(140h) Brownian Dynamics Simulations on Spontaneous Extension of DNA on Cationic Lipid Bilayers Along Grooved Structures

When DNA adsorbed on grooved glass covered with cationic lipid bilayers, they extend spontaneously along the roots of the grooves where the surface curvature is positive. The phenomenon is spontaneous and thus it suggests there exists a deep energy well for DNA. This 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 the DNA extension and the strip width somewhat deviates from the theoretical predictions. We suspect the deviation is related to the shape of the energy well that is assumed to be a deep square in the theories. To verify our argument, we use Brownian dynamics with the bead-rod model to simulate DNA trapped by the energy well with different shapes, depths and widths. The shape of energy well was found to have a strong effect on DNA extension. Moreover, when the depth of energy well is fixed, DNA extension was found decreased with increasing the width of energy well. On the other hand, when the width of confinement is fixed, DNA extension gradually increases as the energy well gets deeper. We have also simulated the cases that the depth of energy well decreases with the increasing width of confinement to mimic the real situation in our experiments. The results are in qualitative agreement with the experimental observation. In conclusion, the simulation results support our argument that the energy well is not a deep square in our system. This finding also bridges the gap between the theoretical predictions and experimental observation for DNA behavior in strip confinement.