Unusual binding of ethidium to a deoxyoligonucleotide containing a B-Z junction

Equilibrium binding studies are reported that describe the interaction of the simple intercalator ethidium with a hexadecadeoxynucleotide (BZ-1) that contains a stable B-Z junction. The transition of BZ-1 from its low-salt right-handed form to its high-salt hybrid form containing the junction between left- and right-handed DNA was found to greatly facilitate ethidium binding. Ethidium binding to all conformational forms of BZ-1 was found to be complex and highly cooperative, a result that indicates an unusually robust conformational mobility in the molecule. Binding results were quantitatively analyzed by using an allosteric model that provides a description of energetics of the conformational transitions in BZ-1, in addition to estimates of the binding constants for ethidium binding to the different conformations. These results provide a quantitative description of a structurally specific intercalator-DNA interaction.