Nucleic acid electrophoresis is a widely used technique for separating DNA or RNA fragments by the mobilities of fragments in electrophoresis gels. Nucleic acid samples to be analyzed are loaded into gels, where an electric field induces the negatively charged nucleic acid molecules to migrate towards the positive pole. The charge, size and shape of a molecule affect its mobility rate. In addition, the type and percentage of gels, the ionic strength of the buffer, the concentration of dyes, and the type of instrument system used are also key factors affecting the migration of nucleic acids.
The separation matrixes of nucleic acid electrophoresis include agar, agarose, polyacrylamide, and composite agarose-acrylamide gels. Among them, agarose and polyacrylamide are the two most used gels in nucleic acid electrophoresis. Polyacrylamide gels are suitable for separating nucleic acid molecules smaller than 1000 bp.
Nucleic acid fragment size is usually reported in "nucleotides", "base pairs (bp)" or "kb” depending upon whether single- or double-stranded nucleic acid has been separated. Fragment size is usually determined by comparison with nucleic acid standards that contain fragments of known length.
The easiest way to see the results of a gel electrophoresis experiment is to stain the gel with a nucleic acid stain. Ethidium bromide (EtBr) is a common stain in agarose and polyacrylamide gels. EtBr binds to DNA molecules by intercalating between adjacent base pairs and emits an intense red-orange fluorescence under UV light.
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