Experimental and Simulation Study on Spontaneous Unravelling of Dna on Grooved Lipid Bilayers
Hou-Jun Guo/郭厚均1, Ching-Kuan Wang/王靜寬1, Chih-Chen Hsieh/謝之真1*
1Chemical Engineering, National Taiwan University, Taipei, Taiwan
* presenting author:Chih-Chen Hsieh, email:ccjhsieh@ntu.edu.tw
We have recently developed a novel platform for optical mapping of genomic DNA in order to rapidly recognize the DNA identity. The platform is simply a grooved glass slide covered with cationic lipid bilayers[1]. When DNA molecules reach the lipid bilayers, they first adsorb on the bilayers and then spontaneously gather and extend along the grooves where the curvature is positive. On this simple platform, the degree of DNA extension can reach more than 80% of its contour length. Although the phenomenon seems rather simple, its mechanism and DNA behaviour are not well understood. In this study, we have first investigated the mechanism by experiments. We have found the phenomenon is governed by the geometry of the grooves, the shape of lipid molecules and the surface charge density of the lipid bilayers. The corresponding thermodynamic calculation also supports our findings. In the second part of the study, we have investigated DNA extension as a function of curvature and the span of the curved surface. When DNA are trapped and extended along the grooves, they can be thought as a polymer trapped in a strip-like confinement proposed by de Gennes[2]. However, the experimental results are in qualitative but not in quantitative agreement with the theoretical predictions. We have used Brownian dynamics with a bead-rod model to simulate DNA behaviour in this situation. The results indicate that the deviation is caused by the difference between the presumed and the real electrostatic energy well.


References
1. Hochrein, M.B., et al., DNA localization and stretching on periodically microstructured lipid membranes. Physical Review Letters, 2006. 96(3): p. 4.
2. Wall, F.T., et al., Statistics of self-avoiding walks confined to strips and capillaries. Proceedings of the National Academy of Sciences of the United States of America, 1978. 75(5): p. 2069-2070.


Keywords: DNA, Lipid bilayers, DNA unravelling, Brownian dynamics