♦ After the gel electrophoresis has been completed, the next step is to analyze agarose gel for DNA fragments. Unfortunately, DNA embedded in the agarose gel can not be seen by the naked eye or with special instrumentation.
♦ The most routinely used method to visualize DNA in agarose gel is to stain DNA using nucleic acid staining dyes.
♦ These staining dyes bind to DNA and emit light when excited with an appropriate wavelength of light. The emitted light can be seen by the naked eye as the emitted light is in the visible spectral range. Since these dyes are excited by UV light, a shield to protect our eyes from UV rays is used regularly.
♦ You can find more information about nucleic acid staining dyes in the section ‘Nucleic Acid Staining Dyes for Detection of DNA in Agarose Gel’.
♦ DNA staining dyes are either added to the agarose gel while casting (precast method) or after the electrophoresis, agarose gel is stained with dye by submerging it in a solution containing dye (post staining method). Another method that consumes a very little staining dye can also be used. In this method, staining dye is mixed with the DNA sample (pre-loading method) and then the sample is loaded into the wells of agarose gel. However, this method does not work with all available dyes and is also not suitable for quantitation purposes.