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Title: Enhanced Photo-Cross-Linking of Thymines in DNA Holliday Junction-Templated Squaraine Dimers

Abstract

Programmable self-assembly of dyes using DNA templates to promote exciton delocalization in dye aggregates is gaining considerable interest. New methods to improve the rigidity of the DNA scaffold and thus the stability of the molecular dye aggregates to encourage exciton delocalization are desired. In these dye–DNA constructs, one potential way to increase the stability of the aggregates is to create an additional covalent bond via photo-cross-linking reactions between thymines in the DNA scaffold. Specifically, we report an approach to increase the yield of photo-cross-linking reaction between thymines in the core of a DNA Holliday junction while limiting the damage from UV irradiation to DNA. We investigated the effect of the distance between thymines on the photo-cross-linking reaction yields by using linkers with different lengths to tether the dyes to the DNA templates. By comprehensively evaluating the photo-cross-linking reaction yields of dye–DNA aggregates using linkers with different lengths, we conclude that interstrand thymines tend to photo-cross-link more efficiently with short linkers. A higher cross-linking yield was achieved due to the shorter intermolecular distance between thymines influenced by strong dye–dye interactions. Furthermore, our method establishes the possibility of improving the stability of DNA-scaffolded dye aggregates, thereby expanding their use in exciton-based applicationsmore » such as light harvesting, nanoscale computing, quantum computing, and optoelectronics.« less

Authors:
ORCiD logo [1]; ORCiD logo [1]; ORCiD logo [1]; ORCiD logo [1]; ORCiD logo [1]; ORCiD logo [1]; ORCiD logo [1]
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  1. Boise State University, ID (United States)
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 (MSE)
OSTI Identifier:
2234021
Grant/Contract Number:  
SC0020089
Resource Type:
Accepted Manuscript
Journal Name:
Biochemistry
Additional Journal Information:
Journal Volume: 62; Journal Issue: 22; Journal ID: ISSN 0006-2960
Publisher:
American Chemical Society (ACS)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; Adjacent thymines; Interstrand photo−crosslinking; Short linker length; Squaraine dye; Dye−dye interactions; Dyes and pigments; Genetics; Nucleic acid structure; Oligomers; Thymine

Citation Formats

Basu, Shibani, Roy, Simon K., Barcenas, German, Li, Lan, Yurke, Bernard, Knowlton, William B., and Lee, Jeunghoon. Enhanced Photo-Cross-Linking of Thymines in DNA Holliday Junction-Templated Squaraine Dimers. United States: N. p., 2023. Web. doi:10.1021/acs.biochem.3c00471.
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Basu, Shibani, Roy, Simon K., Barcenas, German, Li, Lan, Yurke, Bernard, Knowlton, William B., & Lee, Jeunghoon. Enhanced Photo-Cross-Linking of Thymines in DNA Holliday Junction-Templated Squaraine Dimers. United States. https://doi.org/10.1021/acs.biochem.3c00471
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Basu, Shibani, Roy, Simon K., Barcenas, German, Li, Lan, Yurke, Bernard, Knowlton, William B., and Lee, Jeunghoon. Tue . "Enhanced Photo-Cross-Linking of Thymines in DNA Holliday Junction-Templated Squaraine Dimers". United States. https://doi.org/10.1021/acs.biochem.3c00471.
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@article{osti_2234021,
title = {Enhanced Photo-Cross-Linking of Thymines in DNA Holliday Junction-Templated Squaraine Dimers},
author = {Basu, Shibani and Roy, Simon K. and Barcenas, German and Li, Lan and Yurke, Bernard and Knowlton, William B. and Lee, Jeunghoon},
abstractNote = {Programmable self-assembly of dyes using DNA templates to promote exciton delocalization in dye aggregates is gaining considerable interest. New methods to improve the rigidity of the DNA scaffold and thus the stability of the molecular dye aggregates to encourage exciton delocalization are desired. In these dye–DNA constructs, one potential way to increase the stability of the aggregates is to create an additional covalent bond via photo-cross-linking reactions between thymines in the DNA scaffold. Specifically, we report an approach to increase the yield of photo-cross-linking reaction between thymines in the core of a DNA Holliday junction while limiting the damage from UV irradiation to DNA. We investigated the effect of the distance between thymines on the photo-cross-linking reaction yields by using linkers with different lengths to tether the dyes to the DNA templates. By comprehensively evaluating the photo-cross-linking reaction yields of dye–DNA aggregates using linkers with different lengths, we conclude that interstrand thymines tend to photo-cross-link more efficiently with short linkers. A higher cross-linking yield was achieved due to the shorter intermolecular distance between thymines influenced by strong dye–dye interactions. Furthermore, our method establishes the possibility of improving the stability of DNA-scaffolded dye aggregates, thereby expanding their use in exciton-based applications such as light harvesting, nanoscale computing, quantum computing, and optoelectronics.},
doi = {10.1021/acs.biochem.3c00471},
journal = {Biochemistry},
number = 22,
volume = 62,
place = {United States},
year = {Tue Oct 31 00:00:00 EDT 2023},
month = {Tue Oct 31 00:00:00 EDT 2023}
}
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