Summary & Purpose
Molecular excitons play a foundational role in chromophore aggregates found in light-harvesting systems and offer potential applications in engineered excitonic systems. Controlled aggregation of chromophores to promote exciton delocalization has been achieved by covalently tethering chromophores to deoxyribonucleic acid (DNA) scaffolds. Although many studies have documented changes in the optical properties of chromophores upon aggregation using DNA scaffolds, more limited work has investigated how structural modifications of DNA via bridged nucleotides and chromophore covalent attachment impact scaffold stability as well as the configuration and optical behavior of attached aggregates. Here we investigated the impact of two types of bridged nucleotides, LNA and BNA, as a structural modification of duplex DNA-templated cyanine (Cy5) aggregates. The bridged nucleotides were incorporated in the domain of one to four Cy5 chromophores attached between adjacent bases of a DNA duplex. We found that bridged nucleotides increase the stability of DNA scaffolds carrying Cy5 aggregates in comparison with natural nucleotides in analogous constructs. Exciton coupling strength and delocalization in Cy5 aggregates were evaluated via steady-state absorption, circular dichroism, and theoretical modeling. Replacing natural nucleotides with bridged nucleotides resulted in a noticeable increase in the coupling strength (≥10 meV) between chromophores and increased H-like stacking behavior (i.e., more face-to-face stacking). Our results suggest that bridged nucleotides may be useful for increasing scaffold stability and coupling between DNA templated chromophores.
Date of Publication or Submission
This research was supported wholly by the U.S. Department of Energy, Idaho National Laboratory, Laboratory Directed Research and Development project through blanket master contract 154754 between Battelle Energy Alliance and Boise State University, Release 15, except for the following: the circular dichroism spectrometer was made available through the Biomolecular Research Center (BRC) supported by NIH awards P20GM103408 and P20GM109095, the MJ Murdock Charitable Trust, and the Idaho State Board of Education. Molecular graphics images in Figure 6 were produced by using the UCSF Chimera package from the Resource for Biocomputing, Visualization, and Informatics at the University of California, San Francisco (supported by NIH P41 RR-01081) All authors have given approval to the final version of the manuscript.
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Roy, Simon K. and Knowlton, William B., "Dataset for Exciton Delocalization and Scaffold Stability in Bridged Nucleotide-Substituted, DNA Duplex-Templated Cyanine Aggregates" (2023). Quantum DNA Research Group Data. 1.