Migration of DNA molecules through entropic trap arrays: a dissipative particle dynamics study

Dissipative particle dynamics (DPD) simulations of worm-like chain bead-spring models are used to explore the electrophoresis migration of DNA molecules traveling through narrow constrictions. The DPD is a relatively new numerical approach that is able to fully incorporate hydrodynamic interactions. Two mechanisms are identified that cause the size-dependent trapping of DNA chains and thus mobility differences. First, small molecules are found to be trapped in the deep region due to higher Brownian mobility and crossing of electric field lines. Second longer chains have higher probability to form hernias at the entrance of the gap and can pass the entropic barrier more easily. Consequently, longer DNA molecules have higher mobility and travel faster than shorter chains. The present DPD simulations show good agreement with existing experimental data as well as published numerical data.