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

Abstract

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, wemore » 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.« less

Authors:
; ORCiD logo; ; ; ;
Publication Date:
Research Org.:
Boise State Univ., ID (United States)
Sponsoring Org.:
USDOE; USDOE Office of Science (SC), Basic Energy Sciences (BES). Materials Sciences & Engineering Division
OSTI Identifier:
1873576
Alternate Identifier(s):
OSTI ID: 1873523
Grant/Contract Number:  
SC0020089
Resource Type:
Published Article
Journal Name:
Molecules
Additional Journal Information:
Journal Name: Molecules Journal Volume: 27 Journal Issue: 13; Journal ID: ISSN 1420-3049
Publisher:
MDPI AG
Country of Publication:
Switzerland
Language:
English
Subject:
77 NANOSCIENCE AND NANOTECHNOLOGY; Photocrosslinking; Thymine Modifiers; Holliday Junctions; Adjacent Dimers; Transverse Dimers; Excitonic Coupling; Squaraine; Kasha; Quantum Computing; Tetramer

Citation Formats

Basu, Shibani, Cervantes-Salguero, Keitel, Yurke, Bernard, Knowlton, William B., Lee, Jeunghoon, and Mass, Olga A. Photocrosslinking Probes Proximity of Thymine Modifiers Tethering Excitonically Coupled Dye Aggregates to DNA Holliday Junction. Switzerland: N. p., 2022. Web. doi:10.3390/molecules27134006.
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Basu, Shibani, Cervantes-Salguero, Keitel, Yurke, Bernard, Knowlton, William B., Lee, Jeunghoon, & Mass, Olga A. Photocrosslinking Probes Proximity of Thymine Modifiers Tethering Excitonically Coupled Dye Aggregates to DNA Holliday Junction. Switzerland. https://doi.org/10.3390/molecules27134006
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Basu, Shibani, Cervantes-Salguero, Keitel, Yurke, Bernard, Knowlton, William B., Lee, Jeunghoon, and Mass, Olga A. Wed . "Photocrosslinking Probes Proximity of Thymine Modifiers Tethering Excitonically Coupled Dye Aggregates to DNA Holliday Junction". Switzerland. https://doi.org/10.3390/molecules27134006.
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@article{osti_1873576,
title = {Photocrosslinking Probes Proximity of Thymine Modifiers Tethering Excitonically Coupled Dye Aggregates to DNA Holliday Junction},
author = {Basu, Shibani and Cervantes-Salguero, Keitel and Yurke, Bernard and Knowlton, William B. and Lee, Jeunghoon and Mass, Olga A.},
abstractNote = {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.},
doi = {10.3390/molecules27134006},
journal = {Molecules},
number = 13,
volume = 27,
place = {Switzerland},
year = {Wed Jun 22 00:00:00 EDT 2022},
month = {Wed Jun 22 00:00:00 EDT 2022}
}
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