Simulating the Spontaneous Unraveling of DNA on Lipid Bilayers

• Main Authors: Ching-Kuan Wang, 王靜寬
• Other Authors: Chih-Chen Hsieh
• Format: Others
• Language: zh-TW
• Published: 2016
• Online Access: http://ndltd.ncl.edu.tw/handle/45670104325660006928

碩士 === 國立臺灣大學 === 化學工程學研究所 === 104 === When DNA adsorbed on grooved glass with cationic lipid bilayers, they extend along the roots of the side wall of the grooves where the surface curvature is positive. The phenomenon is spontaneous and is expected to be caused by a deep energy well there. Such energy well can be considered as a strip-like confinement for DNA, and the width of the strip can be inferred from the width of area with positive curvature. However, the experimentally determined relationship between DNA extension and strip width somewhat deviates from the theoretical predictions made by de Gennes and Odijk. We suspect this deviation is related to the shape of the energy well which is assumed to be a deep square but is more likely to be nearly parabolic in reality. To support our argument, we use Brownian dynamics to simulate DNA behavior in a strip confinement. DNA is represented by a bead-spring model that includes Lennard-Jones excluded-volume force, spring force and bending force. The force applied by lipid molecules is simulated by a random force. The model was tested in a strip confinement with infinitely deep well and the results were founded to match predictions by de Gennes and Odijk. At first we simulate DNA extension in a fixed depth of energy well with varying confinement width. DNA extension was found decreases with increasing width of energy well. As we expected, the simulation results are not in agreement with theoretical prediction. As the second step, we simulate DNA extension under a fixed width of confinement with varying depth of energy well. We found that DNA extension gradually increases as the energy well gets deeper. If the depth of energy well is below the thermal energy of the system, DNA starts to cross the boundary of confinement and the degree of DNA extension drops rapidly. With further reducing the depth of the energy well, DNA can no longer be confined by the well. We also simulate the cases that the depth of energy well decrease while the width of confinement increase because such scenario is closer to the real situation in experiments. We find that the relative rate of change between the depth of energy well and the width of confinement has critical influence to DNA extension. Employing a relationship between the depth of energy well and the width of confinement similar to experimental condition, we found the simulation results show very similar deviation from theoretical prediction as the experiments do. In conclusion, the simulation results support our argument that the energy well is not a deep square in reality. This finding also bridges the gap between the theoretical predictions and experimental observation for DNA behavior in strip confinement.