How does ethidium bromide interact with duplex DNA at the molecular level?

Introduction / Context:
Ethidium bromide is a classical fluorescent dye used to visualize DNA. Understanding its interaction with DNA explains both its staining properties and its mutagenic potential.

Given Data / Assumptions:

• Analyte: duplex DNA.
• Ligand: ethidium bromide (planar polycyclic compound).

Concept / Approach:
Ethidium bromide intercalates—slides between stacked base pairs—expanding the helical rise and unwinding DNA slightly. Intercalation enhances fluorescence by restricting rotational freedom and shielding the dye from solvent quenching.

Step-by-Step Solution:
1) Consider structural complementarity: a flat aromatic dye fits between base pairs.2) Predict effects: intercalation increases contour length and reduces superhelical density.3) Conclude: the mechanism is intercalation, not specific base or phosphate binding.

Verification / Alternative check:
Viscosity and circular dichroism changes, along with topological experiments, confirm intercalative binding; phosphate-binding agents yield different signatures.

Why Other Options Are Wrong:
Adenine-only binding: inconsistent with non-specific intercalation between any adjacent base pairs.Phosphate binding: typical of cationic groove binders, not ethidium intercalation.No interaction: contradicted by strong fluorescence upon DNA addition.

Common Pitfalls:
Assuming base-specific hydrogen bonding or mistaking groove-binding for intercalation.

Final Answer:
It intercalates between bases