Molecular Dynamic Studies of Dye–Dye and Dye–DNA Interactions Governing Excitonic Coupling in Squaraine Aggregates Templated by DNA Holliday Junctions
Abstract
Dye molecules, arranged in an aggregate, can display excitonic delocalization. The use of DNA scaffolding to control aggregate configurations and delocalization is of research interest. Here, we applied Molecular Dynamics (MD) to gain an insight on how dye–DNA interactions affect excitonic coupling between two squaraine (SQ) dyes covalently attached to a DNA Holliday junction (HJ). We studied two types of dimer configurations, i.e., adjacent and transverse, which differed in points of dye covalent attachments to DNA. Three structurally different SQ dyes with similar hydrophobicity were chosen to investigate the sensitivity of excitonic coupling to dye placement. Each dimer configuration was initialized in parallel and antiparallel arrangements in the DNA HJ. The MD results, validated by experimental measurements, suggested that the adjacent dimer promotes stronger excitonic coupling and less dye–DNA interaction than the transverse dimer. Additionally, we found that SQ dyes with specific functional groups (i.e., substituents) facilitate a closer degree of aggregate packing via hydrophobic effects, leading to a stronger excitonic coupling. This work advances a fundamental understanding of the impacts of dye–DNA interactions on aggregate orientation and excitonic coupling.
- Publication Date:
- Research Org.:
- Boise State Univ., ID (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Basic Energy Sciences (BES). Materials Sciences & Engineering Division; USDOE Office of Nuclear Energy (NE)
- OSTI Identifier:
- 1957860
- Alternate Identifier(s):
- OSTI ID: 1958620
- Grant/Contract Number:
- SC0020089; AC07-05ID14517
- Resource Type:
- Published Article
- Journal Name:
- International Journal of Molecular Sciences (Online)
- Additional Journal Information:
- Journal Name: International Journal of Molecular Sciences (Online) Journal Volume: 24 Journal Issue: 4; Journal ID: ISSN 1422-0067
- Publisher:
- MDPI AG
- Country of Publication:
- Switzerland
- Language:
- English
- Subject:
- 77 NANOSCIENCE AND NANOTECHNOLOGY; excitonic delocalization; molecular dynamics; squaraine dyes; DNA Holliday junctions; dye placement; hydrophobic effects; excitonic coupling; DNA nanotechnology; dye aggregates
Citation Formats
Barcenas, German, Biaggne, Austin, Mass, Olga A., Knowlton, William B., Yurke, Bernard, and Li, Lan. Molecular Dynamic Studies of Dye–Dye and Dye–DNA Interactions Governing Excitonic Coupling in Squaraine Aggregates Templated by DNA Holliday Junctions. Switzerland: N. p., 2023.
Web. doi:10.3390/ijms24044059.
Barcenas, German, Biaggne, Austin, Mass, Olga A., Knowlton, William B., Yurke, Bernard, & Li, Lan. Molecular Dynamic Studies of Dye–Dye and Dye–DNA Interactions Governing Excitonic Coupling in Squaraine Aggregates Templated by DNA Holliday Junctions. Switzerland. https://doi.org/10.3390/ijms24044059
Barcenas, German, Biaggne, Austin, Mass, Olga A., Knowlton, William B., Yurke, Bernard, and Li, Lan. Fri .
"Molecular Dynamic Studies of Dye–Dye and Dye–DNA Interactions Governing Excitonic Coupling in Squaraine Aggregates Templated by DNA Holliday Junctions". Switzerland. https://doi.org/10.3390/ijms24044059.
@article{osti_1957860,
title = {Molecular Dynamic Studies of Dye–Dye and Dye–DNA Interactions Governing Excitonic Coupling in Squaraine Aggregates Templated by DNA Holliday Junctions},
author = {Barcenas, German and Biaggne, Austin and Mass, Olga A. and Knowlton, William B. and Yurke, Bernard and Li, Lan},
abstractNote = {Dye molecules, arranged in an aggregate, can display excitonic delocalization. The use of DNA scaffolding to control aggregate configurations and delocalization is of research interest. Here, we applied Molecular Dynamics (MD) to gain an insight on how dye–DNA interactions affect excitonic coupling between two squaraine (SQ) dyes covalently attached to a DNA Holliday junction (HJ). We studied two types of dimer configurations, i.e., adjacent and transverse, which differed in points of dye covalent attachments to DNA. Three structurally different SQ dyes with similar hydrophobicity were chosen to investigate the sensitivity of excitonic coupling to dye placement. Each dimer configuration was initialized in parallel and antiparallel arrangements in the DNA HJ. The MD results, validated by experimental measurements, suggested that the adjacent dimer promotes stronger excitonic coupling and less dye–DNA interaction than the transverse dimer. Additionally, we found that SQ dyes with specific functional groups (i.e., substituents) facilitate a closer degree of aggregate packing via hydrophobic effects, leading to a stronger excitonic coupling. This work advances a fundamental understanding of the impacts of dye–DNA interactions on aggregate orientation and excitonic coupling.},
doi = {10.3390/ijms24044059},
journal = {International Journal of Molecular Sciences (Online)},
number = 4,
volume = 24,
place = {Switzerland},
year = {Fri Feb 17 00:00:00 EST 2023},
month = {Fri Feb 17 00:00:00 EST 2023}
}
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