Ethidium bromide(EtBr) is most commonly used dye for detecting DNA/RNA bands in agarose gel electrophoresis. It is a flat molecules for ideal intercalating agent which resembles a DNA base pair. Thus, it is used as fluorescent tag for nucleic acid as it can fluorescent under UV light when intercalated into the DNA strand. Any band more than ~20 ng DNA in agarose gel may visible if visualizing it with UV light. EtBr is a strong mutagen, it is toxic and known as harmful by all routes of entry; inhalation, ingestion or skin absorption. Therefore, it is important to wear gloves when handling with EtBr. In addition, there are other safer alternatives can be used such as GelRed, which is able to bind to the minor groove.  It has UV absorbance maxima at 300 and 360nm, also able to absorb energy from nucleotides excited at 260nm. The absorbed energy is emitted as orange/yellow light at 590nm.

 

Furthermore, it is important to mix loading buffers with mix DNA as they are visible under natural light (as opposed to UV light for EtBr stained DNA). Bromophenol blue are common dyes can be found in loading buffers. Illuminator apparatus can be used for flurorescent dye for taking the image after illuminated with UV radiation. The DNA appear in the gel as reddish-orange as it has intercalated with DNA. Next, the gel can be photographed by using a digital or polaroid camera, the image normally shown in black and white.

 

On the other hand, the most common used for visualization in SDS-PAGE is Coomassie Brilliant Blue, was first described by the German scientist Volker Neuhoff. It is an anionic dye, which is high sensitivity, low background (protein will be detected as blue), large linear range, and ease of use. Unbound Coomassie Blue absorbs light maximally at a wavelength of 465 nm, while the absorption maximum is at 595 nm when the dye is bound to protein. The two kinds of the Coomassie dyes are R-250 and G-250.