Investigation of DNA binding modes for a symmetrical cyanine dye trication: Effect of DNA sequence and structure

The DNA binding behavior of a tricationic cyanine dye (DiSC(3+)(5)) was stu died using the [Poly(dA-dT)](2), [Poly(dI-dC)](2) and Poly(dA)(.)Poly(dT) d uplex sequences and the Poly(dA)(.)2Poly(dT) tripler. Optical spectroscopy and viscometry results indicate that the dye binds to the tripler structure by intercalation, to the nonalternating Poly(dA)(.)Poly(dT) duplex through minor groove binding and to the alternating [Poly(dA-dT)](2) duplex by a c ombination of two binding modes: intercalation at low concentration and dim erization within the minor groove at higher concentration. Dimerization occ urs at lower dye concentrations for the [Poly(dI-dC)](2) sequence, consiste nt with our previous investigations on an analogous monocationic cyanine dy e. [Seifert, J.L., et al. (1999) J. Am. Chem. Sec. 121, 2987-2995] These st udies illustrate the diversity of DNA binding modes that are available to a given ligand structure.