1H-NMR studies of a monointercalating drug into a d(CpGpApTpCpG)2 minihelix

The structure of the complex formed between the 7H-pyridocarbazole monomer [[(2-piperidyl)-2,1-ethane-yl] [10-methoxy-7H-pyrido[4,3-c]carbazolium] dimethane sulfonate] and the autocomplementary hexanucleotide d(CpGpApTpCpG)2 in aqueous solution is analyzed by 270- and 400-MHz 1H-nmr. The large upfield shifts observed for both the drug and the self-complementary hexanucleotide protons provide evidence for intercalated complexes. The observation of intermolecular nuclear Overhauser effects between drug and the hexanucleotide protons gives a privileged orientation of the drug in the intercalation site with the quaternarizing ethyl piperidine chain protruding in the major groove. Moreover, the data suggest an intercalation based on the neighbor exclusion site principle in the three alternating sequences.