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 ϳ1-100 m 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 HϷ10S b , where H is the channel width and S b 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/S b Ӷ1), 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/S b are in good agreement with scaling theories. In agreement with the results of Harden and Doi ͓J. Phys. Chem. 96, 4046 ͑1992͔͒, 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 ͑1977͔͒; that relationship does not account for the interaction between chain and wall.

Double-Stranded DNA Diffusion in Slitlike Nanochannels

“…The remaining assumption that the walls do not increase the drag on individual blobs should be examined if future experimental results cannot be brought into line with the theory. 27,47 Also important to note, in both Figures 3 and 4, there is no dramatic change in trend at smaller channel heights even though our channels are in the range predicted for the onset of the Odijk regime. 3 This implies the transition to the Odijk regime is smooth for diffusion in slitlike channels (unlike relaxation in square channels).…”

“…Simulations have recently investigated polymer behavior in confinement. Jenderjack et al 27 used a Brownian dynamics simulation of the polymer dynamics coupled with a numerical solver for the solvent motion. In square channels, the scalings obtained did not match theoretical predictions.…”

Confined dynamics of a single DNA molecule

“…This observation confirms that HI is implicitly taken into account in our model and hence the presence of the wall modifies the dynamics even in the early stages of relaxation. For a complete discussion see Jendrejack et al [9], in which the comparison of a free-draining model and that with explicit hydrodynamic interaction allows us to attribute the modification of the relaxation dynamics to the confinement only when HI is considered. In figure 3a, the more confined case is h = 5.…”

“…However, this approach is difficult to apply in confined geometries because the hydrodynamics interaction tensor cannot be calculated analytically and a numerical procedure is required (see also [9,10]). To overcome this difficulty, many groups have used an appropriate beads-springs model with a coarse-grained solvent whose momentum transport is explicitly computed (e.g.…”

Simulation of DNA electrophoresis in systems of large number of solvent particles by coarse‐grained hybrid molecular dynamics approach

“…As a computationally efficient explicitsolvent method, CGH-MD is potentially useful for simulating systems of large number of water particles to complement more rigorous methods. It may also be applied to the study of polar and hydrophobic effects, 13 nonuniformly distributed electrostatic interactions, and the effects associated with bound and sequestered water molecules 12,13 in various bio-macromolecular and nanofluidic systems such as the electrophoresis of DNA, 36 proteins, 60 viral particles, and complexes 61 in nanofluidic, 34,58,59,62 microfluidic, 63,64 and microstructure array 16,65 systems. …”