Effect of 1-methyladenine on double-helical DNA structures and stabilities.

Yang, Hao.Thesis (M.Phil.)--Chinese University of Hong Kong, 2009.Includes bibliographical references (leaves 53-57).Abstract also in Chinese.Title Page --- p.iThesis Committee --- p.iiAbstract (English version) --- p.ivAbstract (Chinese version) --- p.viAcknowledgment --- p.viiTable of Contents --- p.viiiList of Tables --- p.xiList of Figures --- p.xiiList of Abbreviations and Symbols --- p.xvChapter 1 --- Introduction --- p.1Chapter 1.1 --- DNA Methylation --- p.1Chapter 1.2 --- DNA Methylation Repair --- p.2Chapter 1.3 --- Objectives of This Work --- p.2Chapter 1.4 --- DNA Structure --- p.3Chapter 1.4.1 --- Nomenclature Scheme for DNA --- p.3Chapter 1.4.2 --- Base Pair Scheme --- p.4Chapter 1.4.3 --- Sugar Conformation --- p.5Chapter 1.4.4 --- Backbone Conformation --- p.5Chapter 2 --- Materials and Methods --- p.7Chapter 2.1 --- Sample Design --- p.7Chapter 2.2 --- Sample Preparation --- p.7Chapter 2.3 --- UV Optical Melting Study --- p.8Chapter 2.4 --- NMR Study --- p.9Chapter 2.4.1 --- NMR Melting Study --- p.10Chapter 2.4.2 --- Resonance Assignment --- p.10Chapter 2.4.3 --- Determination of Sugar Conformation --- p.12Chapter 2.4.4 --- Determination of Backbone Conformation --- p.13Chapter 3 --- Effect of 1-Methyladenine on Double-Helical DNA Structures --- p.14Chapter 3.1 --- NMR Resonance Assignments --- p.14Chapter 3.1.1 --- TA-oligo Resonance Assignments --- p.14Chapter 3.1.2 --- TmlA-oligo Resonance Assignments --- p.16Chapter 3.2 --- DNA Double-Helical Structures upon 1-Methylation of Adenine --- p.18Chapter 3.2.1 --- Base Pairing Mode --- p.18Chapter 3.2.2 --- Sugar Puker --- p.21Chapter 3.2.3 --- Backbone Conformation --- p.22Chapter 3.3 --- Summary --- p.24Chapter 4 --- Effect of 1-Methyladenine on Double-Helical DNA Stabilities --- p.25Chapter 4.1 --- Thermodynamic Studies --- p.26Chapter 4.1.1 --- Influence of m6A on UV Melting Studies --- p.26Chapter 4.1.2 --- Thermodynamics by NMR Melting Studies --- p.28Chapter 4.2 --- "NMR Structural Studies on Gm1A-, Am1A- and Cm1A-oligo" --- p.33Chapter 4.2.1 --- Gml A-oligo --- p.33Chapter 4.2.1.1 --- Gm1A-oligo Resonance Assignments --- p.33Chapter 4.2.1.2 --- Base Pair Structures of Gm1A-oligo --- p.35Chapter 4.2.2 --- AmiA-oligo --- p.37Chapter 4.2.2.1 --- Am1A-oligo Resonance Assignments --- p.37Chapter 4.2.2.2 --- Base Pair Structures of Am1A-oligo --- p.39Chapter 4.2.3 --- Cm1A-oligo --- p.43Chapter 4.2.3.1 --- Cm1A-oligo Resonance Assignments --- p.43Chapter 4.2.3.2 --- Base Pair Structures of Cm1A-oligo --- p.45Chapter 4.3 --- Summary --- p.46Chapter 5 --- Conclusion and Future work --- p.47Appendix I Proton chemical shift values of TA-oligo --- p.48Appendix II Proton chemical shift values of TmlA-oligo --- p.49Appendix III Proton chemical shift values of GmlA-oligo --- p.50Appendix IV Proton chemical shift values of Am1A-oligo --- p.51Appendix V Proton chemical shift values of CmlA-oligo --- p.52References --- p.5