| The DNA local structure is associated with DNA mutation since high DNA repairing efficiency, which is determined by the DNA local structure, prevents mutations from occurring in the genes. This thesis focuses on what these sources are and how they control the DNA local structure which affects its biological functions through recognition. A detailed study of the mechanism of DNA local structure alteration will certainly push forward our understanding on DNA mutation mechanism.;Initially, a DNA hairpin d(CGGTCCATTAGGACCG) containing HKNPC-EBV LMP1 mutant codon 335 (GAC(Asp)) is studied in order to explore the structure and the underlying chemistry of the unique 'Chinese type of LMP1 sequence' in the EBV strain. Without advanced NMR instruments, complicated NMR pulse sequences and isotope labeling of DNA, efforts have been made to develop novel methods, particularly the use of computational methods, to determine DNA structure.;The SingrMM method has been developed and verified to successfully derive the endocyclic sugar torsion angle constraints suitable for the structure determination of solution DNA molecules, and is also shown to be applicable to the study of RNA type molecules. Through incorporation of a E-COSY experiment and the SingrMM method, useful information on both P and gamma can also be determined. It is also demonstrated that alpha, gamma, beta, epsilon and the "noncontact" information could be obtained from 13C chemical shifts, 3JH3'P and 3JCP4' values by performing HSQC experiments and the absence of NOE intensities in NOESY experiments respectively.;Through a detailed analysis of the structure, it has been shown that the relaxation mechanism of the purine-pyrimidine clash assists the process of DNA separation. In addition, the comparison between the structural results for the native (GGC) and the mutant codon (GAC) reveals the presence of a relationship between the sequence and the flexibility.;Analysis of the structural data obtained in this work together with those collected from the PDB demonstrated that the structural flexibility (DeltaSigmaS/DeltaT) and the entropy (DeltaS) is highly correlated and it explains the origin of the structure-stability relationship of DNA tetramer units reported earlier by us. There are at least three mechanisms unveiled, which are depended on the sequence, for the DNA structural changes. Based on a consideration of structural flexibility, a signaling region appears for AT-rich sequences. The redistribution of both solvent molecules and local structures of DNA tetramers are believed to be the origin responsible for the resulting entropy.;Finally, the DFT calculation confirms that the proton transfer in the nucleobase affects the conformation of DNA sugar ring and its backbone conformation, and hence it contributes to the flexibility of DNA which is known to affect its biological function. The protonation of the electronegative atom involved in the hydrogen bonding affects the planarity of DNA basepair and its helical structure. Thus, the process of proton transfer plays a significant role in DNA structural changes. |
