Ethidium bromide
IUPAC name	3,8-Diamino-5-ethyl-6-phenylphenanthridinium 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
Identifiers
CAS number	[1239-45-8]
PubChem	14710
EINECS number	214-984-6
KEGG	C11161
RTECS number	SF7950000
SMILES	[Br-].CC[n+]3c4cc(N)ccc4c1ccc(N)cc1c3c2ccccc2
Properties
Molecular formula	C21H20BrN3
Molar mass	394.308 g/mol
Appearance	Purple-red solid
Melting point	260 - 262 °C Image File history File links This is a lossless scalable vector image. ... IUPAC nomenclature is a system of naming chemical compounds and of describing the science of chemistry in general. ... CAS registry numbers are unique numerical identifiers for chemical compounds, polymers, biological sequences, mixtures and alloys. ... PubChem is a database of chemical molecules. ... The EINECS number (for European Inventory of Existing Chemical Substances) is a registry number given to each chemical substance commercially available in the European Union between 1 January 1971 and 18 September 1981. ... KEGG PATHWAY Database is one of the important databases in bioinformatics. ... RTECS, also known as Registry of Toxic Effects of Chemical Substances, is a database of toxicity information compiled from the open scientific literature that is available for charge. ... The simplified molecular input line entry specification or SMILES is a specification for unambiguously describing the structure of chemical molecules using short ASCII strings. ... This article or section does not cite any references or sources. ... Molar mass is the mass of one mole of a chemical element or chemical compound. ... The melting point of a crystalline solid is the temperature at which it changes state from solid to liquid. ...
Solubility in water	~ 40 g/l
Hazards
NFPA 704	Solubility refers to the ability for a given substance, the solute, to dissolve in a solvent. ... Impact from a water drop causes an upward rebound jet surrounded by circular capillary waves. ... NFPA 704 is a standard maintained by the U.S. National Fire Protection Association. ... Image File history File links NFPA_704. ... 0 2 0
R-phrases	R36/37/38, R46
S-phrases	S22, S24/25, S26, S36/37/39, S45, S53
Flash point	> 100 °C
Except where noted otherwise, data are given for materials in their standard state (at 25 °C, 100 kPa) Infobox disclaimer and references

Absorption spectrum of ethidium bromide

Ethidium bromide (sometimes abbreviated as EtBr) is an intercalating agent commonly used as a nucleic acid stain in molecular biology laboratories for techniques such as agarose gel electrophoresis. When exposed to ultraviolet light, it will fluoresce with a red-orange color, intensifying almost 20-fold after binding to DNA. Ethidium bromide is a very strong mutagen, and may possibly be a carcinogen or teratogen. R-phrases are defined in Annex III of European Union Directive 67/548/EEC: Nature of special risks attributed to dangerous substances and preparations. ... S-phrases are defined in Annex IV of European Union Directive 67/548/EEC: Safety advice concerning dangerous substances and preparations. ... The flash point of a flammable liquid is the lowest temperature at which it can form an ignitable mixture with air. ... In chemistry, the standard state of a material is its state at 1 bar (100 kilopascals) and 25 degrees Celsius (298. ... Image File history File links Size of this preview: 800 × 535 pixelsFull resolution (1665 × 1114 pixel, file size: 78 KB, MIME type: image/png) 200. ... Image File history File links Size of this preview: 800 × 535 pixelsFull resolution (1665 × 1114 pixel, file size: 78 KB, MIME type: image/png) 200. ... Intercalation induces structural distortions. ... Look up nucleic acid in Wiktionary, the free dictionary. ... Staining is a biochemical technique of adding a class-specific (DNA, proteins, lipids, carbohydrates) dye to a substrate to qualify or quantify the presence of a specific compound. ... Molecular biology is the study of biology at a molecular level. ... Digital image of 3 plasmid restriction digests run on a 1% w/v agarose gel, 3 Volts/cm, stained with ethidium bromide. ... Note: Ultraviolet is also the name of a 1998 UK television miniseries about vampires. ... Fluorescence induced by exposure to ultraviolet light in vials containing various sized Cadmium selenide (CdSe) quantum dots. ... The structure of part of a DNA double helix Deoxyribonucleic acid (DNA) is a nucleic acid that contains the genetic instructions for the development and function of living organisms. ... In biology, a mutagen (Latin, literally origin of change) is a physical or chemical agent that changes the genetic information (usually DNA) of an organism and thus increases the number of mutations above the natural background level. ... The hazard symbol for carcinogenic chemicals in the Globally Harmonized System. ... Teratogenesis is a medical term from the Greek, literally meaning monster making. ...

