Single molecule study of DNA collision with elliptical nanoposts conveyed by hydrodynamics

Abstract

Periodic arrays of micro-or nano-pillars constitute solid state matrices with excellent properties for DNA size separation. Nanofabrication technologies offer many solutions to tailor the geometry of obstacle arrays, yet most studies have been conducted with cylinders arranged in hexagonal lattices. In this report, we investigate the dynamics of single DNA collision with elliptical nanoposts using hydrodynamic actuation.Our data shows that the asymmetry of the obstacles has minor effect on unhooking dynamics, and thus confirms recent predictions obtained by Brownian dynamics simulations. In addition, we show that the disengagement dynamics are correctly predicted by models of electrophoresis, and propose that this consistency is associated to the confinement in slit-like channels. We finally conclude that elliptical posts are expected to marginally improve the performances of separation devices.Size separation of DNA molecules with electrophoresis is a key process of molecular biology, which has been widely investigated over decades [1]. Separation cannot be performed in free solution [2], requiring the use of matrices to achieve size-dependent DNA mobilities. Slab gels are the most common separation matrices, but optimal performances have been reached with capillaries of hundreds of µm in diameter filled with concentrated polymer solutions. This technology features excellent physical properties associated to rapid heat dissipation and reduction of convection [3], and the chemical composition of polymer solutions has been tailored to enhance the resolution of separation experiments, which now reach base-pair (bp) resolution for fragments up to ~500-1000 bp [4]. Despite these successes, the nanoscale arrangement of polymer solutions is intrinsically disordered, making it difficult to precisely control the migration of DNA at the molecular level. Therefore Volkmuth and Austin proposed to use micro or nanofabricated solid state artificial matrices for DNA separation [5]. These systems consist of arrays of posts etched in glass or silicon with exquisite control over their size, spacing, and shape from the nano to the millimeter scale. This approach showed impressive results for long DNA chains of ~100.10 3 base pairs (100 kbp) [6] that were separated in tens of seconds in comparison to hours otherwise [7]. For shorter DNA fragments, artificial matrices of nanoposts of ~200 nm in radius have been devised, also showing exquisite performances [8].Machining technologies offer many choices for the design of the matrix, yet hexagonal arrays of cylindrical obstacles have been predominantly characterized in the literature [9]. The idea of using asymmetric obstacles to separate biomolecules has nevertheless been documented in the context of e.g.Brownian ratchet devices [10], which enable to perform spatial separations of DNA based on the size dependence of its diffusion coefficient [11]. Dense and asymmetric obstacles have also been incorporated into artificial matrices to test their separation power [12], and it was...

Confinement and partitioning of a single polymer chain in a dense array of nanoposts

“…Previously, a post array has been utilized to separate large DNA molecules based on their lengthdependent hooking and unhooking dynamics under the external electric field. [5][6][7][8][9][10][11] In addition, it was proposed that a nanopost array can template the self-assembly of block copolymers to form specific patterns. [12][13][14] Recent advances in the nano-fabrication may find more versatile uses of the nanopost system, thanks to the ability to prepare an array of nanoposts with a wide range of dimensions and morphologies.…”

Field-driven polyelectrolyte–polymer collisions in nanochannels

“…Figure 3(d) shows an example: the instantaneous polyelectrolyte CM velocity is minimum at the inflection point t = tI of the xe(t) vs t curve; this defines the velocity vI-see Eq. (8). The trajectory of the uncharged polymer [Fig.…”

“…5 Surprisingly, Barron et al 6 showed in a seminal 1994 paper that ultra-dilute polymer solutions can be used in capillary electrophoresis to separate large DNA molecules, forcing us to revisit the concept of sieving. 7 Polymer collisions have thus been extensively studied; examples include DNA molecules colliding with cylindrical poles, [2][3][4] gel fibers, 5 various types of obstacles, 8,9 and uncharged polymers. 10 Excellent review articles have covered this field.…”

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