Helical Aggregation of Cyanine Dyes on DNA Templates: Effect of Dye Structure on Formation of Homo- and Heteroaggregates

UV−visible and circular dichroism (CD) spectroscopic experiments were used to characterize DNA-templated helical aggregates formed from a variety of symmetrical, cationic cyanine dyes. Two types of electronic couplings can be observed in these aggregates:  face-to-face interactions between dye monomers and end-to-end interactions between dye dimers. The face-to-face interactions yield approximately 4-fold stronger couplings due to greater orbital overlap. Variation of the heterocyclic groups on the dye reveals that aggregation on DNA follows the following trend:  quinoline > benzothiazole > benzoxazole > dimethylindole. This trend follows the tendency of these dyes to aggregate in aqueous solution. Within the benzothiazole class of dyes, a dicarbocyanine dye (pentamethine bridge) aggregates much more readily than the carbocyanine (trimethine bridge) analogue. However, a tricarbocyanine dye (heptamethine bridge) aggregates less readily than the dicarbocyanine, in contrast to their relative tendency to aggr...