Taxonomy of Finfish (1+2)

6.2.7 Agarose Electrophoresis

The electrophoretic technique used to characterize DNA and RNA is through agarose gels. The mobility of nucleic acid in agarose gels is influenced by agarose concentration and the size and shape of the nucleic acid. Agarose concentration of 0.5 to 3% is most effective for nucleic acid separations. Gels with agarose concentration less than 0.5% are rather fragile and must be used in a horizontal slab arrangement or in a refrigerated chamber. Like proteins, nucleic acids migrate at a rate that is inversely proportional to the logarithm of their molecular weights; hence molecular weight can be estimated from electrophoretic results using standard nucleic acids of known molecular weight. Passage of a molecule through a gel is influenced by the shape and size of the molecule. A small, compact molecule would be expected to have a greater mobility than rod like, linear molecules.

Most agarose gel electrophoresis experiments are carried out with horizontal slab gels. This method is chosen over vertical mode because low agarose concentration can be used for maximum mobility.