Binding mode of 4′,6-diamidino-2-phenylindole and ethidium to poly(dG)·poly(dC)·poly(dC)⁺ triplex and poly(dG)·poly(dC) duplex

Optical spectroscopic properties of 4′,6-diamidino-2-phenylindole (DAPI) and ethidium bromide complexed with poly(dG)·poly(dC)·poly(dC)+ triplex and poly(dG)·poly(dC) duplex were compared in this study. When complexed with both duplex and triplex, ethidium is characterized by hypochromism and a red shift in the absorption spectrum, a complicate induced circular dichroism (CD) band in the polynucleotide absorption region, and a negative reduced linear dichroism signal in both polynucleotide and drug absorption regions. The spectral properties for both duplex- and triplex-bound ethidium are identical and both can be understood by the intercalation binding mode. In contrast, the absorption and CD spectra of DAPI complexed with triplex differ from those of the DAPI-duplex complex, although both complexes can be understood by the intercalation binding mode. Considering that the third strand runs along the major groove of the template duplex, we conclude that the DAPI molecule partially intercalates near the major groove of the duplex, where the third strand can affect its spectroscopic properties.