Studies of the Binding Thermodynamics and Mechanism between DNA Aptamer and Its Ligand by Isothermal Titration Calorimetry and Circular Dichroism

• Main Authors: Shih-lun Yen, 顏仕倫
• Other Authors: 陳文逸
• Format: Others
• Language: zh-TW
• Published: 2007
• Online Access: http://ndltd.ncl.edu.tw/handle/57924779423762886421

碩士 === 國立中央大學 === 化學工程與材料工程研究所 === 95 === Aptamers are macromolecules composed of nucleic acids, such as RNA or DNA, that bind tightly to a specific molecular target. In this study, we used Isothermal Titration Microcalorimetry (ITC) and Circular Dichroism (CD) to study the binding mechanism between a DNA aptamer and L-tyrosinamide. In order to gain further insights into the binding driven force in the recognizing behavior and the thermodynamic discrepancy, binding enthalpy measurements at different system parameters such as salt ion temperature pH value and analogues were carried out. Noteworthily, stabilizing the aptamer structure and enhanced target-aptamer complex formation by magnesium cation was also demonstrated in this study. ITC results indicate that the binding behavior is an enthalpy driven and entropy cost process. The thermodynamic signature, along with the coupled CD spectral changes, suggest that the binding behavior is an induced-fit process and the conformation of DNA aptamer changes from B-form to A-from like in the binding process. In addition, binding mechanism analysis suggest that the interaction driven force in the binding process may include electrostatic interactions, hydrophobic interactions, hydrogen bonding and binding-linked protonation process. Furthermore, Mg2+ could not only help the forming of the complex by stable the conformation of the DNA aptamer but also change the structure of DNA aptamer.