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

The Journal of Chemical Physics
Loni KringleAndrew H Marcus

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. Here 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 th...Continue Reading

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Citations

Jan 22, 2020·Physical Chemistry Chemical Physics : PCCP·Maria A CastellanosAdam P Willard
Nov 24, 2020·Proceedings. Mathematical, Physical, and Engineering Sciences·Gregory D Scholes
Jun 15, 2021·Chemical Science·Sara H SohailGregory S Engel
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Nov 2, 2018·The Journal of Physical Chemistry. a·Jenny W FothergillLan Li
Jul 25, 2020·The Journal of Physical Chemistry. B·Paul D CunninghamJoseph S Melinger
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Oct 15, 2020·The Journal of Physical Chemistry. B·Olga A MassWilliam B Knowlton
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Oct 29, 2021·The Journal of Physical Chemistry. a·Brian S RolczynskiJoseph S Melinger
Dec 14, 2021·The Journal of Physical Chemistry. B·Simon K RoyWilliam B Knowlton

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