Understanding the properties of electronically interacting molecular chromophores, which involve internally coupled electronic-vibrational motions, is important to the spectroscopy of many biological systems. Here we apply linear absorption, circular dichroism, and two-dimensional fluorescence spectroscopy to study the local structure and excited state dynamics of excitonically coupled cyanine dimers that are rigidly positioned within the sugar-phosphate backbones of the DNA. Dimer probes were positioned within the double-stranded DNA duplex and at the single-strand/double-stranded DNA junction to examine the positional dependence of the structural variation and fluctuations. We interpret spectroscopic measurements in terms of the Holstein vibronic dimer model, from which we obtain information about the local conformation of the dimer probe locally within their respective DNA environments. We show that the exciton-coupling strength of the dimer-DNA construct can be systematically varied with temperature below the double-stranded – single-strand DNA denaturation transition. Using time-resolve 2DFS measurements we observed long lived vibronic coherences in the system. The properties of the cyanine 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 biomolecular arrays.
This dissertation contains previously published and unpublished co-authored material.
| Identifer | oai:union.ndltd.org:uoregon.edu/oai:scholarsbank.uoregon.edu:1794/23749 |
| Date | 06 September 2018 |
| Creators | Kringle, Loni |
| Contributors | Cina, Jeffrey |
| Publisher | University of Oregon |
| Source Sets | University of Oregon |
| Language | en_US |
| Detected Language | English |
| Type | Electronic Thesis or Dissertation |
| Rights | All Rights Reserved. |
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