Ethidium bromide

Last updated
Ethidium bromide
Ethidium bromide.svg
Ethidium-bromide-from-monohydrate-xtal-1971-3D-balls-B.png
Ethidium-bromide-monohydrate-xtal-1971-3D-SF.png
Names
Preferred IUPAC name
3,8-Diamino-5-ethyl-6-phenylphenanthridin-5-ium bromide
Other names
  • 2,7-Diamino-10-ethyl-6-phenylphenanthridinium bromide
  • 2,7-Diamino-10-ethyl-9-phenylphenanthridinium bromide
  • 3,8-Diamino-1-ethyl-6-phenylphenantridinium bromide
  • 5-Ethyl-6-phenyl-phenanthridine-3,8-diamine bromide
  • Ethidium bromide
  • Homidium bromide
  • EtBr
  • EthBr
Identifiers
3D model (JSmol)
3642536
ChEBI
ChEMBL
ChemSpider
ECHA InfoCard 100.013.622 OOjs UI icon edit-ltr-progressive.svg
EC Number
  • 214-984-6
KEGG
PubChem CID
RTECS number
  • SF7950000
UNII
UN number 2811
  • InChI=1S/C21H19N3.BrH/c1-2-24-20-13-16(23)9-11-18(20)17-10-8-15(22)12-19(17)21(24)14-6-4-3-5-7-14;/h3-13,23H,2,22H2,1H3;1H Yes check.svgY
    Key: ZMMJGEGLRURXTF-UHFFFAOYSA-N Yes check.svgY
  • InChI=1/C21H19N3.BrH/c1-2-24-20-13-16(23)9-11-18(20)17-10-8-15(22)12-19(17)21(24)14-6-4-3-5-7-14;/h3-13,23H,2,22H2,1H3;1H
    Key: ZMMJGEGLRURXTF-UHFFFAOYAD
  • CC[n+]1c2cc(N)ccc2c3ccc(N)cc3c1c4ccccc4.[Br-]
Properties
C21H20BrN3
Molar mass 394.294 g/mol
AppearancePurple-red solid
Melting point 260 to 262 °C (500 to 504 °F; 533 to 535 K)
~40 g/l
Pharmacology
QP51DX03 ( WHO )
Hazards [1]
GHS labelling:
GHS-pictogram-skull.svg GHS-pictogram-silhouette.svg
Danger
H302, H330, H341
P201, P202, P260, P284, P301+P312, P304+P340+P310
NFPA 704 (fire diamond)
NFPA 704.svgHealth 4: Very short exposure could cause death or major residual injury. E.g. VX gasFlammability 1: Must be pre-heated before ignition can occur. Flash point over 93 °C (200 °F). E.g. canola oilInstability 0: Normally stable, even under fire exposure conditions, and is not reactive with water. E.g. liquid nitrogenSpecial hazards (white): no code
4
1
0
Flash point >100 °C (212 °F; 373 K)
Except where otherwise noted, data are given for materials in their standard state (at 25 °C [77 °F], 100 kPa).
Yes check.svgY  verify  (what is  Yes check.svgYX mark.svgN ?)

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. It is commonly abbreviated as EtBr, which is also an abbreviation for bromoethane. To avoid confusion, some laboratories have used the abbreviation EthBr for this salt. When exposed to ultraviolet light, it will fluoresce with an orange colour, intensifying almost 20-fold after binding to DNA. Under the name homidium, it has been commonly used since the 1950s in veterinary medicine to treat trypanosomiasis in cattle. [5] The high incidence of antimicrobial resistance makes this treatment impractical in some areas, where the related isometamidium chloride is used instead. Despite its reputation as a mutagen, tests have shown it to have low mutagenicity without metabolic activation. [6] [7]

Contents

Structure, chemistry, and fluorescence

Absorption spectrum of ethidium bromide Ethidium-bromide-abs.png
Absorption spectrum of ethidium bromide

As with most fluorescent compounds, ethidium bromide is aromatic. Its core heterocyclic moiety is generically known as a phenanthridine, an isomer of which is the fluorescent dye acridine. Absorption maxima of EtBr in aqueous solution are at 210 nm and 285 nm, which correspond to ultraviolet light. As a result of this excitation, EtBr emits orange light with wavelength 605 nm. [8] [9]

