Structural-based study of the DNA duplexes with a single mismatch pair

Autor: Jing-Yi Zeng, 曾靜儀
Rok vydání: 2019
Druh dokumentu: 學位論文 ; thesis
Popis: 107
Genetic information is ensured by proofreading of DNA polymerase and mismatch repair system. If the DNA repair system is unable to recognize and repair the mismatches, it may lead to highly elevated rates of various mutations which results in genetic instabilities and ultimately lead to the cancers and the other genetic defects. Presence of a single mismatch may cause local distortions in the DNA duplex structures, and accumulation of mismatches may eventually alter the structural topology of the DNA. In order to understand the effects of presence of single mismatches on the DNA duplex structures, we designed a d(GTCGGCXCAC/GTGXGCCGAC) sequence (where, X = A, T, C or G) which can form a single mismatch pair in the DNA duplex. Initially, we utilize the circular dichroism spectroscopy (CD) analysis to understand the effects of single mismatches on DNA conformations. The CD spectra indicate that there are similar conformations to the B-DNA in the DNA structures of different mismatches along with Watson-Crick base paired duplexes. On the other hand, the melting temperature analysis shows that the base pair stability is in the range of CC＜AC＜TC＜TT＜AA＜GT＜AG＜GG＜AT＜GC for the mismatch and Watson-Crick DNAs. We then solved the crystal structures of the DNA containing G:T, A:G and A:C mismatches at the position 7 in the duplexes. We also solved the structures of the DNA duplexes containing Watson-Crick pairs A:T and G:C at the mismatch sites for comparison. Using Web 3 DNA server to analyze the DNA parameters and torsion angle, we found that all these duplexes belongs to A-form of DNA. The DNA parameters such as shear and stretch distances, opening and twist angles showed significant perturbations at the mismatch sites. These differences present at the mismatch sites may be the key recognition factors for the mismatched repair proteins. In addition, we also compared the effects of changing the terminal base pair in the G:T mismatched DNA duplex from G/C to T/A. Interestingly, we found that the substitution of terminal base pair able to transform the DNA duplex from A-DNA to a B-DNA conformation. Our crystallographic results suggest that the DNA conformation may be associated with single nucleotide polymorphisms. In the future, we can use these characteristics of the mismatched DNA duplexes to develop drugs similar to the role of repair proteins.
Databáze: Networked Digital Library of Theses & Dissertations
Externí odkaz: