Gel-on-a-chip: continuous, velocity-dependent DNA separation using nanoscale lateral displacement

1) NanoDLD devices can be used as continuous polymer fractionation tools.
2) dsDNA in the range of 100-10,000 base pairs can be separated with a size-selective resolution of 200 bp.
3) The developed model helps fine-tune separation efficiency and resolution based on flow velocity.

Abstract

We studied the trajectories of polymers being advected while diffusing in a pressure driven flow along a periodic pillar nanostructure known as nanoscale deterministic lateral displacement (nanoDLD) array. We found that polymers follow different trajectories depending on their length{,} flow velocity and pillar array geometry{,} demonstrating that nanoDLD devices can be used as a continuous polymer fractionation tool. As a model system{,} we used double-stranded DNA (dsDNA) with various contour lengths and demonstrated that dsDNA in the range of 100–10 000 base pairs (bp) can be separated with a size-selective resolution of 200 bp. In contrast to spherical colloids{,} a polymer elongates by shear flow and the angle of polymer trajectories with respect to the mean flow direction decreases as the mean flow velocity increases. We developed a phenomenological model that explains the qualitative dependence of the polymer trajectories on the gap size and on the flow velocity. Using this model{,} we found the optimal separation conditions for dsDNA of different sizes and demonstrated the separation and extraction of dsDNA fragments with over 75% recovery and 3-fold concentration. Importantly{,} this velocity dependence provides a means of fine-tuning the separation efficiency and resolution{,} independent of the nanoDLD pillar geometry.

Access paper here