Tunable and robust optical and structural properties of a cooperative squaraine-dye aggregate-DNA DX-DAE tile system†

Molecular excitons, which are excitations delocalized over multiple dyes in a wavelike manner, are of interest for a wide range of applications, including quantum information science. Numerous studies have templated a variety of synthetic dyes via a DNA scaffold to induce dye aggregation to create molecular excitons upon photoexcitation. Dye aggregate optical properties are critically dependent on relative dye geometry and local environment; therefore, an understanding of dye–dye and DNA–dye interactions is critical for advancing toward more complex DNA–dye systems. The extensively studied DNA Holliday junction (HJ) and less-studied double-crossover (DX) tile motif are fundamental test beds for designing complex and ultimately modular DNA–dye architectures. Here, we report the first study of single-linked squaraine dye aggregation and exciton delocalization on a larger and more stable (compared with the HJ) DX tile motif. We first highlight a few DNA–dye constructs that support single dyes and aggregates with distinct optical properties that are both tunable—through sample design, buffer conditions, and heat treatment—and robust to environment changes, including transfer to solid phase. Next, we assess several experimental and design considerations that demonstrate directed dye-driven assembly of a novel double-tile DNA configuration. Our results demonstrate that single-linked squaraine dyes templated to DX tiles provide a viable research path to design and evaluate dye aggregate networks that support exciton delocalization. We include herein the first report of exciton delocalization in the solid phase in a DNA–dye construct. Additionally, our findings indicate that dye aggregation impacts the assembly of the DNA–dye construct, and, in some cases, thereby cooperates with the DNA to determine a final robust system configuration. Finally, we show that a controlled annealing schedule can be employed to promote the homogeneous assembly of DNA–dye constructs. The findings in this study contribute to the understanding of DNA–dye systems and the relevant factors involved in their directed assembly to achieve specific constructs with desirable properties.