INTERACTION OF 4',6-DIAMIDINO-2-PHENYLINDOLE (DAPI) WITH POLY[D(G-C)2] AND POLY[D(G-M(5)C)2] - EVIDENCE FOR MAJOR GROOVE BINDING OF A DNA PROBE

The interactions of DAPI with poly[d(G-C)2] and poly[d(G-m5C)2] are characterized by optical spectroscopic methods. DAPI is found to bind to poly[d(G-C)2] with its molecular long-axis roughly perpendicular but with its plane more parallel to the belix axis of the polynucleotide, probably being bound in a non-intercalated way in the major groove of the polynucleotide. In poly[d(G-m5C)2], DAPI is bound with its molecular plane perpendicular to the helix axis, probably partially intercalated from the major groove. The conclusions are supported by fluorescence quenching results. Together with the earlier established minor groove binding mode of DAPI in the AT regions, our results demonstrate a heterogeneous nature of the interaction of a small ligand with DNA. We conclude that the conventional classification of a ligand as being either intercalator, minor groove binder, or major groove binder may not be adequate since the mode of binding clearly depends also on the base sequence.