Ethidium bromide is a common intercalating agent used to visualize DNA in electrophoresis gels by associating with the DNA in the gels and fluorescing under UV light to reveal bands. How does ethidium bromide associate with the DNA?

EtBr inserts between the stacked bases in the DNA double helix.

Explanation:

EtBr is used for visualizing DNA bands as it fluoresces under the UV illumination. EtBr is an aromatic compound that is capable of inserting itself between the stacked bases of the DNA double helix. The hydrophobic environment around the base pairs where the EtBr intercalates is responsible for the fluorescence. As the EtBr molecule intercalates between these base pairs the cation of EtBr sheds the water molecules associated with it and this causes it to fluoresce under UV light as water is a quencher of fluorescence.

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