Journal
RSC ADVANCES
Volume 12, Issue 43, Pages 28063-28078Publisher
ROYAL SOC CHEMISTRY
DOI: 10.1039/d2ra05045e
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Funding
- Department of the Navy, Office of Naval Research (ONR), via ONR [N00014-19-1-2615]
- Office of Nuclear Energy of the U.S. Department of Energy
- Nuclear Science User Facilities [DE-AC07-05ID14517]
- U.S. Department of Energy (DoE), Office of Basic Energy Sciences, Division of Materials Science and Engineering through the Established Program to Stimulate Competitive Research (EPSCoR) [DESC0020089]
- NRL
- NRL Institute for Nanoscience
- ONR [770 N0001419WX01811]
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Dye aggregates and their excitonic properties are of interest for various applications, and DNA scaffolding has been effective in promoting controllable dye aggregation. Molecular dynamics simulations show that dye attachment locations on DNA Holliday junctions can affect dye-DNA interactions and resulting dye orientations. Transverse dyes exhibited smaller inter-dye separations and more stacked configurations compared to adjacent dyes.
Dye aggregates and their excitonic properties are of interest for their applications to organic photovoltaics, non-linear optics, and quantum information systems. DNA scaffolding has been shown to be effective at promoting the aggregation of dyes in a controllable manner. Specifically, isolated DNA Holliday junctions have been used to achieve strongly coupled cyanine dye dimers. However, the structural properties of the dimers and the DNA, as well as the role of Holliday junction isomerization are not fully understood. To study the dynamics of cyanine dimers in DNA, molecular dynamics simulations were carried out for adjacent and transverse dimers attached to Holliday junctions in two different isomers. It was found that dyes attached to adjacent strands in the junction exhibit stronger dye-DNA interactions and larger inter-dye separations compared to transversely attached dimers, as well as end-to-end arrangements. Transverse dimers exhibit lower inter-dye separations and more stacked configurations. Furthermore, differences in Holliday junction isomer are analyzed and compared to dye orientations. For transverse dyes exhibiting the smaller inter-dye separations, excitonic couplings were calculated and shown to be in agreement with experiment. Our results suggested that dye attachment locations on DNA Holliday junctions affect dye-DNA interactions, dye dynamics, and resultant dye orientations which can guide the design of DNA-templated cyanine dimers with desired properties.
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