Dynamics of DNA polymers in post arrays: Comparison of single molecule experiments and simulations

Understanding the dynamics of biopolymers in complex flows is critical for the successful design of lab-on-a-chip devices. In this paper, we demonstrate the first direct comparison of experiments and simulations of DNA transport in a pressure-driven post array flow. High aspect ratio ordered silicon posts arrays were microfabricated, and single molecule experiments were employed to examine the dynamics of DNA traversing through arrays of ordered obstacles. Three different geometries with varying post spacing were tested, and probability distributions of DNA hooking location and fractional DNA lengths were generated. It is demonstrated that the appropriate design of post array geometry can be used to control DNA conformation and guide the location of hooking events. Finally, agreement between experimental and Brownian dynamics simulation results is good, validating the simulations that can be used to guide future array designs.