Hydrodynamic manipulation of DNA in nanopost arrays: unhooking dynamics and size separation

Abstract

Micro- or nanofabricated obstacle arrays are widely used as model matrices to perform fast DNA separations by electrophoresis. In this report, a gallery of obstacles of radii spanning from 40 to 250 nm are used to investigate the dynamics of hydrodynamic-field-driven DNA-nanopost collisions at the single-molecule level. The data shows that DNA disengagement dynamics are reasonably well described by conventional electrophoretic models in the limit of a large spacing between obstacles and for moderate migration velocities. It is also demonstrated that the use of hydrodynamic flow fields to convey DNA molecules is associated with changes in the configurational space of hooking events, and to altered relaxation dynamics between consecutive collisions. This study defines experimental conditions for the efficient separation of DNA fragments of tens of base pairs, and provides a complete framework by which to understand the behavior of DNA in the course of hydrodynamic-driven migrations through nanopost arrays.