Fig. 1. Electronic structure of dimer aggregates, dye structures and schematics, and proposed packing arrangements for SQ and SR dimers templated in a DNA Holliday junction.

a Energy-level diagrams for an excitonically coupled dimer, where G, E’, and E” denote ground, low-lying, and high-lying excitonic states, respectively. Solid and dashed horizontal lines indicate optically accessible and inaccessible states, respectively. Adjacent to each state is a schematic of the associated dye transition dipole moment orientations. Colored, gray, and black arrows indicate optical absorption transitions, non-radiative transitions, and transitions to the ground state, respectively. b Representative structures for an SQ dye, a rotaxane ring, and an SR composite molecule. The exact chemical structures of the SQ dye and SR composite molecule are proprietary. The SQ structure (left) can be aniline-based, where six-membered rings are bound to the central squarate moiety, or it can incorporate substituents such as indolenines, where a five-membered ring is conjugated with the central squarate moiety via a methine bridge. The rotaxane ring (middle) forms hydrogen bonds with the squarate moiety via its amide groups. The rotaxane ring is visualized as a red toroid shape. The SR (right) represents a composite molecule combining the SQ dye and a rotaxane ring. Both SQ and SR dyes are tethered to the DNA backbone via an amide bond between the dye and a non-nucleosidic serinol linker (Supplementary Note 1). c Proposed packing for dimers of SQs and SRs templated using a four-armed DNA Holliday junction. Dashed boxes separately highlight the H-aggregate packing proposed for the SQ dimer and the oblique aggregate packing proposed for the SR dimer. Note that the schematic is primarily intended to depict the proposed aggregate packing arrangements, not the conformation of the specific DNA Holliday junction.