The Flow and Adsorption of DNA Polymers Near Surfaces

Abstract

We discuss how agreement between single‐molecule imaging methods applied to DNA molecules in flow and Brownian dynamics simulations using bead‐spring or bead‐rod course‐grained models can be extended to study the interactions of flowing DNA polymers with surfaces, which are of importance in the development of microfluidic devices for processing of DNA and other large molecules for genomics, bio‐assays, combinatorial polymer science, etc. Using single‐molecule experiments and Brownian dynamics simulations we review work on isolated DNA molecules near adsorbing and non‐adsorbing walls in the presence of a simple shearing flow and in an evaporating droplet. The former flow is predicted to produce highly stretched adsorbed molecules due to the prevalence of end‐sticking, following by regular unraveling from one end to the other and laying down of the molecule onto the surface. In the drying‐droplet flow, this process is inhibited by the downward convection, which drives the molecule towards the surface, resulting in complete adhesion before unraveling is complete. Experimental studies using surfaces treated with APTES (3‐aminopropyltriethoxysilane) to produce strong sticking of DNA confirm the Brownian dynamics predictions for the drying flow containing DNA. In simple shearing flow, an unusual, and unexplained, interaction of DNA with the surface inhibits stretching, at distances as great as 20 microns from the surface. © 2004 American Institute of Physics