One of the most common methods of DNA and RNA analysis is agarose or acrylamide gel electrophoresis. Samples are loaded into precast gels, and as an electrical current is passed through the gel, nucleic acid fragments are separated on the basis of size. Larger fragments move more slowly through the gel matrix, while smaller fragments move more quickly. The gels containing the separated fragments are stained with a fluorescent dye that bind nucleic acids, such as ethidium bromide, SYBR® Green or SYBR® Gold but are not specific to RNA. The separated fragments then can be visualized by excitation of the fluorescent dye bound to the nucleic acid.
RNA concentration can be qualitatively measured by comparing the relative fluorescence intensity of the RNA bands to that of known RNA standards, or quantitatively by sophisticated equipment that uses software to analyze an image of the gel, known as gel densitometry. General information about RNA integrity can be obtained by observing the staining intensity of the major ribosomal RNA (rRNA) bands and any degradation products. For mammalian rRNA, a 28S:18S rRNA ratio of 2:1 is generally representative of good-quality RNA. Genomic DNA contamination of RNA samples can be visualized in the sample, as genomic DNA typically runs much slower through the gel matrix than RNA (Figure 3).