{"doi":"10.1039/d5nr00863h","title":"Tunable and robust optical and structural properties of a cooperative squaraine-dye aggregate-DNA DX-DAE tile system","abstract":"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.","journal":"Nanoscale","year":2025,"id":545726,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":1,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9634,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1437451,"name":"Nolan Olaso","orcid":null,"position":1,"is_corresponding":false},{"id":327245,"name":"Paul H. Davis","orcid":"0000-0001-7333-8748","position":2,"is_corresponding":false},{"id":679953,"name":"Olga A. Mass","orcid":"0000-0002-2309-2644","position":3,"is_corresponding":false},{"id":1294679,"name":"Keitel Cervantes‐Salguero","orcid":"0000-0001-8834-8711","position":4,"is_corresponding":false},{"id":679958,"name":"Jeunghoon Lee","orcid":"0000-0002-1909-4591","position":5,"is_corresponding":false},{"id":679961,"name":"Ryan D. Pensack","orcid":"0000-0002-1302-1770","position":6,"is_corresponding":false},{"id":1436998,"name":"John A. Hall","orcid":"0000-0001-8845-4311","position":7,"is_corresponding":false},{"id":679959,"name":"Bernard Yurke","orcid":"0000-0003-3913-2855","position":8,"is_corresponding":false},{"id":679960,"name":"William B. Knowlton","orcid":"0000-0003-3018-2207","position":9,"is_corresponding":false},{"id":679951,"name":"Simon K. Roy","orcid":"0000-0001-8652-1277","position":0,"is_corresponding":true}],"reference_count":83,"raw_metadata":null,"created_at":"2026-07-19T02:53:27.751050Z","pmid":"40748332","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}