Towards tunable exciton delocalization in DNA Holliday junction-templated indodicarbocyanine 5 (Cy5) dye derivative heterodimers.

We studied the exciton delocalization of indodicarbocyanine 5 dye derivative (Cy5-R) heterodimers templated by a DNA Holliday junction (HJ), which was quantified by the exciton hopping parameter . These dyes were modified at the 5 and 5' positions of indole rings with substituent (R) H, Cl, Bu, Peg, and hexyloxy (Hex) groups that exhibit different bulkiness and electron-withdrawing/donating capacities. The substituents tune the physical properties of the dyes, such as hydrophobicity (log ) and solvent-accessible surface area (SASA). We tuned the of heterodimers by attaching two Cy5-Rs in adjacent and transverse positions along the DNA-HJ. Adjacent heterodimers exhibited smaller compared to transverse heterodimers, and some adjacent heterodimers displayed a mixture of H- and J-like aggregates. Most heterodimers exhibited values within the ranges of the corresponding homodimers, but some heterodimers displayed synergistic exciton delocalization that resulted in larger compared to their homodimers. We then investigated how chemically distinct Cy5-R conjugated to DNA can interact to create delocalized excitons. We determined that heterodimers involving Cy5-H and Cy5-Cl and a dye with larger substituents (bulky substituents and large SASA) such as Cy5-Peg, Cy5-Hex, and Cy5-Bu resulted in larger . The combination provides steric hindrance that optimizes co-facial packing (bulky Cy5-R) with a smaller footprint (small SASA) that maximizes proximity. The results of this study lay a groundwork for rationally optimizing the exciton delocalization in dye aggregates for developing next-generation technologies based on optimized exciton transfer efficiency such as quantum information systems and biomedicine.