Gel electrophoresis is developed as a method for separation, purification and analysis of bio molecules (DNA, RNA, Proteins etc) based on their size and charge.
Agarose or polyacrylamide gels usually are used to separate DNA fragments electrophoretically. In the process of gel electrophoresis charged molecules are placed in an electrical field and allowed to migrate towards the positive and negative poles. The molecules separate because they move at different rates due to their differences in charge and size. Because DNA is negatively charged, it is loaded into wells at the negative pole of the gel and migrates towards the positive terminal. Each fragment’s migration rate is inversely proportional to the log of its molecular weight. That is to say, the smaller a fragment is, the faster it moves through the gel.
Migration rate of substrate is also a function of gel density. In practice, this means that higher concentrations of gel material (agarose or acrylamide) provide better resolutions of gel material (agarose or acrylamide) provide better resolution of small fragments and vice versa.
Shorter molecules move faster and can migrate more length than longer ones because shorter molecules can easily migrate through the pores of gel. This phenomenon is called sieving. Gel electrophoresis can also be used to separation of nano particles.
Gel elctrophoresis uses a gel as an anticonvective medium or sieving medium during electrophoresis.
DNA that has not been digested with restriction enzymes is usually supercoiled. For this and other reasons, DNA is usually cut with restriction endonucleases prior to electrophoresis.