SIMULTANEOUS AND DIFFERENT BINDING MECHANISMS OF 4',6-DIAMIDINO-2-PHENYLINDOLE TO DNA HEXAMER (D(CGATCG))(2)

The solution structure of the complex between 4',6-diamidino-2-phenyli ndole (DAPI) and DNA oligomer (d(CGATCG))(2) at a 2:1 drug/duplex rati o has been characterized by combined use of proton one- and two-dimens ional NMR spectroscopy, molecular mechanics, and molecular dynamics co mputations. Intermolecular nuclear Overhauser effects (NOEs), DNA stru cture perturbations, and resonance shifts induced by binding provide e vidence that DAPI interacts with DNA hexamer by two different binding mechanisms, in fast exchange on the NMR. time scale, without any signi ficant distortion of the B-type conformation of DNA hexamer, The resul ts indicate that the ligand binds into the minor groove of the central 5'-ATC-3' region of the hexamer and on the outside of the oligomer by a pi pi-stacking interaction with the terminal C1:G6 base pairs, A mo del for both binding mechanisms that accounts for all experimental dat a was generated by molecular mechanics and dynamics calculations based on experimental NOEs, In the minor groove binding, N2 amino group of G2 precludes a deep insertion of phenyl ring of DAPI into the groove, Position and orientation of the drug in the external stacking interact ion resemble those suggested for intercalation of DAPI between C:G bas e pairs.