Spontaneous assembly of helical cyanine dye aggregates on DNA nanotemplates

3,3'-Diethylthiadicarbocyanine (DiSC(2)(5)) is a symmetrical cationic cyani ne dye consisting of two N-ethylated benzothiazole groups linked by a penta methine bridge. Spectroscopic analysis indicates dimerization of the dye in the presence of duplex DNA sequences consisting of alternating adenine/thy mine (AIT) or inosine/cytosine (I/C) residues, based on the following obser vations: (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 g roove, a conclusion that is supported by viscometric analysis. Spectroscopi c studies with short synthetic oligonucleotide duplexes demonstrate that di merization is highly cooperative: binding of one dimer greatly facilitates binding of a second dimer. For longer binding sites, this cooperativity lea ds to the formation of extended helical cyanine dye aggregates consisting o f dimers aligned in an end-to-end fashion within the minor groove of the DN A. The DNA structure strictly controls the dimensions of the aggregate, per mitting distinction between inter- and intradimer interactions.