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

Abstract

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. Based on the results of these two types of experiments, we conclude that the electrophoretic mobility is not dependent on the array order but that band broadening in the device is greater in the disordered array.

Capillary electrophoresis applied to DNA: determining and harnessing sequence and structure to advance bioanalyses (2009–2014)

“…Channels with nanoscale dimensions, pillar arrays, and self-assembling colloidal crystals are examples of artificial matrices. Many studies utilizing pillar arrays examined the effects of geometry [ 171 ], size [ 172 ], order [ 173 ], and space [ 174 , 175 ] on separation performance. Square and rectangular pillars with different orientations were used to show that electric field distribution, velocity, and motion are impacted by pillar geometry and packing [ 171 ].…”

“…Square and rectangular pillars with different orientations were used to show that electric field distribution, velocity, and motion are impacted by pillar geometry and packing [ 171 ]. Improvements in resolution have been obtained by decreasing pillar diameter [ 172 ], decreasing convective steering by increasing spacing [ 174 ], maintaining order of the array [ 173 ], and creating a more uniform electric field through the use of a nanofence rather than a traditional hexagonal pillar array [ 175 ]. Motion within sparse hexagonal ordered arrays has been proven to be driven by a non-uniform electric field [ 176 ], which causes conformational changes in DNA leading to band broadening [ 175 ].…”

Tilted post arrays for separating long DNA

“…One idea is to make a random arrangement of posts to break up the ordering due to the channels 25,26 while maintaining a pattern that can still be produced using typical microfabrication. 21 If the array is sufficiently dilute, then this strategy can increase the frequency of collisions compared to an ordered array of the same density. 26 Unfortunately, once the array density increases to that used for successful separations in micropost arrays (e.g., the post size and center-to-center distance used in our experiments), the DNA will often engage with multiple posts in the denser regions of the system, leading to increased band broadening 21 due to the wide variance in holdup times for such long-lived collisions.…”

“…21 If the array is sufficiently dilute, then this strategy can increase the frequency of collisions compared to an ordered array of the same density. 26 Unfortunately, once the array density increases to that used for successful separations in micropost arrays (e.g., the post size and center-to-center distance used in our experiments), the DNA will often engage with multiple posts in the denser regions of the system, leading to increased band broadening 21 due to the wide variance in holdup times for such long-lived collisions. [33][34][35] As a result, it is not surprising that there are no experimental data available for separations in micropatterned, disordered 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. 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.…”