Sugar pucker geometries at the intercalation site of propidium diiodide into miniature RNA and DNA duplexes in solution.

We have evaluated the sugar pucker geometry at the intercalation site of propidium diiodide into the self-complementary dinucleoside monophosphate duplexes cytidylylguanosine and deoxycytidylyldeoxyguanosine as a function of the nucleotide/drug ratio in aqueous solution. Our solution results support the observation by Sobell and coworkers [Sobell, H.M., Tsai, C.C., Jain, S.C. & Gilbert, S.G. (1977) J. Mol. Biol. 114, 333--365] of a C3' endo (3'-5')C2' endo sugar pucker geometry in the 2:2 intercalation complex of ethidium bromide into the iodocytidylylguanosine duplex in the crystalline state. We demonstrate further that the mixed sugar pucker observed for the intercalation of propidium diiodide into the miniature RNA duplex in solution persists in the intercalative complex of this trypanocidal drug into the corresponding miniature DNA duplex in solution.