RNA and Protein electrophoresis

The electrophoresis of RNA and proteins has a longer history than DNA electrophoresis. This is because these molecules are shorter in length than DNA in a cell and techniques did not need to be developed that either made a discrete segment of DNA (PCR) or detected that segment (Southern Blotting). RNA and proteins have other properties, however, that influence the electrophoresis methods used to separate them. One property is the formation of a secondary structure. Both molecules are single chains of subunits and these subunits can interact, forming loops, hairpins or sheets. If the molecule retains this secondary structure in the gel, it's mobility will not be directly related to it's length. This can be remedied by treating the molecules physically or chemically to eliminate secondary structure. RNA can be coated with formaldahyde or dimethyl formamide while protein can be treated with a detergent called sodium dodecyl sulfate (SDS). The treated molecules do not retain their secondary structure and thus move through an electrophoresis gel as linear chains. An additional issue with proteins is that the amino acid subunits will each have their chemical properties. Some amino acids have a negative charge, some a positive charge and some no charge at a given pH. The amino acid charges will determine the overall charge of a protein and thus how it moves in an electrophoresis gel. Treating proteins with SDS tends to create a uniform negative charge on the molecule. Proteins treated with SDS will thus have a negative charge, no secondary structure and an SDS gel will separate proteins based on their length. Thus the electrophoresis method has wide applications in molecular genetics but requires modifications based on the molecule of interest and the question being addressed.