Effect of ethidium bromide on deoxyribonucleic acid internal motions.

We have used 31P and 1H NMR to show that DNA internal motions are stopped or greatly hindered when ethidium bromide intercalates into DNA. We show that the effect is localized to a 2 base pair long DNA region at the binding site and that internal motions outside the binding site are nearly unaffected. Based upon the nearly independent behavior of bound and free DNA regions, we conclude that in B-DNA individual base pairs experience internal motion which is independent of the motion of their neighbors.