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Permanent link (DOI): https://doi.org/10.7939/R33T9DD2S

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Initial Excited-State Structural Dynamics and Damage Kinetics of Nucleic Acid Derivatives and a Rhodopsin Analogue Open Access

Descriptions

Other title
Subject/Keyword
nucleic acids
Resonance Raman spectroscopy
initial excited-state structural dynamics
Type of item
Thesis
Degree grantor
University of Alberta
Author or creator
Sasidharanpillai, Swaroop
Supervisor and department
Loppnow, Glen (Chemistry)
Examining committee member and department
Wolfgang, Jaeger (Chemistry)
Charles, Lucy (Chemistry)
David, McCamant (Chemistry),
Alexander, Brown (Chemistry)
Loppnow, Glen (Chemistry)
Department
Department of Chemistry
Specialization

Date accepted
2013-07-23T14:12:03Z
Graduation date
2013-11
Degree
Doctor of Philosophy
Degree level
Doctoral
Abstract
Photochemical reactions resulting from the absorption of ultraviolet light are one of the main causes of DNA damage. For any excited-state photochemical reaction, it is the structural changes in the excited state after the absorption of the photon that ultimately decide the photochemical fate of the molecule. In this thesis, I have explored the initial excited-state structural dynamics of nucleic acid derivatives and a rhodopsin analogue to understand the structural distortions upon photon absorption and the correlation between the observed structural dynamics and the known photochemistry. Resonance Raman spectroscopy was used to probe the initial excited-state structural dynamics of 5,6-dimethyluracil, to understand the effect of mass changes at the C5 and C6 positions, and found that the observed initial excited-state structural dynamics are similar to those of thymine. This study showed that the methyl groups at the C5 and C6 positions are a major factor in determining how the initial excited-state structural dynamics are partitioned between the CH bending and C5=C6 stretching modes, which is directly related to the difference in the photochemistry of uracil and thymine. The resonance Raman-derived initial excited-state structural changes of homopentamer oligonucleotides lie along similar modes as in the corresponding nucleobases or nucleotides, but with smaller distortions. The smaller excited-state distortions suggest that the initial excited-state structural dynamics are restricted by the polymeric structure. The observed homopentamer homogeneous broadening is consistent with this model. The sequence dependence of UV-induced miRNA damage was also studied on a microarray platform. The results suggest that guanine provides a protective effect and sequences with cytosine and uracil are more susceptible to damage, although the errors are large. The visible resonance Raman spectroscopic studies on a rhodopsin analogue show similar initial molecular distortions along the C=C bond during the isomerization as in rhodopsin. The hydrogen out-of-plane (HOOP) mode is absent in N-alkyalated indanylidene-Pyrroline (NAIP), as expected due to the absence of C-H modes. The computed excited-state trajectories are consistent with the experimentally observed initial distortions along the C=C bond.
Language
English
DOI
doi:10.7939/R33T9DD2S
Rights
Permission is hereby granted to the University of Alberta Libraries to reproduce single copies of this thesis and to lend or sell such copies for private, scholarly or scientific research purposes only. Where the thesis is converted to, or otherwise made available in digital form, the University of Alberta will advise potential users of the thesis of these terms. The author reserves all other publication and other rights in association with the copyright in the thesis and, except as herein before provided, neither the thesis nor any substantial portion thereof may be printed or otherwise reproduced in any material form whatsoever without the author's prior written permission.
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