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 ch aracterized 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 molecul ar plane perpendicular to the helix axis, probably partially intercala ted from the major groove. The conclusions are supported by fluorescen ce quenching results. Together with the earlier established minor groo ve binding mode of DAPI in the AT regions, our results demonstrate a h eterogeneous nature of the interaction of a small ligand with DNA. We conclude that the conventional classification of a ligand as being eit her intercalator, minor groove binder, or major groove binder may not be adequate since the mode of binding clearly depends also on the base sequence.