Structure, chemistry, fluorescence

As with most fluorescent compounds, it is aromatic. The main portion of the molecule is a tricyclic structure with aniline (aminobenzene) groups on either side of a pyridine (a six-atom, nitrogen-containing, aromatic ring). The dibenzopyridine structure is known as a phenanthridine. A chemical compound is a chemical substance of two or more different chemically bonded chemical elements, with a fixed ratio determining the composition. ... In chemistry, an aromatic molecule is one in which electrons are free to cycle around circular arrangements of atoms, which are alternately singly and doubly bonded to one another. ... Aniline, phenylamine or aminobenzene (C6H5NH2) is an organic chemical compound which is a primary aromatic amine consisting of a benzene ring and an amino group. ... Pyridine is a chemical compound with the formula C5H5N. It is a liquid with a distinctively putrid odour. ...

The reason for 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 abut 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 fluorescent quencher, the removal of these water molecules allows the ethidium to fluoresce. In chemistry, the phenyl group or phenyl ring (often abbreviated as -Ph) is the functional group with the formula -C6H5 Picture where the six carbon atoms are arranged in a cyclic manner. ... Look up moiety in Wiktionary, the free dictionary. ... In chemistry, hydrophobic or lipophilic species, or hydrophobes, tend to be electrically neutral and nonpolar, and thus prefer other neutral and nonpolar solvents or molecular environments. ... In chemistry, hydrophobic or lipophilic species, or hydrophobes, tend to be electrically neutral and nonpolar, and thus prefer other neutral and nonpolar solvents or molecular environments. ...

Applications

Ethidium bromide is commonly used to detect nucleic acids in the lab. 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 a UV lamp. Since ultraviolet light is harmful to eyes and skin, a camera is used for recording ethidium bromide fluorescence. In other cases, a protective screen is put between the observer and the UV source. In the cytogenetic laboratory the intercalating properties have long been utilized to minimize chromosomal condensation when a culture exposed to mitotic arresting agents during harvest. The resulting slide preparations permit a higher degree of resolution and thus confidence, in determining structural integrity of chromosomes upon microscopic analysis. Highly simplified diagram of a double-stranded nucleic acid. ... The structure of part of a DNA double helix Deoxyribonucleic acid (DNA) is a nucleic acid that contains the genetic instructions for the development and function of living organisms. ... Wikipedia does not yet have an article with this exact name. ... A restriction digest is a molecular biology procedure used to prepare DNA for analysis or other processing. ... Ribonucleic acid (RNA) is a nucleic acid polymer consisting of nucleotide monomers, that acts as a messenger between DNA and ribosomes, and that is also responsible for making proteins out of amino acids. ... Base pairs, of a DNA molecule. ... Digital image of 3 plasmid restriction digests run on a 1% w/v agarose gel, 3 Volts/cm, stained with ethidium bromide. ... “UV” redirects here. ... Fluorescence induced by exposure to ultraviolet light in vials containing various sized Cadmium selenide (CdSe) quantum dots. ...

Alternatives

There are alternatives to ethidium bromide in the lab. ^[1] Several SYBR or or SYBR Safe stains are used by some as a safer alternative. SYBR dyes have been found to be less carcinogenic than EtBr and to give cleaner, higher powered staining. However, they are suspended in DMSO which can rapidly pass through skin. ^{[2] [3]}. However, many researchers still prefer ethidium bromide for difficult detections. Note that Sigma-Aldrich claims a similar detection limit for the SYBR stain.^[4] Chemical Structure of SYBR Green I Spectrogram of SYBR Green I SYBR Green I (SG) is an asymmetrical cyanine dye used as a nucleic acid stain in molecular biology. ... Dimethyl sulfoxide (DMSO) is the chemical compound (CH3)2SO. This colorless liquid is an important dipolar aprotic solvent. ... Sigma-Aldrich Corporation NASDAQ: SIAL, headquartered in St. ...

