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Proton chemical shift prediction of A·A mismatches in B-DNA duplexes.

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

Identiferoai:union.ndltd.org:cuhk.edu.hk/oai:cuhk-dr:cuhk_326100
Date January 2007
ContributorsLai, Kin Fung., Chinese University of Hong Kong Graduate School. Division of Chemistry.
Source SetsThe Chinese University of Hong Kong
LanguageEnglish, Chinese
Detected LanguageEnglish
TypeText, bibliography
Formatprint, xvi, 97 leaves : ill. ; 30 cm.
RightsUse of this resource is governed by the terms and conditions of the Creative Commons “Attribution-NonCommercial-NoDerivatives 4.0 International” License (http://creativecommons.org/licenses/by-nc-nd/4.0/)

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