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Femtosecond Transient Absorption Study Of Femtosecond Transient Absorption Study of Excited-State Dynamics in DNA Model Systems: Thymine-dimer Containing Trinucleotides, Alternate Nucleobases, and Modified Backbone Dinucleosides DISSERTATION Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Jinquan Chen Graduate Program in Chemistry The Ohio State University 2012 Dissertation Committee: Bern Kohler, Co-adviser Terry L. Gustafson, Co-adviser John M. Herbert Dongping Zhong Copyright by Jinquan Chen 2012 ABSTRACT DNA is the genomic information carrier for all life on Earth. The nucleobases that build up DNA absorb strongly in the UV region of the spectrum. A thorough understanding of the relaxation pathways for the energy gained from the UV radiation in DNA is critical to our knowledge of life. The aim of this work is to answer three major questions: (1) can a excited purine base repair the adjacent thymine dimer by a photolyase-like electron transfer mechanism; (2) what are the excited state lifetimes of several xanthine derivatives; (3) what is the origin of the long-lived excited states exist in single- and double-stranded DNA. Transient absorption study was carried on single strand model purine-containing trinucleotide. No evidence was found for that the adjacent purines adenine and guanine could repair thymine dimer by a photolyase-like electron transfer mechanism within experimental uncertainty. Excited-state dynamics of alternate nucleobases were studied by femtosecond transient absorption spectroscopy. Subpicosecond excited-state lifetimes were observed in hypoxanthine and several methylxanthine derivatives. All the compounds studied could be the candidates of possible precursor of today’s canonical nucleobases because of their photostablility property. At last, transient absorption study of adenine dinucleosides with different backbones reveals that the origin of the long-lived states in DNA oligomers is base stacking and base stacking is still presented even at high ii temperature. Meanwhile, experimental results on conjugated AT oligonucleotides suggest that the ultrafast monomer-like excited state nonradiative decay channel is presented in the well-stacked DNA systems. iii Dedication This work is dedicated to my family. iv ACKNOWLEDGMENTS I would like first to thank my advisor, Bern Kohler, for his helping along this five years graduate school study. I would also like to thank Terry L. Gustafson for willing to being my advisor after Bern left Ohio State University and his encouragement for me during my research project. I would like to thank the current and former members of Kohler group for their assistance and company through graduate school. Special thanks to Joseph Henrich who has taught me everything since I joined this group and his useful help from Coherent. I also want to thank Wolfgang Schreier for his guide in how to do good science in lab as well as all the travels and dinners we did together. Finally, I would like to thank all my family members for their support during my study abroad time. Special thanks to my wife Mengyi Liu for all the encouragement and understanding during the last three years. v Vita June 4, 1984 ...................................................Born - Chongqing, China 2007................................................................B.S. Chemistry, Nanjing University 2007 - present ................................................Graduate Teaching and Research Associate, The Ohio State University Publications 1. Chen, J. and Kohler, B., “Ultrafast Nonradiative Decay by Hypoxanthine and Several Methylxanthines in Aqueous and Acetonitrile Solution” Physical Chemistry Chemical Physics, 14, 10677-10682 (2012) 2. Pan, Z.; Chen, J.; Schreier, W.J.; Kohler, B.; Lewis, F.D., “Thymine Dimer Photoreversal in Purine-Containing Trinucleotides” Journal of Physical Chemistry B, 116, 698-704 (2012) Fields of Study Major Field: Chemistry vi Table of Contents Abstract ............................................................................................................................... ii Dedication ........................................................................................................................... v Acknowledgments............................................................................................................... v Vita ..................................................................................................................................... vi List of Tables .................................................................................................................... xii List of Figures .................................................................................................................. xiii List of Schemes .............................................................................................................. xviii Chapter 1: Introduction ...................................................................................................... 1 References ...................................................................................................................... 6 Chapter 2: Methods ........................................................................................................... 11 2.1 Transient absorption spectrometers ....................................................................... 11 2.1.1UV-pump/UV-Visible-probe measurements ................................................. 12 2.2. Steady-state measurements ................................................................................... 14 2.2.1. UV/Vis absorption measurements ............................................................... 14 2.2.2. Circular dichroism measurements ................................................................ 14 2.3. Sample handling.................................................................................................... 15 vii 2.3.1 Materials ....................................................................................................... 15 2.3.2 Spinning cell and temperature-controlled flow cell ...................................... 15 2.4 Data treatment ........................................................................................................ 16 References .................................................................................................................... 18 Chapter 3: Thymine dimer photoreversal in purine-containing trinucleotides ................ 26 3.1 Introduction ............................................................................................................ 26 3.2 Results .................................................................................................................... 28 3.2.1 Steady-state UV absorption measurements ................................................. 28 3.2.2 Transient absorption measurements of cis-syn thymine dimer .................... 30 3.2.3 Transient absorption measurements of purine-containing trinucleotides .... 31 3.3 Discussion .............................................................................................................. 31 3.3.1 Direct photoreversal of thymine dimer under UV irradiation ...................... 31 3.3.2 Conditional quantum yield ............................................................................ 33 3.3.3 Transient absorption signals from aqueous cis-syn thymine dimer solution 37 3.3.4 Transient absorption aignals from purine-containing trinucleotides ........... 40 3.4 Conclusions ............................................................................................................ 42 Reference ..................................................................................................................... 42 Chapter 4: UV hardiness of alternate nucleobasses .......................................................... 65 4.1 Introduction ............................................................................................................ 65 viii 4.2 Results .................................................................................................................... 67 4.2.1 Steady-state UV absorption measurements .................................................. 67 4.2.2 Transient absorption measurements .............................................................. 68 4.3 Discussion .............................................................................................................. 70 4.3.1. Ultrafast lifetimes observed in hypoxanthine and xanthine derivatives ...... 70 4.3.2. Comparison of excited-state decay mechanism between canonical and alternate nucleobases ................................................................................... 72 4.4 Conclusions ............................................................................................................ 74 References .................................................................................................................... 74 Chapter 5: Long-lived excited states in adenine dinucleosides with different backbones and conjugated AT system ........................................................... 90 5.1 Introduction ............................................................................................................ 90 5.2 Results .................................................................................................................... 93 5.2.1 Steady-state UV-Vis absorption
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