EtBr binds to DNA at:
Ethidium bromide exhibits two binding modes to DNA. Primary high-affinity interaction involves intercalation between adjacent base pairs, causing helix unwinding and lengthening. Secondary electrostatic interaction occurs in minor groove where phenanthridinium ring contacts phosphate backbone. Crystallographic and spectroscopic studies indicate preferential residence in minor groove environment with partial intercalation, enhancing fluorescence quantum yield. Major groove binding is less favored due to steric hindrance. Sugar backbone and phosphate alone do not account for fluorescence enhance
Ref: NCERT Biology Class XII Principles on Klenow fill-in labeling, Lehninger Chapter 9 DNA cloning techniques, and Molecular Cloning by Sambrook Chapter 10 documenting end-labeling of cohesive termini.
