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Binding of the frameshift mutagen ethidium bromide to eight dinucleoside phosphates of different complementary base sequences, to trinucleoside diphosphates with mismatched bases capable of forming bulged structures (CpUpG and GpUpG + CpC), and to calf thymus DNA at different counterion concentrations was studied by optical methods, notably UV-visible spectroscopy, circular dichroism (CD), and fluorescence-detected circular dichroism (FDCD). The ethidium ion intercalated between the base pairs of the minihelix formed by the complementary dimers and displaced the mismatched bases to form bulged structures with the trimers. The stoichiometry of the complexes was 2:1 oligonucleotide:dye (or 1:1:1 for non-self-complementary species). Equilibrium constants for complex formation showed a general preference for dye binding to complementary sequences. Above 300 nm, where only the dye absorbs light, the induced CD spectra of the complexes had bands at 510, 375, 330, and 307 nm, with the magnitude of the 307-nm band, per bound dye, being the largest and sequence dependent. The CD spectra down to 220 nm of some complexes were obtained by FDCD measurements; between 220 and 300 nm, both the positions and the magnitudes of the bands were sequence dependent. At very low ionic strength, complexes of calf thymus DNA plus ethidium ion inmore » different salt concentrations showed that the 307-nm CD magnitude increased with decreasing counterion concentration. Implications of the results for theories of the induced CD spectrum of the ethidium ion are discussed.« less

Structural effects on the circular dichroism of ethidium ion nucleic acid complexes