Complex formation between naphthothiopheneethanolamines and deoxyribonucleic acids

Reduced viscosities, viscometric titrations, fluorescence, and flow dichroism measurements indicate that the aromatic ring system of naphthothiopheneethanolamines (NA) is intercalated on binding to DNA. No marked change in binding was found on substituting a dibutylamino group for a piperidyl ring on the side chain. Ionic strength studies, however, did indicate that the positive charge on the side chain is quite important for binding. Both the binding equilibrium constant and the number of binding sites, as determined from a Scatchard plot of spectrophotometric results, decreased on increasing the sodium chloride concentration. The increase in Tm for several DNA samples, caused by adding NA to DNA at a fixed ratio, showed a marked dependence on the percentage of AT base pairs. The conclusion drawn from these data is that the DNA-NA complex involves high specificity of the NA for AT base pairs, intercalation of the aromatic ring system, and binding of the NA side chain in the DNA minor groove with strong interaction between the positively charged side chain and the DNA phosphate groups.