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

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Initial Excited-State Structural Dynamics and Damage Kinetics of Nucleic Acid Derivatives and a Rhodopsin Analogue University of Alberta Initial Excited-State Structural Dynamics and Damage Kinetics of Nucleic Acid Derivatives and a Rhodopsin Analogue by Swaroop Sasidharanpillai A thesis submitted to the Faculty of Graduate Studies and Research in partial fulfillment of the requirements for the degree of Doctor of Philosophy Department of Chemistry c Swaroop Sasidharanpillai Fall 2013 Edmonton, Alberta 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. Dedicated to My Family 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 ho- mopentamer oligonucleotides lie along similar modes as in the corresponding nu- cleobases 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. Acknowledgements Apart from the efforts from my side, this thesis would not have been possible without the help, support, encouragement and guidelines of many others. I would like to express by deep sense of gratitude towards my Ph D supervisor, Prof. Glen R. Loppnow for his guidance, supervision, patience and constant motivation. His knowledge and expertise in the field of research has helped me to understand the science better and look at research in different perspective. I thank him for the freedom and choices he gave us in shaping the research and the training in making me a better researcher. Being a great teacher and administrator, discussion with him, both scientific and non-scientific, were fruitful and interesting. His way of preparing ourselves for presentations and talk in group meetings and individual meeting and his critical reviews and suggestions helped us to become better speakers. I am in debt to him, for being a great supervisor and good friend during Ph D career. I thank Prof. Charles Lucy and Prof. Alexander Brown for being in my supervisory committee and monitoring the progress of my research at different stages of my Ph D career. Their guidance and suggestion helped me use time more efficiently in research. They were always available when I needed some guidance. I also thank, Prof. Wolfgang Jaeger, Juli Gibbs-Davis, Prof. Janice Cooke and Prof. David C. McCamant for serving in candidacy and Ph D defense committees. I am in debt to my colleagues Dr. Amira El Yazbi, Sindhu Nair and Faranak Teimoory, for their help, friendship and understanding. I am also thankful to our former group members Dr. Sulayman Adeyemi Oladepo, Steve Dempster, Christine Pinnock and Zahra Shire. I gratefully acknowledge the services from Molecular Biology Service Unit (MBSU) especially Dr. Anthony Cornish and Troy Locke, for the help and support with microarray printing and teaching me how to use the microarray scanners and the analysis softwares. I am equally grateful to Dr. Walid El Kayal for the great discussions on microarrays and his help with microarray analysis software and design. Helps from people of Analytical and Instrumentation Laboratory, machine shop and glass shop are worth mentioning. The help and support from Wayne Moffat in Analytical and Instrumentation Laboratory need special mention. I am grateful to my friends Dr. Saneej Balakrishnapillai, Dr. Praveen Veluthedathukuzhi and Dr. Archana Kandakkathara for their time and help in formatting the thesis and their support. I am thankful to my all friends and their families in Canada and India for their understanding and moral support. I am grateful to department of chemistry, FGSR and GSA, university of Alberta for the teaching assistanceship, financial support and travel awards. The help and support from Dr. Norman and Dr. Anna Jordan are gratefully acknowledged. I would like to express my deep sense of gratitude towards my previous research guides Prof. C. T Aravindakumar, Dr. Indira Priyadharsini and Dr. Beena Singh for their encouragement, support and making be a better researcher. Last, but not least, I would like to thanks my parents and my family for their encouragement, support and understanding. Contents 1 Introduction 1 1.1 ResonanceRamanSpectroscopy. 4 1.1.1 Vibrational Spectroscopy . 4 1.1.2 RamanSpectroscopy.. .. .. .. .. .. .. 4 1.1.3 Theory of Raman Spectroscopy . 8 1.1.4 Resonance Raman Spectroscopy . 9 1.1.5 Resonance Raman Spectra and Absorption Spectra . 10 1.1.6 Initial Excited-State Structural Dynamics . 10 1.1.7 Overtone and Combination Bands . 15 1.1.8 Applications ........................... 15 1.2 Nucleic Acid Properties and Damage . 16 1.2.1 NucleicAcids ........................... 16 1.2.2 Central Dogma of Biology . 17 1.2.3 Different Types of RNA . 20 1.2.4 SmallRNAs............................ 20 1.2.5 MicroRNAs............................ 21 1.2.6 Electronic Properties of Nucleic Acids . 21 1.2.7 Vibrational Properties of Nucleic Acid . 23 1.2.8 DNA Photochemistry and UV Damage . 23 1.2.9 Fluorescence Spectroscopy . 27 1.2.10 Hairpin Probes and Damage Detection . 28 1.2.11 DNA/RNA Microarrays . 29 1.3 Researchoutline ............................. 30 2 Initial Excited-state Structural Dynamics Of 5,6-Dimethyluracil Using Resonance Raman Spectroscopy 41 2.1 Introduction................................ 41 2.2 Experimental ............................... 43 2.3 ResultsandDiscussion. .. .. .. .. .. .. .. 46 2.4 Conclusions ................................ 57 3 Initial Excited-State Structural Dynamics of DNA Oligonucleotide Homopentamers using Resonance Raman Spectroscopy 60 3.1 Introduction................................ 60 3.2 Experimental ............................... 62 3.3 Results................................... 66 3.4 Discussion................................. 87 3.5 Conclusions ................................ 91 4 UV-Induced miRNA Damage on a Microarray Platform 99 4.1 Introduction................................ 99 4.2 Experimental ............................... 102 4.3 ResultsandDiscussion. 109 4.4 Conclusions ................................ 118 5 Initial Excited-State Structural Dynamics of an N-Alkylated Indanylidene-Pyrroline Rhodopsin Analog 124 5.1 Introduction................................ 124 5.2 Experimental and Computational Methods . 125 5.3 ResultsandDiscussion. 129 5.4 Conclusions ................................ 139 6 Conclusion and Future Works 145 6.1 Generalconclusions. .. .. .. .. .. .. .. .. 145 6.1.1 Chapter2............................. 146 6.1.2 Chapter3............................. 147 6.1.3 Chapter4............................. 148 6.1.4 Chapter5............................. 149 6.2 Futurework................................ 149 6.2.1 Initial excited-state structural dynamics of 5,6-DMU and photochemistry. .. .. .. .. .. .. .. 149 6.2.2 Initial excited-state structural dynamics of oligonucleotides andphotochemistry . 151 6.2.3 Kinetics of nucleic acid damage . 151 6.2.4 Techniques to detect nucleic acid damage . 152 Appendix A Resonance Raman Spectra and Twostate (Model-2) for Homopentamers 156 Appendix B Kinetics and Correlation Plots
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