Role of Ethidium bromide in agarose gel electrophoresis and Cytogenetics

The role of EtBr in agarose electrophoresis is to intercalate with DNA and helps in the identification of DNA fragments. Yet, it plays a significant role in cytogenetics as well. In this article, We will discuss the role of EtBr in molecular genetics and cytogenetics.

Ethidium bromide is commonly used as a nucleic acid tagging agent in life science research. However, during the mid 19th century, EtBr was used as an anti-trapynosomal drug in cattle.

It was believed that it can kill the mitochondrial DNA, named kinetoplast (kDNA) and prevent cattle from the Trypanosoma infection. Still, the role of EtBr was unclear in killing kDNA.

Chemical name: Ethidium bromide

Abbreviation: EtBr, etbr, EB

Chemical formula: C21H20N3Br

Molecular weight: 394.4

Colour emission: orange

The image represents the structure of EtBr.

EtBr is an aromatic molecule and has a heterocyclic moiety. Due to the intercalating property of EtBr, it is used as an intercalating agent in molecular biology. Majorly, the EtBr is most popular in gel electrophoresis of DNA. However, it has routinely used in cytogenetics too.

We have covered an entire series on agarose gel electrophoresis. please read all the articles here,

  1. DNA gel loading dye
  2. Agarose gel electrophoresis buffer
  3. Agarose gel electrophoresis

Role of EtBr in gel electrophoresis

Agarose gel electrophoresis is routinely used in the separation of molecules like DNA, RNA and protein. Under the influence of constant current, the negatively charged DNA migrates toward the positive charge.

The fragments of DNA is separated into gel metrics based on the size of DNA fragments. Nonetheless, DNA does not have its own colour, hence it is impossible to visualize DNA without any colour.

EtBr work as a separating agent in agarose gel electrophoresis. EtBr intercalates between DNA base pairs and emits fluorescence under UV light. With the use of a standard orange filter, it emits orange colour at 470nm wavelength. 

Read an interesting article: Role of alcohol in DNA extraction

EtBr contains the tricyclic phenanthridine ring system. This ring interacts with the hydrophobic interior of the DNA bases with the strong van der walls bond. Approximately one EtBr molecule will binds per 2.5 base pairs of DNA.

The hydrophobic environment present in between the basepairs increases the intensity of the fluorescence. Water is a highly efficient quencher of fluorescent. After intercalating between base pairs, under the hydrophobic environment,  the EtBr removes water as it moves away from the buffer and emits fluorescence, increasingly.

The image represents the intercalation of EtBr in DNA base pairs


Additionally, as the concentration of EtBr increases the intensity of fluorescence will increase. The standard concentration of EtBr for gel electrophoresis is 0.5μg/ml for 50ml of gel.

EtBr is used for the identification of PCR products specifically the double-stranded DNA. Single-stranded DNA can also be visualised by EtBr.

Likewise, It is used for the identification of genomic DNA, restriction digestion products and RNA identification.

Intercalated EtBr changes several properties of DNA such as mobility, molecular weight and even the charge of DNA.

Sigmon J and Larcom LL in 1966, was studied the effect of EtBr intercalation on double-stranded DNA. They used the different concentration of EtBr for the same fragment of DNA and each time as the concentration of EtBr increases the mobility of DNA fragment decreases. 

You can read their research paper here: The effect of ethidium bromide on the mobility of DNA fragments in agarose gel electrophoresis.

Their finding suggests that intercalated EtBr alters the conformational and physical properties of DNA. In spite of that, it is mostly used for DNA confirmation studies (whether the fragment of our interest is presented or not) in Genetics.

Two different methods are used for addition of EtBr:

  • Direct addition of EtBr into the gel
  • Staining of the gel by EtBr

The first method is widely accepted across all molecular laboratories. 

The required amount of agarose is dissolved into the buffer and boiled until a clear solution is obtained (all agarose is dissolved). After the temperature become touchable, EtBr can be added to the gel.

Read further on our PCR related articles,

  1. Function of taq DNA polymerase in PCR
  2. PCR primer design guidelines
  3. Role of MgCl2 in PCR reaction

In spite of the wide acceptance of this method, it has several common problems.

