Fabrication of nano-pillar chips by a plasma etching technique for fast DNA separation

Tilted post arrays for separating long DNA

“…Increasing the post density requires sophisticated nanopatterning methods, 6,[10][11][12][13] which are available for prototyping and somewhat more challenging to implement for mass production. Note that this strategy cannot be extended down to an arbitrarily small gap between the posts; as the post density increases, the transport mechanism will switch eventually from the cyclic rope-over-pulley model 8,28,29 to biased reptation in a tight (artificial) gel.…”

“…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.…”

Electrokinetic transport of DNA in nanoslits

“…However, as soon as the DNA molecules collide with the obstacles, their mobility became length dependent. This fundamental result has been confirmed by a number of subsequent separation experiments using micron-scale obstacles 136,137 and submicron-scale obstacles 44,45,[138][139][140][141] . In the context of nanopillar arrays, one particularly interesting question is the role of the array geometry 44,45 .…”

“…The last few years have witnessed a number of experiments on DNA electrophoresis in nanoslits [11][12][13][14][15][16][17][18][19][20][21][22] , nanochannels [23][24][25][26][27][28][29][30][31][32][33][34] , channels with nanosize entropic traps and pillars [35][36][37][38][39][40][41][42][43][44][45] and with nanopores and other structures [46][47][48][49][50] . The materials used for these nanofluidics experiments can develop a relatively strong surface potential depending on the buffer used for the experiment.…”

“…For a macromolecule such as DNA, the transition towards nanoscale structures also leads to non-trivial confinement effects when the device length scales approach the pertinent length scales characterizing the DNA, such as its radius of gyration and persistence length (see section 2.2). The last several years have witnessed extensive experimental work on DNA transport in nano slits [11][12][13][14][15][16][17][18][19][20][21][22] , channels [23][24][25][26][27][28][29][30][31][32][33][34] , entropic traps and pillars [35][36][37][38][39][40][41][42][43][44][45] and pores and other structures [46][47][48][49][50] . This chapter aims to explore the extent to which the available knowledge on the physicochemical properties of DNA in gels and the separation mechanisms underlying gel electrophoresis can be used to understand and interpret the results that have appeared thus far for DNA electrophoresis in nanostructures.…”