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How does one visualize DNA on an agar gel?

Last updated date: 21st Jun 2024
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Hint: Gel electrophoresis also known as submarine or horizontal electrophoresis. Nucleic acids are usually visualized by adding ethidium bromide directly to agarose gel or by dipping agarose gel in dye. Ethidium bromide is embedded between the bases of the DNA molecule.

Complete answer:
Agarose gel electrophoresis is a highly efficient and simple method for the isolation, identification and purification of DNA fragments. Separation is carried out under an electric field applied to a gel matrix. Since phosphate is negatively charged in the spine, DNA molecules migrate to the anode.
Migration rate of a linear DNA fragment is inversely proportional to its molecular weight ratio. The separation of the DNA molecule is very much based on size. The smallest fragments are constantly moving in the gel because they can move through the small pores in the gel compared to the larger molecules.
In each of these electrophoresis techniques, the position of DNA or RNA fragments in the gel can be detected by various methods. Ethidium bromide staining-One common method is the addition of ethidium bromide, a stain that is introduced to a non-specific site in nucleic acids and can be made visible when exposed to ultraviolet light.
EtBr is intercalated in the main DNA channel and fluoresces under UV light. The intercalation depends on the DNA concentration and therefore the high intensity band shows more DNA than the low intensity band. then stained after electrophoresis.
UV light excites electrons in the ethidium bromide aromatic ring, and once they return to their ground state, light is released, causing DNA and ethidium bromide to glow.

EtBr is an aromatic molecule and has heterocyclic units. Due to the intercalation properties of EtBr, it is used as an intercalation agent in molecular biology. Although EtBr is the most popular In gel DNA electrophoresis, it also has important uses in cytogenetics. As the EtBr concentration increases, the fluorescence intensity increases.
Ethidium bromide stacks between the double-stranded DNA bases, we can't identify the single-stranded DNA from EtBr. PCR products and other genomic DNA were visualized and identified using EtBr during electrophoresis. DNA also visualized by autoradiography.