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:

Kringle, Loni  ^[1];

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• Search DOE PAGES for ORCID "0000-0003-0152-2401"

Sawaya, Nicolas P. D. ^[2]; Widom, Julia ^[3]; Adams, Carson ^[1]; Raymer, Michael G. ^[4]; Aspuru-Guzik, Alán  ^[5];

• Search DOE PAGES for author "Aspuru-Guzik, Alán"
• Search DOE PAGES for ORCID "0000-0002-8277-4434"

Marcus, Andrew H.  ^[1]

• Search DOE PAGES for author "Marcus, Andrew H."
• Search DOE PAGES for ORCID "0000-0003-2109-327X"

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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:

Mon Feb 26 00:00:00 EST 2018

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)