Linear dichroism studies of binding site structures in solution. Complexes between DNA and basic arylmethane dyes

The interaction between B-form DNA and twelve cationic triaryl-methane dyes was studied with respect to optical properties and stabilities, using linear dichroism (LD) and aqueous two-phase partition techniques. Monovalent dyes derived from crystal violet as a rule form a single strong complex (K1 ca 10(5) M-1; site density per nucleotide base n1 ca 0.1 at 0.1M ionic strength) in which the plane of the dye is at an angle of less than 50 degrees to the local DNA helix axis. The complex with fuchsin is weaker (10(4) M-1) but can be explained by a similar orientation. For some of the dyes (those with pseudo-C2v symmetry) the angular orientations of two molecule-fixed axes can be obtained. For the divalent methyl green a second complex appears to be formed at low ionic strength. Methyl green (and to some extent 2-thiophene green and malachite green) show exciton splitting in the LD spectrum and circular dichroism assignable to exciton coupling between transition dipoles roughly parallel to the helical strands, indicating a dye-dye interaction. The optical data, supported by fitting experiments with space-filling models, suggests a general structure for the binding site. The dye is not intercalated but is bound to exposed hydrophobic regions in the major groove. The ligand is in part (the charged amino groups) in contact with the phosphoribose chain but its main surface lies against the hydrophobic base-pair stack. For a diphenylmethane dye, Michler's hydro blue, a perpendicular orientation was observed, possibly due to intercalation.