Structural Insight into a Sixteen Cyanine Dye Construct via Exciton–Exciton Annihilation

Molecular (dye) aggregates play a prominent role in light harvesting and are of interest in quantum information science; however, there are limited reports that programmably assemble many (>4) dye aggregates featuring strong coupling and exciton delocalization. Using oligonucleotides with four Cy5s covalently linked in series along the phosphate backbone, we bring 4, 8, and 16 Cy5s in close proximity by assembling four-armed junctions. We elucidate their structure via gel electrophoresis and steady-state and transient optical spectroscopy. We find that Cy5 has a strong propensity to form tetramer clusters, where the exciton is delocalized over all 4 Cy5s, that the exciton is not delocalized beyond tetramer clusters in the 8 and 16 Cy5 constructs, and that the 16 Cy5 construct may consist of pairs of tetramer clusters that are isolated from one another. Many-dye aggregates such as these may serve useful as antennae for their intense light absorption and spatially directed energy transfer.