Ethidium bromide

CA Index Name Phenanthridinium, 3,8-diamino-5-eth-yl-6-phenyl-, bromide (1 1) 

Other Names 3,8-Diamino-5-ethyl-6-phenylphenan-thridinium bromide Phenanthridinium, 3,8-diamino-5-ethyl-6-phenyl-, bromide 2,7-Diamino-lO-ethyl-9-phe-nylphenanthridinium bromide 2,7-Diamino-9-phenyl-10-ethylphenanthridinium bromide 2,7-Diamino-9-phe-nylphenanthridine ethobromide Eiromilac Ethidium bromide Homidium bromide Merck Index Number 4731 

Chemical/Dye Class Phenanthridine Molecular Formula C2iH2oBrN3 Molecular Weight 394.31 Physical Form Dark red crystals 

Solubility Soluble in water, chloroform, dimethyl sulfoxide, ethanol 

Emission (Xmax) 605 nm, 620 nm Synthesis Synthetic methods Staining Applications Nucleic acids  

LABORATORY CHEMICAL SAFETY SUMMARY ETHIDIUM BROMIDE  

Substance Ethidium bromide (Dromilac, homidium bromide) CAS 1239-45-8 

Physical Properties Dark red crystals mp 260 to 262 °C Soluble in water (5 g/100 mL) 

Flammability and Explosibility Ethidium bromide does not pose a flammability hazard (NFPA rating = 1). 

Storage and Handling Ethidium bromide should be handled in the laboratory using the basic prudent practices described in Chapter 5.C. Because of its mutagenicity, stock solutions of this compound should be prepared in a fume hood, and protective gloves should be worn at aU times while handling this substance. Operations capable of generating ethidium bromide dust or aerosols of ethidium bromide solutions should be conducted in a fume hood to prevent exposure by inhalation. 

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As an alternative to radiation, a stain such as ethidium bromide is used to visualize DNA. The ethidium may be incorporated into the stmcture of DNA either before or after electrophoresis. The gel is then visualized under a fluorescent lamp. 

The mechanism of interaction with DNA is suggested. Ethidium bromide (EB) displacement assay was performed. We determine the binding constant of Tb-E to DNA to be in the order of Ig K = 6.47 0.4. The bathochromic and hypsochromic effects in the absorption spectra of investigated complex were observed and the interaction is assumed to be mainly of the mono-intercalating type. 

Deoxyribonucleic acid (from plasmids). Purified by two buoyant density ultracentrifugations using ethidium bromide-CsCl. The ethidium bromide was extracted with Et20 and the DNA was dialysed against buffered EDTA and lyophilised. [Marmur and Doty J Mol Biol 5 109 1962 Guerry et al. J Bacteriol II6 1064 1973.] See p. 504. 

Aromatic macrocycles, flat hydrophobic molecules composed of fused, heterocyclic rings, such as ethidium bromide, acridine orange, and actinomycin D... 

The most commonly used dye in fluorescence studies on nucleic acids is ethidium bromide. The dye has broad excitation bands centered around 280 and 460 nm and a strong emission around 600 nm. When the dye hinds to DNA by an intercalative mechanism, its emission is greatly enhanced and slightly shifted in wavelength. In the simplest case with ethidium bromide saturating intercalating sites,... 

The sensitivity of the fluorescence methods varies considerably with the instrument used. Advances in modern instrumentation and the power of today s computers allow for a much improved sensitivity. Using commercially available instruments and modern computers equipped with appropriate software, detection limits down to 10 pg of calf thymus DNA can be achieved using ethidium bromide. (We have achieved such levels using several Perkin-Elmer MPF66 Instruments at various locations.)... 

It should be pointed out that when using ethidium bromide the sensitivity of the assays varies depending on the physical state of the nucleic acids (see Table I). Ethidium does not discriminate between RNA and DNA, although dyes are available which bind DNA exclusively, so the relative amounts of each may be determined by taking two sets of measurements. Alternatively, nucleases (DNA-ase or RNA-ase) can be used to exclusively remove one or the other in a mixture. Nucleic acids from different sources (see Table II) also show a variation in sensitivity, and the fluorescence assay lacks the selectivity of the hybridization technique. Nevertheless, for rapid screening or quality-control applications the fluorescence assay is still the method of choice. 

Cariello, N., Keohavong, P., Sanderson, B., Thilly, W. DNA damage produced by ethidium bromide staining and exposure to ultraviolet light. Nucleic Acids Research, Vol. 16, No.9, (May 1988), pp. 4157-4161, ISSN 0305-1048... 

DNA has also been tested as a carrier for ethidium bromide, a drug used in the treatment of protozoal diseases. When compared with free drug, the DNA-bound drug showed decreased toxicity and higher therapeutic efficacy in mice infected with Trypanosoma cruzi [231]. 

Intercalators with asymmetric substituents, such as the phenyl and ethyl groups of ethidium bromide (21), frequently cause a smaller increase in DNA length than expected from the simple model described above. In such cases these groups are inserted into the minor groove of the DNA helix with concomitant bending of the double helix towards the major groove. This alternative type of complexation is supported by X-ray studies on model systems, 25). 

The permeability coefficient of 2.6x 10 locm/s at 296 K measured by Deamer is sufficient to supply the enzyme in the liposomes with ADP. How could it be shown that RNA formation actually does take place in the vesicles The increase in the RNA synthesis was detected by observing the fluorescence inside the vesicles. In the interior of the liposomes, the reaction rate is only about 20% of that found for the free enzyme, which shows that the liposome envelope does limit the efficiency of the process. The fluorescence measurements were carried out with the help of ethidium bromide, a fluorescence dye often used in nucleic acid chemistry. 

BioMarker products for accurate sizing of dsDNA bands over different ranges, with nine bands of equal ethidium bromide intensity. 

DNA molecules on gel are stained with ethidium bromide and observed using epi-fluorescent microscopy. 

Several complexes that involve intercalation of an acridine in a portion of a nucleic acid have been studied by X-ray crystallographic techniques. These include complexes of dinucleoside phosphates with ethidium bromide, 9-aminoacridine, acridine orange, proflavine and ellipticine (65-69). A representation of the geometry of an intercalated proflavine molecule is illustrated in Figure 6 (b) this is a view of the crystal structure of proflavine intercalated in a dinucleoside phosphate, cytidylyl- -S ) guano-sine (CpG) (70, TV). For comparison an example of the situation before such intercalation is also illustrated in Figure 6 (a) by three adjacent base pairs found in the crystal structure of a polynucleotide (72, 73). In this latter structure the vertical distance (parallel to the helix axis) between the bases is approximately... 

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