Photocrosslinking Probes Proximity of Thymine Modifiers Tethering Excitonically Coupled Dye Aggregates to DNA Holliday Junction

• Published in: Molecules (Basel, Switzerland) Vol. 27; no. 13; p. 4006
• Main Authors: Basu, Shibani, Cervantes-Salguero, Keitel, Yurke, Bernard, Knowlton, William B., Lee, Jeunghoon, Mass, Olga A.
• Format: Journal Article
• Language: English
• Published: Basel MDPI AG 22.06.2022; MDPI
• Subjects: Aggregates; Configurations; Cycloaddition; Deoxyribonucleic acid; dimer; DNA; DNA probes; Dyes; Electrophoresis; exciton; excitonic coupling; Excitons; Kasha; Optoelectronics; Polyacrylamide; Proximity; Quantum computing; squaraine; Tethering; Thermal stability; Thymine
• ISSN: 1420-3049; 1420-3049
• DOI: 10.3390/molecules27134006

A DNA Holliday junction (HJ) has been used as a versatile scaffold to create a variety of covalently templated molecular dye aggregates exhibiting strong excitonic coupling. In these dye-DNA constructs, one way to attach dyes to DNA is to tether them via single long linkers to thymine modifiers incorporated in the core of the HJ. Here, using photoinduced [2 + 2] cycloaddition (photocrosslinking) between thymines, we investigated the relative positions of squaraine-labeled thymine modifiers in the core of the HJ, and whether the proximity of thymine modifiers correlated with the excitonic coupling strength in squaraine dimers. Photocrosslinking between squaraine-labeled thymine modifiers was carried out in two distinct types of configurations: adjacent dimer and transverse dimer. The outcomes of the reactions in terms of relative photocrosslinking yields were evaluated by denaturing polyacrylamide electrophoresis. We found that for photocrosslinking to occur at a high yield, a synergetic combination of three parameters was necessary: adjacent dimer configuration, strong attractive dye–dye interactions that led to excitonic coupling, and an A-T neighboring base pair. The insight into the proximity of dye-labeled thymines in adjacent and transverse configurations correlated with the strength of excitonic coupling in the corresponding dimers. To demonstrate a utility of photocrosslinking, we created a squaraine tetramer templated by a doubly crosslinked HJ with increased thermal stability. These findings provide guidance for the design of HJ-templated dye aggregates exhibiting strong excitonic coupling for exciton-based applications such as organic optoelectronics and quantum computing.