Effect of confinement on DNA dynamics in microfluidic devices

Abstract

The dynamics of dissolved long-chain macromolecules are different in highly confined environments than in bulk solution. A computational method is presented here for detailed prediction of these dynamics, and applied to the behavior of ∼1–100 μm DNA in micron-scale channels. The method is comprised of a self-consistent coarse-grained Langevin description of the polymer dynamics and a numerical solution of the flow generated by the motion of polymer segments. Diffusivity and longest relaxation time show a broad crossover from free-solution to confined behavior centered about the point H≈10Sb, where H is the channel width and Sb is the free-solution chain radius of gyration. In large channels, the diffusivity is similar to that of a sphere diffusing along the centerline of a pore. For highly confined chains (H/Sb≪1), Rouse-type molecular weight scaling is observed for both translational diffusivity and longest relaxation time. In the highly confined region, the scaling of equilibrium length and relaxation time with H/Sb are in good agreement with scaling theories. In agreement with the results of Harden and Doi [J. Phys. Chem. 96, 4046 (1992)], we find that the diffusivity of highly confined chains does not follow the scaling relation predicted by Brochard and de Gennes [J. Chem. Phys. 67, 52 (1977)]; that relationship does not account for the interaction between chain and wall.