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

TL;DR

This study investigates how temperature affects the conformations and exciton-coupling of Cy3 dimers in DNA using advanced spectroscopy, revealing insights into their local structure and disorder, with implications for understanding bio-molecular energy transfer.

Contribution

The paper demonstrates temperature-dependent modulation of exciton coupling in Cy3 dimers within DNA and interprets spectroscopic data using the Holstein vibronic dimer model, providing new insights into their conformational dynamics.

Findings

Exciton-coupling strength varies systematically with temperature.

Spectroscopic analysis reveals local conformations and static disorder.

Cy3 dimers in DNA can serve as models for studying protein-DNA interactions.

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 (CD), and two-dimensional fluorescence spectroscopy (2DFS) 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 (ss) - 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.