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Title: Temperature-dependent conformations of exciton-coupled Cy3 dimers in double-stranded DNA

Abstract

Understanding the properties of electronically interacting molecular chromophores, which involve internally coupled electronic-vibrational motions, is important to the spectroscopy of many biologically relevant systems. In this paper, we apply linear absorption, circular dichroism, and two-dimensional fluorescence spectroscopy to study the polarized collective excitations of excitonically coupled cyanine dimers (Cy3)2 that are rigidly positioned within the opposing sugar-phosphate backbones of the double-stranded region of a double-stranded (ds)–single-stranded (ss) DNA fork construct. We show that the exciton-coupling strength of the (Cy3)2-DNA construct can be systematically varied with temperature below the ds–ss DNA denaturation transition. We interpret spectroscopic measurements in terms of the Holstein vibronic dimer model, from which we obtain information about the local conformation of the (Cy3)2 dimer, as well as the degree of static disorder experienced by the Cy3 monomer and the (Cy3)2 dimer probe locally within their respective DNA duplex environments. The properties of the (Cy3)2-DNA construct we determine suggest that it may be employed as a useful model system to test fundamental concepts of protein-DNA interactions and the role of electronic-vibrational coherence in electronic energy migration within exciton-coupled bio-molecular arrays.

Authors:
ORCiD logo [1];  [2];  [3];  [1];  [4]; ORCiD logo [5]; ORCiD logo [1]
  1. Univ. of Oregon, Eugene, OR (United States). Dept. of Chemistry and Biochemistry, Center for Optical, Molecular and Quantum Science
  2. Harvard Univ., Cambridge, MA (United States). Dept. of Chemistry and Chemical Biology
  3. Univ. of Michigan, Ann Arbor, MI (United States).Dept. of Chemistry
  4. Univ. of Oregon, Eugene, OR (United States). Dept. of Physics, Center for Optical, Molecular, and Quantum Science
  5. Harvard Univ., Cambridge, MA (United States). Dept. of Chemistry and Chemical Biology; Canadian Inst. for Advanced Research (CIFAR), Toronto, ON (Canada)
Publication Date:
Research Org.:
Energy Frontier Research Centers (EFRC), Washington, D.C. (United States). Center for Excitonics (CE)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES)
OSTI Identifier:
1470511
Alternate Identifier(s):
OSTI ID: 1422667
Grant/Contract Number:  
SC0001088
Resource Type:
Accepted Manuscript
Journal Name:
Journal of Chemical Physics
Additional Journal Information:
Journal Volume: 148; Journal Issue: 8; Related Information: CE partners with Massachusetts Institute of Technology (lead); Brookhaven National Laboratory; Harvard University; Journal ID: ISSN 0021-9606
Publisher:
American Institute of Physics (AIP)
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; 59 BASIC BIOLOGICAL SCIENCES; 71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSICS; solar (photovoltaic); solid state lighting; photosynthesis (natural and artificial); charge transport; optics; synthesis (novel materials); synthesis (self-assembly); synthesis (scalable processing)

Citation Formats

Kringle, Loni, Sawaya, Nicolas P. D., Widom, Julia, Adams, Carson, Raymer, Michael G., Aspuru-Guzik, Alán, and Marcus, Andrew H. Temperature-dependent conformations of exciton-coupled Cy3 dimers in double-stranded DNA. United States: N. p., 2018. Web. doi:10.1063/1.5020084.
Kringle, Loni, Sawaya, Nicolas P. D., Widom, Julia, Adams, Carson, Raymer, Michael G., Aspuru-Guzik, Alán, & Marcus, Andrew H. Temperature-dependent conformations of exciton-coupled Cy3 dimers in double-stranded DNA. United States. doi:10.1063/1.5020084.
Kringle, Loni, Sawaya, Nicolas P. D., Widom, Julia, Adams, Carson, Raymer, Michael G., Aspuru-Guzik, Alán, and Marcus, Andrew H. Mon . "Temperature-dependent conformations of exciton-coupled Cy3 dimers in double-stranded DNA". United States. doi:10.1063/1.5020084. https://www.osti.gov/servlets/purl/1470511.
@article{osti_1470511,
title = {Temperature-dependent conformations of exciton-coupled Cy3 dimers in double-stranded DNA},
author = {Kringle, Loni and Sawaya, Nicolas P. D. and Widom, Julia and Adams, Carson and Raymer, Michael G. and Aspuru-Guzik, Alán and Marcus, Andrew H.},
abstractNote = {Understanding the properties of electronically interacting molecular chromophores, which involve internally coupled electronic-vibrational motions, is important to the spectroscopy of many biologically relevant systems. In this paper, we apply linear absorption, circular dichroism, and two-dimensional fluorescence spectroscopy to study the polarized collective excitations of excitonically coupled cyanine dimers (Cy3)2 that are rigidly positioned within the opposing sugar-phosphate backbones of the double-stranded region of a double-stranded (ds)–single-stranded (ss) DNA fork construct. We show that the exciton-coupling strength of the (Cy3)2-DNA construct can be systematically varied with temperature below the ds–ss DNA denaturation transition. We interpret spectroscopic measurements in terms of the Holstein vibronic dimer model, from which we obtain information about the local conformation of the (Cy3)2 dimer, as well as the degree of static disorder experienced by the Cy3 monomer and the (Cy3)2 dimer probe locally within their respective DNA duplex environments. The properties of the (Cy3)2-DNA construct we determine suggest that it may be employed as a useful model system to test fundamental concepts of protein-DNA interactions and the role of electronic-vibrational coherence in electronic energy migration within exciton-coupled bio-molecular arrays.},
doi = {10.1063/1.5020084},
journal = {Journal of Chemical Physics},
number = 8,
volume = 148,
place = {United States},
year = {2018},
month = {2}
}

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