Agarose and Polyacrylamide Gel Electrophoresis

Electrophoresis through agarose or polyacrylamide gels is a standard method used to separate, identify, and purify nucleic acids. The technique is simple, rapid to perform and capable of resolving fragments that differ by as little as 0.2% in size. Electrophoresis occurs under the influence of an electric field: Charged molecules such as nucleic acids migrate in the direction of the electrode having the opposite charge (anode). The electrophoretic mobility of nucleic acids is determined by a number of parameters, but molecules of linear double-stranded DNA migrate through gel matrices at rates that are inversely proportional to the log₁₀ of the number of base pairs (1 ) and therefore larger molecules migrate more slowly because of the greater frictional drag (see Note 1 ). Other factors affecting electrophoretic mobility include the pK value, base composition, concentration of gel matrix, composition and ionic strength of the electrophoresis buffer, temperature and the use of intercalating dyes such as ethidium bromide.