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

Journal Article · · Journal of Chemical Physics
DOI: https://doi.org/10.1063/1.5020084 · OSTI ID:1470511
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)
+ Show Author Affiliations

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.

Research Organization:
Energy Frontier Research Centers (EFRC), Washington, D.C. (United States). Center for Excitonics (CE)
Sponsoring Organization:
USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22)
Grant/Contract Number:
SC0001088
OSTI ID:
1470511
Journal Information:
Journal of Chemical Physics, Journal Name: Journal of Chemical Physics Journal Issue: 8 Vol. 148; ISSN 0021-9606
Publisher:
American Institute of Physics (AIP)Copyright Statement
Country of Publication:
United States
Language:
English

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Cited By (2)

Measuring local conformations and conformational disorder of (Cy3) 2 dimer labeled DNA fork junctions using absorbance, circular dichroism and two-dimensional fluorescence spectroscopy journal January 2019
On the design of molecular excitonic circuits for quantum computing: the universal quantum gates journal January 2020

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