Agarose Gel Electrophoresis of RNA

Abstract

Gel electrophoresis is one of the most important techniques currently available for the fractionation of RNA. The experimental procedure is relatively simple, but nevertheless achieves very reproducible results and high resolution. RNA is a polyanion and will therefore migrate toward the positive electrode in an electric field. If the migration occurs through a gel matrix of carefully chosen pore size, the mobility of the RNA molecules is related to the logarithm of the molecular weights: the smallest molecules moving the greatest distance. Suitable gel matrices for the electrophoresis of RNA are polyacrylamide or agarose in the form of rods or slabs. Agarose is generally preferred to acrylamide because of its ease of handling and lower toxicity, although acrylamide gives better resolution of small molecular weight RNA. Slabs have a number of advantages over rod gels: they enable many samples to be fractionated under identical conditions, they can be easily stained and photographed, and following electrophoresis the nucleic acids can be transferred to cellulose nitrate paper (Northern blotting) for hybridization experiments by a procedure similar to that described in Chapter 5 (1).