Resolving DNA Amplification Products Using Polyacrylamide Gel Electrophoresis and Silver Staining

Abstract

The scanning of nucleic acids by amplification produces an array of DNA products that can be resolved using a variety of methods. As originally described, DNA amplification fingerprinting (DAF) (Caetano-Anolles et al. 1991) and arbitrarily primed PCR (AP-PCR) (Welsh and McClelland 1990) use Polyacrylamide gel electrophoresis (PAGE), while random amplified polymorphic DNA (RAPD) analysis (Williams et al. 1990) separates amplification products by electrophoresis in agarose gels. These techniques differ also in the way nucleic acid fragments are detected: DAF uses silver staining, AP-PCR uses autoradiography, and RAPD uses staining with ethidium bromide. These procedures provide simple, fast and low-cost analysis of amplification products. However, many researchers would prefer avoiding the use of radioactivity, acrylamide, and ethidium bromide. Despite its low resolving power, the familiarity and simplicity of agarose gel electrophoresis has made RAPD popular. However, it is a poor strategy for the analysis of complex fingerprints. Alternatively, PAGE has traditionally offered a superior separation of nucleic acids, proteins and polysaccharides. Acrylamide polymerization onto backing supports such as polyester films or glass has simplified gel handling and improved the overall performance of the technique.