Ethidium bromide's intense fluorescence after binding with DNA is probably not due to rigid stabilization of the phenyl moiety, because the phenyl ring has been shown to project outside the intercalated bases. In fact, the phenyl group is found to be almost perpendicular to the plane of the ring system, as it rotates about its single bond to find a position where it will impinge upon the ring system minimally. Instead, the hydrophobic environment found between the base pairs is believed to be responsible. By moving into this hydrophobic environment and away from the solvent, the ethidium cation is forced to shed any water molecules that were associated with it. As water is a highly efficient fluorescence quencher, the removal of these water molecules allows the ethidium to fluoresce.[ citation needed ]

Applications

DNA sample separated using gel electrophoresis of nucleic acids and stained with ethidium bromide, which emits orange light after binding to DNA AgarosegelUV.jpg
DNA sample separated using gel electrophoresis of nucleic acids and stained with ethidium bromide, which emits orange light after binding to DNA

Ethidium bromide is commonly used to detect nucleic acids in molecular biology laboratories. In the case of DNA this is usually double-stranded DNA from PCRs, restriction digests, etc. Single-stranded RNA can also be detected, since it usually folds back onto itself and thus provides local base pairing for the dye to intercalate. Detection typically involves a gel containing nucleic acids placed on or under an ultraviolet lamp. Since ultraviolet light is harmful to eyes and skin, gels stained with ethidium bromide are usually viewed indirectly using an enclosed camera, with the fluorescent images recorded as photographs. Where direct viewing is needed, the viewer's eyes and exposed skin should be protected. In the laboratory the intercalating properties have long been used to minimize chromosomal condensation when a culture is exposed to mitotic arresting agents during harvest. The resulting slide preparations permit a higher degree of resolution, and thus more confidence in determining structural integrity of chromosomes upon microscopic analysis.[ citation needed ]

Ethidium bromide is also used during DNA fragment separation by agarose gel electrophoresis. [10] It is added to running buffer and binds by intercalating between DNA base pairs. When the agarose gel is illuminated using UV light, DNA bands become visible. Intercalation of EtBr can alter properties of the DNA molecule, such as charge, weight, conformation, and flexibility. Since the mobilities of DNA molecules through the agarose gel are measured relative to a molecular weight standard, the effects of EtBr can be critical to determining the sizes of molecules. [11]

Ethidium bromide has also been used extensively to reduce mitochondrial DNA copy number in proliferating cells. [12] The effect of EtBr on mitochondrial DNA is used in veterinary medicine to treat trypanosomiasis in cattle, as EtBr binds molecules of kinetoplastid DNA and changes their conformation to the Z-DNA form. This form inhibits replication of kinetoplastid DNA, which is lethal for trypanosomes. [13]

The chloride salt homidium chloride has the same applications. [3] [4]

Ethidium bromide can be added to YPD media and used as an inhibitor for cell growth. [14]

The binding affinity of the cationic nanoparticles with DNA could be evaluated by competitive binding with ethidium bromide. [15] [16]

Alternatives for gel

There are alternatives to ethidium bromide which are advertised as being less dangerous and having better performance. [17] [18] For example, several SYBR-based dyes are used by some researchers and there are other emerging stains such as "Novel Juice". SYBR dyes are less mutagenic than EtBr by the Ames test with liver extract. [19] However, SYBR Green I was actually found to be more mutagenic than EtBr to the bacterial cells exposed to UV (which is used to visualize either dye). [20] This may be the case for other "safer" dyes, but while mutagenic and toxicity details are available [21] these have not been published in peer-reviewed journals. The MSDS for SYBR Safe reports an LD50 for rats of over 5 g/kg, which is higher than that of EtBr (1.5 g/kg). Many alternative dyes are suspended in DMSO, which has health implications of its own, including increased skin absorption of organic compounds. [19] Despite the performance advantage of using SYBR dyes instead of EtBr for staining purposes, many researchers still prefer EtBr since it is considerably less expensive.[ citation needed ]

Possible carcinogenic activity

Ethidium bromide intercalated between two adenine-thymine base pairs. The intercalation is said by some to motivate a high mutagenicity of DNA. DNA intercalation2.jpg
Ethidium bromide intercalated between two adenine–thymine base pairs. The intercalation is said by some to motivate a high mutagenicity of DNA.