Health hazard

Ethidium bromide is strongly mutagenic and is irritating to the eyes, skin, mucous membranes and upper respiratory tract^{[citation needed]}. The health effects of ethidium bromide exposure have not been thoroughly investigated. It is suspected to be carcinogenic and teratogenic because of its mutagenicity, although there is no direct evidence of either effect. The toxic effects of ethidium bromide may be experienced if swallowed, inhaled or absorbed through the skin. However ethidium bromide is not easily absorbed through the skin because of positive charge and bulky structure. In biology, a mutagen (Latin, literally origin of change) is a physical or chemical agent that changes the genetic information (usually DNA) of an organism and thus increases the number of mutations above the natural background level. ... Health effects, health impacts or health risks are an important consideration in many areas, such as hygiene, pollution studies, workplace safety, nutrition and health sciences in general. ... In pathology, a carcinogen is any substance or agent that promotes cancer. ... Teratogenesis is a medical term from the Greek, literally meaning monster making. ...

Ethidium bromide is thought to act as a mutagen because it intercalates into double stranded DNA, thereby deforming the molecule. This is believed to block or trip biological processes occurring on DNA, like DNA replication and transcription. In biology, a mutagen (Latin, literally origin of change) is a physical or chemical agent that changes the genetic information (usually DNA) of an organism and thus increases the number of mutations above the natural background level. ... The structure of part of a DNA double helix Deoxyribonucleic acid (DNA) is a nucleic acid that contains the genetic instructions for the development and function of living organisms. ... It has been suggested that DNA replicate, Replisome, Replication fork, Lagging strand, Leading strand be merged into this article or section. ... A micrograph of ongoing gene transcription of ribosomal RNA illustrating the growing primary transcripts. ...

Safe handling

Preparation of stock solutions and any operations capable of generating ethidium bromide dust or aerosols should be conducted in a fume hood to prevent inhalation. Gloves should be worn at all times. Latex gloves offer little protection from ethidium bromide – gloves made of nitrile rubber are much more effective. When working with high concentrations (stocks or powder) or for a prolonged period of time, double gloving can further reduce the risk of exposure, especially if the outer glove is replaced whenever significantly contaminated. Nitrile rubber is a synthetic rubber co-polymer of acrylonitrile (ACN) and butadiene. ...

Spills or personal exposure

As with most any chemical, if spilled on skin or eyes, rinse for 15 minutes using a safety shower or eyewash. If inhaled or swallowed, seek medical attention immediately.

For spills, use a spill pillow or absorbent to soak up aqueous ethidium bromide. Carefully clean up solid ethidium bromide to avoid creating dusts. Place in a sealable container and dispose in a medical waste box.

Waste disposal

Ethidium bromide should be handled and disposed of as HAZARDOUS waste. This applies to gloves, test tubes, paper towels, etc., that are grossly contaminated with ethidium bromide as well. All ethidium bromide waste should be considered state regulated hazardous waste.

See also

• Amino group
• Ethyl group
• Phenyl group
• Phenanthridine
• Agarose gel electrophoresis

In chemistry, especially in organic chemistry and biochemistry, an amino group is an ammonia-like functional group. ... In chemistry, an ethyl group is an alkyl functional group derived from ethane (C2H6). ... The structure of the phenyl group In chemistry, the phenyl group or phenyl ring (often abbreviated as -Ph) is the functional group with the formula -C6H5 where the six carbon atoms are arranged in a cyclic ring structure. ... Digital image of 3 plasmid restriction digests run on a 1% w/v agarose gel, 3 Volts/cm, stained with ethidium bromide. ...

References

1. ^ Dean Madden, Safer stains for DNA. accessed 2007-01-31.
2. ^ Huang Q, Fu WL. Comparative analysis of the DNA staining efficiencies of different fluorescent dyes in preparative agarose gel electrophoresis. Clin Chem Lab Med. 2005;43(8):841-2. PMID 16201894
3. ^ Invitrogen, Using SYBR Safe DNA Gel Stain accessed 3 Oct 2006.
4. ^ Sigma-Aldrich, SYBR® Green I nucleic acid gel stain, accessed 3 Oct 2006.

Sigma-Aldrich Corporation NASDAQ: SIAL, headquartered in St. ...

External links

• Borst P. Ethidium DNA agarose gel electrophoresis: how it started. IUBMB Life. 2005 Nov;57(11):745-7. PMID 16511967

• Links to external chemical sources