The activity of EtBr decreases at high temperature. Hence the fluorescence level can decrease. Additionally, if the agarose solution becomes colder quickly EtBr cannot be spread evenly into the gel.

In the second method, after the completion of a gel run, the gel is overnight stained with the mild solution of EtBr. This method is time-consuming and not recommended because of the carcinogenic nature of EtBr.

Role of EtBr in cytogenetic

“A study of chromosome structure, function and location are called as cytogenetics”. The metaphase chromosome is visualized for the identification of structural or numerical anomalies in chromosomes.

Traditionally, the Cytogenetic analysis is a widely accepted method for detection of major anomalies such as Turner Syndrome, Klinefelter Syndrome, Down Syndrome and Patau Syndrome.

The role of EtBr is very crucial in the identification of chromosomes i.e in karyotyping. The normal metaphase chromosomal plates are applicable for identification of numerical chromosomal abnormalities. Yet, we cannot identify smaller deletion or translocation.

Generally, metaphase chromosomes are more condensed as compare to other stages of cell division. Addition of EtBr releases the condensation of the chromosome and chromosome appears longer than the normal size.

Therefore it is easy to identify smaller deletions or addition. This technique is called as high-resolution banding. The number of the bands increases by the addition of EtBr before harvesting the chromosomes.

The image represents the elongated chromosomes and normal chromosomes.

 The chromosomes are cultured for 72 hours and then it is harvested. A couple of hours before harvesting (around ~70th hour), the EtBr can be added.

The EtBr intercalates between the base pairs as explained above and hinder in the condensation process of DNA. Because of that, the protein which packs DNA compactly cannot fold DNA properly. 

The loosely packed DNA makes the chromosome appear longer and the size of the band increases. As the numbers of bands increase the accuracy of the result will increases.

However, some scientist believes that EtBr does not have any significant role in the elongation of the chromosome.

Shinichi Misawa, in 1986 proposed a finding that EtBr does have an important role in chromosomal elongation.  Cultured human bone marrow cells are treated with different doses of EtBr before two hours of harvesting.

When compared without the EtBr culture results, the yield of the result was increased by 2.9 folds and more than 400 bands per haploid cells were achieved by the addition of 10 μg/ml of EtBr.

EtBr treatment resulted in increasing the length of the chromosome by decreasing the condensation of the chromosome. Further, it increases the quality of chromosome in high-resolution banding.

We have covered an article on the condensation process of a chromosome and DNA packaging. Read the article here,

DNA packaging in eukaryotes

Limitations of EtBr

  • EtBr is fluorescent dye and has less shelf life.
  • As it can bind with DNA, it is mutagenic.
  • EtBr is carcinogenic and teratogenic in nature. However, the carcinogenic property of EtBr is not proven. It affects through inhalation, skin absorption and ingestion. 
  • It can not be used for longer times as its activity decreases over a period of time.

My ultimate guide for the handling of EtBr

EtBr is carcinogenic, teratogenic and mutagenic in nature. We should follow some safety guideline while handling EtBr.

  • Always prefer to use liquid and ready to use EtBr solution.
  • While using EtBr, always wear gloves, glasses and a lab coat. Do not touch any of your body parts while handing EtBr.
  • Always wear goggles during the addition of EtBr and during the analysis of gel under UV light.
  • Discard gloves after handling EtBr.
  • Do not dispose of EtBr with regular chemicals. It is highly mutagenic and carcinogenic therefore place it in a separate sealed container and follow waste disposal management guideline for EtBr or do as indicated by manufactures protocol.

Indeed, the role of Etbr in molecular genetics and cytogenetics is significant. I personally prefer to use EtBr during Karyotyping and I always get good quality of karyograms. Next time when you will perform Karyotyping add EtBr at 70th hour of culture and believe me you will get good results.

Sybr Green is the best alternative of EtBr and it is safe as compared with EtBr. However, Sybr Green cannot be useful in karyotyping. So if you are working on molecular genetics and cytogenetics, the EtBr will be the best cost-effective option for you.

Article written by: Tushar Chauhan

Article reviewed by: Binal tailor