Q8 — Ethidium Bromide — DNA Binding and Intercalation

Theoretical 1 Real exam question — full text reproduced under IBO's CC BY-NC-SA 4.0 license

DNA Structure & Replication Nucleotide & Nucleic Acid Chemistry

Ethidium bromide is a fluorescent dye which can intercalate into double-stranded DNA (Figure 1), resulting in a sharp increase in the fluorescence intensity of ethidium bromide. Ethidium bromide can bind to and intercalate in DNA in different ways (Figure 2).

Figure 1. Ethidium bromide structure and its binding to DNA. Figure 1. Ethidium bromide and its binding to DNA.

Figure 2. Four modes of ethidium bromide binding to DNA, labelled A–D. Figure 2. Modes of binding of ethidium bromide to DNA. A — minor groove binding. B — intercalation of ethidium bromide into DNA. C — stacking on the terminal base pairs and insertion mode in DNA. D — major groove intercalation between DNA and minor groove binding.

Using Figures 1 and 2, determine whether the following statements are true or false:

A. The study of complexes between ethidium bromide and DNA allows for the detection of major structural DNA damage caused by different stressful situations.

B. When ethidium bromide is intercalated into a DNA molecule, the base pairs move away from each other to make space for the inserted molecule.

C. In the intercalation shown in Figure 2B, the bases are displaced by overexertion while simultaneously the helix contracts along its axis. This ensures the DNA sugar-phosphate backbone does not rupture during the overexertion.

D. The plane of the intercalated ethidium bromide molecule is approximately parallel to the axis of the DNA helix and perpendicular to the plane of the bases.

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Question reproduced from IBO 2022, Theoretical Paper 1, licensed under CC BY-NC-SA 4.0 — attributed to the International Biology Olympiad. Open the full exam PDF · Community solutions (unofficial)