Most use of ethidium bromide in the laboratory (0.25–1 μg/mL) is below the LD50 dosage, making acute toxicity unlikely. Testing in humans and longer studies in a mammalian system would be required to fully understand the long-term risk ethidium bromide poses to lab workers, but it is clear that ethidium bromide can cause mutations in mammalian and bacterial cells. [22]

Handling and disposal

Ethidium bromide is not regulated as hazardous waste at low concentrations, [23] but is treated as hazardous waste by many organizations. Material should be handled according to the manufacturer's safety data sheet (SDS).[ citation needed ]

The disposal of laboratory ethidium bromide remains a controversial subject. [24] Ethidium bromide can be degraded chemically, or collected and incinerated. It is common for ethidium bromide waste below a mandated concentration to be disposed of normally (such as pouring it down a drain). A common practice is to treat ethidium bromide with sodium hypochlorite (bleach) before disposal. [25] According to Lunn and Sansone, chemical degradation using bleach yields compounds which are mutagenic by the Ames test. Data are lacking on the mutagenic effects of degradation products. Lunn and Sansone describe more effective methods for degradation. [26] Elsewhere, ethidium bromide removal from solutions with activated charcoal or ion exchange resin is recommended. [27] Various commercial products are available for this use. [28]

Drug resistance

Trypanosomes in the Gibe River Valley in southwest Ethiopia showed universal resistance between July 1989 and February 1993. [29] This likely indicates a permanent loss of function in this area against the tested target, T. congolense isolated from Boran cattle. [29]

See also

Related Research Articles

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Agarose gel electrophoresis is a method of gel electrophoresis used in biochemistry, molecular biology, genetics, and clinical chemistry to separate a mixed population of macromolecules such as DNA or proteins in a matrix of agarose, one of the two main components of agar. The proteins may be separated by charge and/or size, and the DNA and RNA fragments by length. Biomolecules are separated by applying an electric field to move the charged molecules through an agarose matrix, and the biomolecules are separated by size in the agarose gel matrix.

<span class="mw-page-title-main">Agarose</span> Heteropolysaccharide found in red algae

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<span class="mw-page-title-main">Gel electrophoresis</span> Method for separation and analysis of biomolecules

Gel electrophoresis is an electrophoresis method for separation and analysis of biomacromolecules and their fragments, based on their size and charge through a supportive medium. It is used in clinical chemistry to separate proteins by charge or size and in biochemistry and molecular biology to separate a mixed population of DNA and RNA fragments by length, to estimate the size of DNA and RNA fragments or to separate proteins by charge.

<span class="mw-page-title-main">Polyacrylamide gel electrophoresis</span> Analytical technique

Polyacrylamide gel electrophoresis (PAGE) is a technique widely used in biochemistry, forensic chemistry, genetics, molecular biology and biotechnology to separate biological macromolecules, usually proteins or nucleic acids, according to their electrophoretic mobility. Electrophoretic mobility is a function of the length, conformation, and charge of the molecule. Polyacrylamide gel electrophoresis is a powerful tool used to analyze RNA samples. When polyacrylamide gel is denatured after electrophoresis, it provides information on the sample composition of the RNA species.

<span class="mw-page-title-main">Gel electrophoresis of nucleic acids</span>

Gel electrophoresis of nucleic acids is an analytical technique to separate DNA or RNA fragments by size and reactivity. Nucleic acid molecules are placed on a gel, where an electric field induces the nucleic acids to migrate toward the positively charged anode. The molecules separate as they travel through the gel based on the each molecule's size and shape. Longer molecules move more slowly because the gel resists their movement more forcefully than it resists shorter molecules. After some time, the electricity is turned off and the positions of the different molecules are analyzed.

