Quantum Chemical Investigations of Structural and Photophysical Properties of Emissive RNA Nucleobase Analogues

  • Author / Creator
    Gedik, Melis
  • The photostability of nucleic acid constituents is crucial in maintaining the integrity of our genetic code. This is achieved by the essential mechanism of ultrafast radiationless decay of the singlet excited state to the electronic ground state of nucleobases. While this mechanism provides resilience against mutations to the genetic code, it results in the non-emissive nature of the canonical building blocks of nucleic acids. Consequently, the conformational dynamics of DNA and RNA are difficult to study by fluorescence spectroscopy and imaging. Investigations on the structure and function of these biomolecules can be achieved with fluorescent probes that mimic the natural components of nucleic acids without perturbing the overall structure. Hence, the design of such "isomorphic" nucleoside analogues is highly desired in the field of bioimaging. The photophysical properties of nucleoside analogues are very sensitive to structural modifications. In particular, the nature of the low-lying excited electronic states, presence of long range excitations, conformational flexibility, tautomerization, and access to non-radiative deactivation pathways such as conical intersections (CIs), have significant impact on fluorescence. The vast majority of fluorescent analogues are also sensitive to their local environment. Base stacking, base sequence dependence and base pairing, i.e., hydrogen bonding interactions, all play pivotal roles in the incorporation of analogues into oligomers and helical structures. This thesis outlines computational investigations of these properties for a variety of isomorphic nucleoside analogues. Initial work in this thesis (Chapter 2) involves the evaluation of the photophysical properties of thieno-modified analogues with time-dependent density functional theory (TD-DFT). These preliminary investigations shed light on the energetics of CI pathways. Meanwhile, the presence of stable tautomers confirmed with computational studies (Chapter 3) helps explain the unique spectral features observed in experimental results. Further investigations on base pairing interactions (Chapter 5) of these analogues illustrate the structural similarities to their natural counterparts. As the analogues studied in this work have potential utility in bioimaging, it is important that they be biocompatible for in vivo applications. Light penetration into biological media is very poor at short wavelengths due to increased absorption and scattering. As a result, multi-photon absorption techniques can be utilized to overcome the disadvantages of one-photon absorption. Multi-photon excitation reduces out-of-focus photobleaching, ensures localization of the incident light, and absorption occurs at higher wavelengths which allows for deeper penetration into biological tissue. The utility of analogues for two-photon fluorescence spectroscopy is analyzed by computation of the two-photon absorption (TPA) cross sections in Chapter 4. Studies on the conformational flexibility of select analogues uncover differences in TPA properties that could account for experimental discrepancies. The ultimate goal of the work done in this thesis is the utilization of the knowledge obtained from computational studies in the design of new analogues with the desired physical and spectral properties. While the aim is to provide computational insight for advances in the development of tuneable isomorphic nucleoside analogues, it is equally important to elucidate the reasons behind undesired properties of analogues. This is a vibrant field of research which requires collaboration between synthetic chemists, spectroscopists, biologists, as well as theoretical chemists.

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  • Graduation date
    Fall 2017
  • Type of Item
  • Degree
    Doctor of Philosophy
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  • License
    This thesis is made available by the University of Alberta Libraries with permission of the copyright owner solely for non-commercial purposes. This thesis, or any portion thereof, may not otherwise be copied or reproduced without the written consent of the copyright owner, except to the extent permitted by Canadian copyright law.
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  • Citation for previous publication
    • Computational Study of the Excited State Properties of Modified RNA Nucleobases M. Gedik and A. Brown J. Photochem. and Photobiol. A. 259 25-32 (2013).
  • Institution
    University of Alberta
  • Degree level
  • Department
  • Supervisor / co-supervisor and their department(s)