Ratchet nanofiltration of DNA.

The DNA nanofilter is a microfabricated electrophoretic separation device consisting of a periodic array of thin slits (circa 60 nm) separated by deeper wells (circa 320 nm). We demonstrate that this device can act as a tuneable, clog-free filter when operating in a low frequency, asymmetric field inversion mode. This filtration occurs by using asymmetric field inversion to achieve bi-directional migration of short (less than 1000 bp) DNA.

Experimental study of the effect of disorder on DNA dynamics in post arrays during electrophoresis.

We used top-down fabrication techniques to create both an ordered hexagonal array and a disordered array of 1 μm diameter cylindrical posts in a silicon dioxide microchannel with the same number of posts per unit area. The electrophoretic mobility and dispersion coefficient of λ DNA in each of the arrays were obtained as a function of the electric field using ensembles of DNA molecules in a double channel device that minimizes experimental artifacts. To deepen our understanding of the transport, we also used fluorescence microscopy to examine the dynamics of single DNA molecules as they interact with the arrays at a fixed value of the electric field.

DNA electrophoresis in a nanofence array.

We present the design and implementation of an oxidized silicon "nanofence array" for long DNA electrophoresis. The device consists of a periodic array of post-filled regions (the nanofences) alternating with empty channel regions. Even in this prototype version, the nanofence array provides the resolving power of a hexagonal nanopost array without requiring any direct-write nanopatterning steps such as electron-beam lithography.

Continuous-time random walk models of DNA electrophoresis in a post array: part I. Evaluation of existing models.

Several continuous-time random walk (CTRW) models exist to predict the dynamics of DNA in micropost arrays, but none of them quantitatively describes the separation seen in experiments or simulations. In Part I of this series, we examine the assumptions underlying these models by observing single molecules of λ DNA during electrophoresis in a regular, hexagonal array of oxidized silicon posts. Our analysis takes advantage of a combination of single-molecule videomicroscopy and previous Brownian dynamics simulations.

Continuous-time random walk models of DNA electrophoresis in a post array: part II. Mobility and sources of band broadening.

Using the two-state, continuous-time random walk model, we develop expressions for the mobility and the plate height during DNA electrophoresis in an ordered post array that delineate the contributions due to (i) the random distance between collisions and (ii) the random duration of a collision. These contributions are expressed in terms of the means and variances of the underlying stochastic processes, which we evaluate from a large ensemble of Brownian dynamics simulations performed using different electric fields and molecular weights in a hexagonal array of 1 μm posts with a 3 μm center-to-center distance. If we fix the molecular weight, we find that the collision frequency governs the mobility.

DNA electrophoresis in a sparse ordered post array.

We present a study of the electrophoresis of long DNA in a strong electric field through a hexagonal array of cylindrical microscale posts spaced such that the pore size is commensurate with equilibrium coil size of the DNA. Experimental mobility, dispersivity, and videomicroscopy data indicate that the DNA frequently collide with the posts, contradicting previous Brownian dynamics studies using a uniform electric field. We demonstrate via simulations that the frequent collisions, which are essential to separations in these devices, are due to the nonuniform electric field, highlighting the importance of accounting for electric-field gradients when modeling DNA transport in microfluidic devices.