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Ethidium bromide12 (EtBr) remains a widely used dye for the visualization of nucleic acids in agarose gels. It is a phenanthridinium intercalator, structurally similar to propidium iodide. EtBr binds DNA with no apparent sequence preference once every 4–5 base pairs (Waring, 1965). In view of the emergence of SYBR Green and SYBR Gold as realistic alternative methods for staining (discussed below), EtBr is really no longer the best choice. In addition, the issue of when to apply the dye is a source of considerable intralaboratory debate. Not only can EtBr be added to the gel, or used to stain the gel at the conclusion of the electrophoresis, EtBr can be added directly to the RNA sample prior to loading the well(s), and otherwise omitted from the gel itself. This latter approach cuts back on the amount of EtBr waste that is generated, and will limit the fluorescence to the lanes in which a sample is loaded. Briefly, prepare a 1 μg/ml stock of EtBr in nuclease-free water. Add 2 μl of EtBr to 18 μl heat-denatured RNA and mix by pipetting up and down, and then load the gel as usual.

Before electing to use EtBr as a staining tool, it is incumbent upon the investigator to weigh four key disadvantages associated with the use of EtBr into this decision:

1.

Ethidium bromide is a powerful mutagen (MacGregor and Johnson, 1977; Fukunaga et al., 1984). Extreme care must be exercised when preparing and manipulating ethidium bromide stock solutions and dilutions thereof. Thus, contaminated buffers must be treated as toxic waste and equipment likewise treated as such; EtBr must be inactivated and disposed of properly (Appendix E; Lunn and Sansone, 1987; 1990).

2.

The presence of ethidium bromide in a gel or added to samples just prior to loading the gel will retard the electrophoretic migration rate of nucleic acids by about 15%. Although this may not seriously delay the progress of an investigation, it should by no means be used as an excuse to increase the applied voltage to compensate for this phenomenon. Remember that slower-running gels demonstrate enhanced resolution.

3.

Continuous exposure to ambient light or, especially, UV light will nick the RNA, making it difficult to work with. Further, EtBr will quickly experience photobleaching, making visualization and quantitative judgments difficult.

4.

The presence of ethidium bromide in a gel will reduce its transfer efficiency. If a tradi-tional method of transfer is utilized, such as passive capillary diffusion (Chapter 11), the transfer period may need to be extended for unacceptably long periods. Destaining the gel may facilitate transfer, although even minute amounts of ethidium bromide remaining in the gel can result in poor transfer.

The only advantage of running samples in the presence of ethidium bromide is that the progress of electrophoresis can be monitored by disconnecting the power and briefly irradiating the casting tray upon which the gel is resting by placing it directly on a transilluminator or irradiating it from above with a low intensity UV light source (remember eye and skin protection). If greater separation is required, the gel can be placed back in the gel box and the power supply reconnected for a suitable interval.

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Ethidium bromide used as a fluorescent dye to detect DNA/RNA.

It is a mutagen as it inserts between double-stranded DNA and deforms the DNA.

Ethidium bromide is an intercalating agent commonly used as a fluorescent tag (nucleic acid stain) in molecular biology laboratories for techniques such as agarose gel electrophoresis. It is commonly abbreviated as "EtBr", which is also an abbreviation for bromoethane.

https://en.wikipedia.org/wiki/Ethidium_bromide

Please see this useful link.

https://ehs.wisc.edu/wp-content/uploads/sites/25/2017/08/CHM-GUI-003-NEW.pdf