<span class="mw-page-title-main">Gel electrophoresis of proteins</span> Technique for separating proteins

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<span class="mw-page-title-main">DAPI</span> Fluorescent stain

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In molecular biology, gel extraction or gel isolation is a technique used to isolate a desired fragment of intact DNA from an agarose gel following agarose gel electrophoresis. After extraction, fragments of interest can be mixed, precipitated, and enzymatically ligated together in several simple steps. This process, usually performed on plasmids, is the basis for rudimentary genetic engineering.

<span class="mw-page-title-main">Propidium iodide</span> Chemical compound

Propidium iodide is a fluorescent intercalating agent that can be used to stain cells and nucleic acids. PI binds to DNA by intercalating between the bases with little or no sequence preference. When in an aqueous solution, PI has a fluorescent excitation maximum of 493 nm (blue-green), and an emission maximum of 636 nm (red). After binding DNA, the quantum yield of PI is enhanced 20-30 fold, and the excitation/emission maximum of PI is shifted to 535 nm (green) / 617 nm (orange-red). Propidium iodide is used as a DNA stain in flow cytometry to evaluate cell viability or DNA content in cell cycle analysis, or in microscopy to visualize the nucleus and other DNA-containing organelles. Propidium Iodide is not membrane-permeable, making it useful to differentiate necrotic, apoptotic and healthy cells based on membrane integrity. PI also binds to RNA, necessitating treatment with nucleases to distinguish between RNA and DNA staining. PI is widely used in fluorescence staining and visualization of the plant cell wall.

<span class="mw-page-title-main">Electrophoretic mobility shift assay</span> Technique used to study DNA and RNA

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<span class="mw-page-title-main">SYBR Green I</span> Dye used for molecular genetics

SYBR Green I (SG) is an asymmetrical cyanine dye used as a nucleic acid stain in molecular biology. The SYBR family of dyes is produced by Molecular Probes Inc., now owned by Thermo Fisher Scientific. SYBR Green I binds to DNA. The resulting DNA-dye-complex best absorbs 497 nanometer blue light and emits green light. The stain preferentially binds to double-stranded DNA, but will stain single-stranded (ss) DNA with lower performance. SYBR Green can also stain RNA with a lower performance than ssDNA.

<span class="mw-page-title-main">Electrophoretic color marker</span>

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<span class="mw-page-title-main">Fluorescence in the life sciences</span> Scientific investigative technique

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<span class="mw-page-title-main">Gel doc</span>

A gel doc, also known as a gel documentation system, gel image system or gel imager, refers to equipment widely used in molecular biology laboratories for the imaging and documentation of nucleic acid and protein suspended within polyacrylamide or agarose gels. Genetic information is stored in DNA. Polyacrylamide or agarose gel electrophoresis procedures are carried out to examine nucleic acids or proteins in order to analyze the genetic data. For protein analysis, two-dimensional gel electrophoresis is employed (2-DGE) which is one of the methods most frequently used in comparative proteomic investigations that can distinguish thousands of proteins in a single run. Proteins are separated using 2-DGE first, based on their isoelectric points (pIs) in one dimension and then based on their molecular mass in the other. After that, a thorough qualitative and quantitative analysis of the proteomes is performed using gel documentation with software image assessment methods on the 2-DGE gels stained for protein visibility. Gels are typically stained with Ethidium bromide or other nucleic acid stains such as GelGreen.

<span class="mw-page-title-main">GelRed</span> DNA gel stain for molecular genetics

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<span class="mw-page-title-main">GelGreen</span> DNA gel stain for molecular genetics

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References

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  7. ↑ "Ethidium Bromide: Swap or Not | UCSB Sustainability". sustainability.ucsb.edu. Retrieved 2023-02-08.
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  29. 1 2 Mulugeta W, Wilkes J, Mulatu W, Majiwa PA, Masake R, Peregrine AS (April 1997). "Long-term occurrence of Trypanosoma congolense resistant to diminazene, isometamidium and homidium in cattle at Ghibe, Ethiopia". Acta Tropica. 64 (3–4). Elsevier: 205–217. doi:10.1016/s0001-706x(96)00645-6. PMID   9107367. S2CID   23878484.
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