Lai, Kin Fung. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2007. / Includes bibliographical references (leaves 92-97). / Abstracts in English and Chinese. / Title Page --- p.i / Thesis Committee --- p.ii / Abstract (In English) --- p.iv / Abstract (In Chinese) --- p.v / Acknowledgement --- p.vi / List of Figures --- p.xii / List of Tables --- p.xiv / List of Symbols and Abbreviations --- p.xvi / Chapter 1. --- Introduction --- p.1 / Chapter 1.1 --- Chemical Shift Predictions of Nucleic Acids --- p.1 / Chapter 1.1.1 --- Chemical Shift --- p.1 / Chapter 1.1.2 --- Chemical Shift Prediction of Double Helical DNA and RNA --- p.1 / Chapter 1.1.3 --- Chemical Shift Prediction of Random Coil DNA --- p.2 / Chapter 1.1.4 --- Applications of Nucleic Acid Chemical Shift Prediction --- p.4 / Chapter 1.2 --- General Review of DNA Structure --- p.4 / Chapter 1.2.1 --- Structure and Nomenclature of Nucleotide --- p.4 / Chapter 1.2.2 --- Structure of Polynucleotide --- p.5 / Chapter 1.2.3 --- Sugar Conformation in Nucleotide --- p.5 / Chapter 1.2.4 --- Double Helical DNA Conformation --- p.7 / Chapter 1.3 --- A.A Mismatches in DNA Duplexes --- p.8 / Chapter 1.3.1 --- Mismatches in DNA Duplexes --- p.8 / Chapter 1.3.2 --- Biological Significance of A． A Mismatches --- p.9 / Chapter 1.4 --- Purpose of the Work --- p.9 / Chapter 2 --- Materials and Method --- p.10 / Chapter 2.1 --- Overview of the Proposed Prediction Method --- p.10 / Chapter 2.1.1 --- Nearest Neighbor Model --- p.10 / Chapter 2.1.2 --- Base Pair Replacement Approach --- p.10 / Chapter 2.2 --- Sample Design --- p.11 / Chapter 2.2.1 --- Reference Sequences for Obtaining Triplet Values and Correction Factors --- p.11 / Chapter 2.2.2 --- Sequences for Verifying the Base Pair Replacement Approach --- p.12 / Chapter 2.2.3 --- Sequences for Testing Chemical Shift Prediction Accuracy --- p.12 / Chapter 2.3 --- Sample Preparation --- p.13 / Chapter 2.4 --- NMR Experiments --- p.14 / Chapter 2.4.1 --- Non-labile Proton Resonance Assignment --- p.14 / Chapter 2.4.2 --- Labile Proton Resonance Assignment --- p.16 / Chapter 2.5 --- Validating the Assumption in Reference Hairpin Model Samples --- p.17 / Chapter 3 --- Establishment of Proton Chemical Shift Prediction method of A.A Mismatches in B-DNA Duplexes --- p.18 / Chapter 3.1 --- Resonance Assignment --- p.18 / Chapter 3.1.1 --- Non-labile Protons --- p.18 / Chapter 3.1.2 --- Labile Protons --- p.20 / Chapter 3.2 --- Validating the Assumption in Reference Hairpin Model Samples --- p.21 / Chapter 3.3 --- Extraction of A.A Mismatch Triplet Chemical Shift Values --- p.22 / Chapter 3.4 --- Calculation of the 5´ة- and 3´ة-Correction Factors --- p.24 / Chapter 3.5 --- Chemical Shift Prediction Using Triplet Values and Correction Factors Extracted from Top Strands of refA.A(XAY) and refA．T(XAY) --- p.27 / Chapter 3.6 --- Chemical Shift Prediction Using Triplet Values and Correction Factors Extracted from Bottom Strands of refA.A(XAY) and refA．T(XAY) --- p.28 / Chapter 4 --- Testing of Proton Chemical Shift Prediction of A.A Mismatches in B- DNA --- p.29 / Chapter 4.1 --- Prediction Result Using Triplet Values and Correction Factors Extracted from the Top Strands of refA.A(XAY) and refA.T(XAY) --- p.29 / Chapter 4.2 --- Prediction Result Using Triplet Values and Correction Factors Extracted from Bottom Strands of refA.A(XAY) and refAT(XAY) --- p.30 / Chapter 4.3 --- Applicability of the Base Pair Replacement Approach --- p.31 / Chapter 4.3.1 --- Chemical Shifts and 3JH1´ةH2´ة of refT.A(XTY) Sequences --- p.31 / Chapter 4.3.2 --- Correction factors Extracted from the Top Strands of refA.A(XAY) and refT.A(XTY) --- p.31 / Chapter 4.3.3 --- Prediction Result Using Correction Factors Extracted from the Top Strands of refA.A(XAY) and refT.A(XTY) --- p.33 / Chapter 5 --- Conclusion --- p.35 / Appendix I NOE Sequential Assignment of refA.T(XAY) - (A) Aromatic Protons at 25 °C; (B) Labile Protons at 25 °C --- p.36 / Appendix II NOE Sequential Assignment of refA.A(XAY) - (A) Aromatic Protons at 25 °C; (B) Labile Protons at 5 °C --- p.40 / Appendix III H1'-H2'/H2´ح region of DQF-COSY Spectra of refA.T(XAY) at 25 °C --- p.44 / Appendix IV H1'- H2'/H2´ح region of DQF-COSY Spectra of refA.A(XAY) at 25 °C --- p.46 / Appendix V H3' region of HSQC Spectra of refA T(XAY) at 25 °C --- p.48 / Appendix VI H3' region of 1H-31̐ư HSQC Spectra of refA.A(XAY) at 25 °C --- p.50 / Appendix VII 3JH1'h2'1H and 31P Chemical Shifts of refA T(XAY) --- p.52 / Appendix VIII 3JH1'H2'and 31P Chemical Shifts of refA.A(XTY) --- p.60 / Appendix IX NOE Sequential Assignment of refT .A(XTY) - (A) Aromatic Protons at 25 °C; (B) Labile Protons at 25 °C --- p.68 / Appendix X H1'-H2'/H2''region of DQF-COSY Spectra of refT.A(XTY) --- p.72 / Appendix XI H3'region of H-31P HSQC Spectra of refT.A(XTY) --- p.74 / Appendix XII 3JH1'H2'1H and 31P Chemical Shifts of refT.A(XTY) --- p.76 / Appendix XIII Chemical Shifts of Testing Sequences --- p.84 / Reference --- p.92

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