Effect of 3-methylthymine on solution structures and thermodynamic stabilities of double-helical deoxyribonucleic acids.

Abstract

Zhong, Yangliu.Thesis (M.Phil.)--Chinese University of Hong Kong, 2011.Includes bibliographical references (leaves 50-57).Abstracts in English and Chinese.Title Page --- p.iThesis Committee --- p.iiAbstract (English Version) --- p.ivAbstract (Chinese Version) --- p.VAcknowledgement --- p.viTable of Contents --- p.viiiList of Tables --- p.XList of Figures --- p.xiiList of Abbreviations and Symbols --- p.xiiiChapter 1 --- Introduction --- p.1Chapter 1.1 --- DNA methylation --- p.1Chapter 1.2 --- Repair of m3T --- p.2Chapter 1.3 --- Objectives of this work --- p.3Chapter 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.7Chapter 2 --- Materials and Methods --- p.9Chapter 2.1 --- Sample design --- p.9Chapter 2.2 --- Sample preparation --- p.10Chapter 2.3 --- NMR analysis --- p.10Chapter 2.3.1 --- Resonance assignment --- p.12Chapter 2.3.2 --- Determination of sugar conformation --- p.13Chapter 2.3.3 --- Determination of backbone conformation --- p.14Chapter 2.4 --- UV melting study --- p.15Chapter 3 --- Effect of m3T on Double-Helical Structures and Stabilities --- p.17Chapter 3.1 --- Resonance assignments --- p.17Chapter 3.2 --- Effect of m3T on double-helical DNA structures --- p.19Chapter 3.2.1 --- Base pairing mode --- p.19Chapter 3.2.2 --- Sugar conformation --- p.21Chapter 3.2.3 --- Backbone conformation --- p.22Chapter 3.3 --- Effect of m3T on double-helical DNA stabilities --- p.25Chapter 3.4 --- Discussion --- p.26Chapter 3.4.1 --- Single-strand requirement in FTO repair --- p.26Chapter 3.4.2 --- Relationship between m3T pairing structure and stability --- p.27Chapter 4 --- Effect of m3T Mispair on Double-Helical DNA Structures and Stabilities --- p.28Chapter 4.1 --- Resonance assignments --- p.28Chapter 4.2 --- Effect of m3T mispair on double-helical DNA structures --- p.32Chapter 4.2.1 --- Pairing mode of T m3T --- p.34Chapter 4.2.2 --- Pairing mode of G m3T --- p.35Chapter 4.2.3 --- Pairing mode of C.m3T --- p.35Chapter 4.3 --- Effect of m3T mispair on double-helical DNA stabilities --- p.36Chapter 4.4 --- Discussion --- p.36Chapter 4.4.1 --- Predominant mutation --- p.37Chapter 4.4.2 --- Relationship between m3T pairing structure and stabilities --- p.37Chapter 5 --- Conclusion and Future Work --- p.39Chapter Appendix I --- Proton chemical shift values (ppm) of AmT --- p.40Chapter Appendix II --- Proton chemical shift values (ppm) of RefAT --- p.41Chapter Appendix III --- Proton chemical shift values of NmT samples --- p.42Chapter Appendix IV --- "Σ1' and %S of TmT, GmT and CmT" --- p.45Chapter Appendix V --- "1H-31P HSQC spectra of (a) TmT, (b) GmT and (c) CmT" --- p.46Chapter Appendix VI --- "1H-31P COSY spectra of (a) TmT, (b) GmT and (c) CmT" --- p.47Chapter Appendix VII --- "31P chemical shifts, 3JH3'P and %Bi of TmT, GmT and CmT" --- p.48Chapter Appendix VIII --- "UV melting curves of RefAT, AmT, TmT, GmT and CmT" --- p.49References --- p.5