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Ethidium bromide (or homidium bromide, [2] chloride salt homidium chloride) [3] [4] is an intercalating agent commonly used as a fluorescent tag (nucleic acid stain) in molecular biology laboratories for techniques such as agarose gel electrophoresis.
The preparation of EtBr stands as a model for the synthesis of bromoalkanes in general. It is usually prepared by the addition of hydrogen bromide to ethene: H 2 C=CH 2 + HBr → H 3 C-CH 2 Br. Bromoethane is inexpensive and would rarely be prepared in the laboratory.
An agarose gel cast in tray, to be used for gel electrophoresis. Agarose gel is a three-dimensional matrix formed of helical agarose molecules in supercoiled bundles that are aggregated into three-dimensional structures with channels and pores through which biomolecules can pass. [3]
Apart from acting as the synthetic equivalent of an ethyl anion synthon for nucleophilic addition, ethylmagnesium bromide may be used as a strong base to deprotonate various substrates such as alkynes: [1]
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The chemicals used in most northern blots can be a risk to the researcher, since formaldehyde, radioactive material, ethidium bromide, DEPC, and UV light are all harmful under certain exposures. [11] Compared to RT-PCR, northern blotting has a low sensitivity, but it also has a high specificity, which is important to reduce false positive results.
Molecules other than proteins can be separated by 2D electrophoresis. In supercoiling assays, coiled DNA is separated in the first dimension and denatured by a DNA intercalator (such as ethidium bromide or the less carcinogenic chloroquine) in the second. This is comparable to the combination of native PAGE/SDS-PAGE in protein separation.
SYBR Green I is marketed as a replacement for ethidium bromide, a potential human mutagen, as both safer to work with and free from the complex waste disposal issues of ethidium bromide. However any small molecule capable of binding DNA with high affinity is a possible carcinogen , including SYBR Green.