CAN ENERGY-TRANSFER BE AN INDICATOR FOR DNA INTERCALATION

Contact energy transfer from DNA bases to various ligands, which can b e represented by the ratio of the fluorescence intensity Q(lambda)/Q(3 10nm), is measured by conventional fluorometer. 4',6-Diamidino-2-pheny lindole and -(4-methyl-1-piperazinyl)-2,5'-bi-1H-benzimidazole can acc ept energy from DNA bases and exhibit the ratio Q(lambda)/Q(310nm), si milar to that of intercalators, although these molecules are known to bind preferentially to the minor groove of the adenine-thymine rich re gion of DNA. When porphyrin is intercalated in DNA or poly[d(G-C)(2)], the shape of the ratio Q(lambda)/Q(310nm) is distinct from that of th e ethidium-DNA complex with two maxima at 250 nm and 280 nm. The ratio Q(lambda)/Q(310nm) of the porphyrin-poly[d(A-T)(2)] complex, in which porphyrin is known to bind 'outside' of the DNA stem, is similar to t hat of intercalators. Therefore, energy from excited DNA bases can be transferred not only to an intercalated ligand through direct contact but also to that bound in the minor groove. It follows from this obser vation that using energy transfer as a criterion for DNA intercalation requires extreme caution.