Onset of channeling during DNA electrophoresis in a sparse ordered post array

Abstract

The "channeling hypothesis" of DNA electrophoresis in sparse, ordered arrays of posts predicts that the DNA will move through the array relatively unhindered if ͑i͒ the spacing between the posts is larger than the DNA coil and ͑ii͒ the electric field lines are straight. We tested this hypothesis by studying the electrophoretic separation of a small plasmid DNA ͑pUC19, 2686 base pairs͒ and a large, linear DNA ͑-DNA, 48 500 base pairs͒ in a hexagonal array of 1 m diameter posts with a pitch of 7 m. At low electric field strengths, these DNAs are separated due to the long-lived, rope-over-pulley collisions of -DNA with the posts. The resolution is lost as the electric field increases due to the onset of channeling by the -DNA. Using a diffusive model, we show that channeling arises at low electric fields due to the finite size of the array. This channeling is not intrinsic to the system and is attenuated by increasing the size of the array. Higher electric fields lead to intrinsic channeling, which is attributed to the disparate time scales for a rope-over-pulley collision and transverse diffusion between collisions. The onset of channeling is a gradual process, in agreement with extant Brownian dynamics simulation data. Even at weak electric fields, the electrophoretic mobility of -DNA in the array is considerably higher than would be expected if the DNA frequently collided with the posts.

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

“…Two dimensional arrays of micron-sized cylindrical posts are proven to rapidly separate long DNA under a dc electric field [1][2][3][4][5][6][7][8]. While the application of a dc electric field using the standard separation matrices (polyacrylamide or agarose gels) fails to produce a size dependent mobility for long DNA ( > ∼ 10 kbp) [9], the increased pore size of microfabricated arrays results in a size dependent mobility for long DNA.…”

Fluctuations of DNA mobility in nanofluidic entropic traps

“…Variations in DNA mobility on the order of 15% for identical experiments run on consecutive days have similarly been observed in microfluidic devices containing an array of posts. 37 The physical mechanism of DNA separation in the devices of Thomas et al 17 is distinct from that studied here since the DNA molecules they used did not have to deform to pass from a deep to shallow region in their devices. The separation process is more analogous to size exclusion chromatography.…”

Tilted post arrays for separating long DNA

“…The reproducibility of the mobility ratio, even in the presence of fluctuations in the elution time, is consistent with previous experiments in post arrays. 16 We also performed experiments up to 80 V/cm in the devices, but we were not able to fit the peaks for electric fields exceeding 50 V/cm. At electric fields around 130 V/cm, the oxide layer suffers electrical break down, 32 so our upper bound of 80 V/cm is a conservative estimate to avoid destroying the device.…”

“…15 The channeling effect described in simulations only dominates when the array is so sparse that the electric field lines are hardly perturbed by the posts. 16 However, since transport across field lines occurs by diffusion, the effects of channeling seem to limit separations in sparse arrays to electric fields in the range of 10-20 V/cm. 4,5,17 At higher electric fields, the time to diffuse onto a "collision" field line is long compared to convection through the array 16 and the separation fails.…”

“…3 Unfortunately, due to the slow migration of long DNA in the net direction of the applied field, pulsed field separations take hours to days to achieve a baseline separation; 3 this time is compared to minutes needed to separate long DNA in post arrays. [4][5][6] Regular arrays of micro-and nano-sized posts, fabricated by semiconductor methods, have been the subject of substantial experimental work [6][7][8][9][10][11][12][13][14][15][16][17][18][19] using a wide variety of materials, post sizes, and post spacing. In addition to microfabricated arrays with perfectly ordered features, results also exist for self-assembled magnetic beads, 4,5,20 which form quasihexagonal arrays, microfabricated arrays with intentional disorder, 21 and nanowire-based posts.…”