Spontaneous Assembly of Helical Cyanine Dye Aggregates on DNA Nanotemplates

3,3'-Diethylthiadicarbocyanine (DiSC2(5)) is a symmetrical cationic cyanine dye consisting of two N-ethylated benzothiazole groups linked by a pentamethine bridge. Spectroscopic analysis indicates dimerization of the dye in the presence of duplex DNA sequences consisting of alternating adenine/thymine (A/T) or inosine/cytosine (I/C) residues, based on the following observations: (i) the absorption maximum shifts from 647 to 590 nm, (ii) exciton splitting is observed in the induced circular dichroism spectrum, and (iii) fluorescence from the dye is strongly quenched. Dimerization on I/C, but not G/C sequences indicates that the cyanine dimers insert into the minor groove, a conclusion that is supported by viscometric analysis. Spectroscopic studies with short synthetic oligonucleotide duplexes demonstrate that dimerization is highly cooperative: binding of one dimer greatly facilitates binding of a second dimer. For longer binding sites, this cooperativity leads to the formation of extended helical cyanine dye aggregates consisting of dimers aligned in an end-to-end fashion within the minor groove of the DNA. The DNA structure strictly controls the dimensions of the aggregate, permitting distinction between inter- and intradimer interactions.