Excitonically Coupled Cyanine Dye Dimers as Optical Energy Transfer Relays on DNA Templates

An attractive strategy to improve the energy transfer properties of synthetic dye networks is to optimize the excitonic coupling between the dyes to increase the energy transfer rates. To explore this possibility, we investigated the use of J-like cyanine dye dimers (Cy3 and Cy5 dimers) on DNA duplexes as energy transfer relays in molecular photonic wires. This approach is based on the use of the collective emission dipole of a J-dimer to enhance the FRET rate between the dimer relay and a remote acceptor dye. Experimentally, we find that in room temperature aqueous buffer conditions, the dimer relay provided no benefit in the energy transfer quantum yield relative to a simple monomer relay. Further investigation led us to determine that enhanced nonradiative relaxation, non-ideal dye orientation within the dimer, and unfavorable dye orientation between the dimer and the acceptor dye limit energy transfer through the dimer relay. We hypothesized that nonradiative relaxation was the largest factor and demonstrated this by placing the sample in a viscous solvent or by cooling the sample, which dramatically improved the energy transfer through the J-like dimer relay. Similar to how the formation of DNA-templated J-like dimers has improved, the practical use of J-like dimers to optimize energy transfer quantum efficiency will require improvements in the ability to control the orientation between dyes to reach its full potential.