Roy Simon K, Olaso Nolan, Davis Paul H, Mass Olga A, Cervantes-Salguero Keitel, Lee Jeunghoon, Pensack Ryan D, Hall John A, Yurke Bernard, Knowlton William B
Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, USA.
Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, USA.
Nanoscale. 2025 Aug 1. doi: 10.1039/d5nr00863h.
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 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.
分子激子是以波的形式在多种染料上离域的激发态，在包括量子信息科学在内的广泛应用中备受关注。众多研究已将多种合成染料模板化到DNA支架上，以诱导染料聚集，从而在光激发时产生分子激子。染料聚集体的光学性质严重依赖于染料的相对几何结构和局部环境；因此，理解染料 - 染料以及DNA - 染料相互作用对于推进更复杂的DNA - 染料系统至关重要。被广泛研究的DNA霍利迪连接体（HJ）和较少研究的双交叉（DX）瓦片基序是设计复杂且最终模块化的DNA - 染料结构的基础测试平台。在此，我们报告了首次关于单链方酸菁染料在比HJ更大且更稳定的DX瓦片基序上的聚集和激子离域的研究。我们首先重点介绍一些支持具有独特光学性质的单染料和聚集体的DNA - 染料构建体，这些光学性质可通过样品设计、缓冲条件和热处理进行调节，并且对环境变化具有鲁棒性，包括转移到固相。接下来，我们评估了几个实验和设计考量因素，这些因素证明了新型双瓦片DNA构型的定向染料驱动组装。我们的结果表明，模板化到DX瓦片上的单链方酸菁染料为设计和评估支持激子离域的染料聚集体网络提供了一条可行的研究途径。我们在此首次报告了DNA - 染料构建体在固相中激子离域的情况。此外，我们的研究结果表明染料聚集会影响DNA - 染料构建体的组装，并且在某些情况下，会与DNA协同作用以确定最终稳健的系统构型。最后，我们表明可以采用可控的退火程序来促进DNA - 染料构建体的均匀组装。本研究中的发现有助于理解DNA - 染料系统以及其定向组装过程中涉及的相关因素，以实现具有理想性质的特定构建体。
