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

Optical spectroscopic properties of 4',6-diamidino-2-phenylindole (DAPI) an d ethidium bromide complexed with poly(dG). poly(dC) poly(dC)(+) tripler an d poly(dG). poly(dC) duplex were compared in this study. When complexed wit h both duplex and tripler, ethidium is characterized by hypochromism and a red shift in the absorption spectrum, a complicate induced circular dichroi sm (CD) band in the polynucleotide absorption region, and a negative reduce d linear dichroism signal in both polynucleotide and drug absorption region s. The spectral properties for both duplex- and tripler-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 tripler diff er from those of the DAPI-duplex complex, although both complexes can be un derstood by the intercalation binding mode. Considering that the third stra nd 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. (C) 2001 El sevier Science B.V. All rights reserved.