffer that keeps pH stable. Some proteins misbehave: tropomyosin, an acidic protein, migrates abnormally in a common protein test because its charge interferes. For truly enormous DNA, over 6 million bases, specialised pulsed-field techniques are needed.
Source: Gel electrophoresis
