Tilted hexagonal post arrays: DNA electrophoresis in anisotropic media

Abstract

Using Brownian dynamics simulations, we show that DNA electrophoresis in a hexagonal array of micron-sized posts changes qualitatively when the applied electric field vector is not coincident with the lattice vectors of the array. DNA electrophoresis in such “tilted” post arrays is superior to the standard “un-tilted” approach; while the time required to achieve a resolution of unity in a tilted post array is similar to an un-tilted array at a low electric field strengths, this time (i) decreases exponentially with electric field strength in a tilted array and (ii) increases exponentially with electric field strength in an un-tilted array. Although the DNA dynamics in a post array are complicated, the electrophoretic mobility results indicate that the “free path”, i.e., the average distance of ballistic trajectories of point sized particles launched from random positions in the unit cell until they intersect the next post, is a useful proxy for the detailed DNA trajectories. The analysis of the free path reveals a fundamental connection between anisotropy of the medium and DNA transport therein that goes beyond simply improving the separation device.

Tilted post arrays for separating long DNA

“…Indeed, these simulations 24 indicate that tilting the post array increases the collision probability while leaving the hold-up time unchanged, so the speed difference between different sized DNA molecules increases upon tilting the array without greatly affecting the dispersion. 24 The model used for these simulations has been well parameterized with post array experiments and has been shown to match single molecule experiments in normal hexagonal post arrays very well. 18 To date, Brownian dynamics simulations 24 are the only evidence supporting the efficacy of tilted post arrays compared to their untilted counterparts.…”

“…22,23 Given the extensive experimental work on DNA electrophoresis in post arrays, let alone the corresponding efforts using computer simulation, 1 it would seem that further work in this area would lead to merely incremental advances in the device performance. In the present contribution, we argue otherwise by exploiting the orientation of the electric field with respect to the lattice vectors of the array, 24 i.e., DNA electrophoresis in a "tilted" post array. This previously underutilized design parameter leads to a substantial improvement in separation resolution and time compared to conventional hexagonal post arrays without introducing any complicated nanofabrication methods.…”

“…The key simulation data 24 suggesting that tilted post arrays would lead to improved separations were obtained using different molecular weights (k and T4 DNA, 169 kbp) with tilt angles at 10 increments from 0 ( Fig. 1(a)) to 30 ( Fig.…”

“…Brownian dynamics simulations 24 indicate that tilted arrays should preserve the cyclic rope-over-pulley mechanism 8,28,29 underlying the separation without producing the dispersive, multi-post collisions that can occur at higher post densities. Indeed, these simulations 24 indicate that tilting the post array increases the collision probability while leaving the hold-up time unchanged, so the speed difference between different sized DNA molecules increases upon tilting the array without greatly affecting the dispersion. 24 The model used for these simulations has been well parameterized with post array experiments and has been shown to match single molecule experiments in normal hexagonal post arrays very well.…”

“…24 The model used for these simulations has been well parameterized with post array experiments and has been shown to match single molecule experiments in normal hexagonal post arrays very well. 18 To date, Brownian dynamics simulations 24 are the only evidence supporting the efficacy of tilted post arrays compared to their untilted counterparts. In the present contribution, we test these simulation results by experiments in a post array with a 15 tilt, as illustrated in Fig.…”