Plasma thinned nanopost arrays for DNA electrophoresis

Jia Ou, Mark N. Joswiak, Samuel J. Carpenter, Kevin D. Dorfman

Research output: Contribution to journalArticlepeer-review

15 Scopus citations


Separating long DNA in a microfabricated post array requires (tens of) thousands of posts in the separation channel. Moving from microposts to nanoposts is thus a fabrication challenge owing to the large area that needs to be nanopatterned. The authors implemented an oxygen plasma etching method in conjunction with conventional optical photolithography and deep trench etching that led to centimeter-long microchannels containing either 360 or 460 nm diameter posts in a hexagonal array with a 3 μm spacing. Separations of the XhoI λ -DNA digest in the device indicate that these sparse nanopost arrays are an improvement over the equivalent micropost array with only a marginal increase in fabrication cost. The fabrication method described here is broadly applicable to biological microfluidic and nanofluidic platforms that require nanoscale features with micrometer-scale spacing.

Original languageEnglish (US)
Article number011025
JournalJournal of Vacuum Science and Technology A: Vacuum, Surfaces and Films
Issue number1
StatePublished - Jan 2011

Bibliographical note

Funding Information:
This material is based on the work supported by the Defense Advanced Research Projects Agency (DARPA) under Award No. N66001-09-1-2103. S.J.C. acknowledges the support of the UROP program at the University of Minnesota. Portions of this work were performed in the University of Minnesota Nanofabrication Center, which receives partial support through the NNIN, and in the Institute of Technology Characterization Facility at the University of Minnesota, a member of the NSF-funded Materials Research Facilities Network ( FIG. 1. (Color online) Fabrication overview. (a) Scanning electron microscope (SEM) image of the 1   μ m diameter post array. (b) SEM image of the 360 nm diameter post array. (c) Schematic illustration of the mask pattern and the rope-over-pulley collision of a DNA molecule in the array. (d) Schematic figure of the microchannel design with shifted- T channels, reservoirs, and the fluorescence detection position. In (c) and (d), the arrow refers to the direction of DNA migration. FIG. 2. (Color online) Fabrication by the oxygen plasma thinning method. (a) Overview of the process. (b) SEM image of the photoresist pattern of 1   μ m posts after development. (c) Photoresist pattern of the same microchannel after 4 min of oxygen plasma thinning. (d) Silicon dioxide pattern of the same microchannel after BOE etching. The scale bar is the same for images (b)–(d). FIG. 3. Sizes of the posts after different etching times. The insets are the SEM images of the corresponding post arrays. The standard deviation in the post size measured by SEM is approximately 1.2% and thus smaller than the size of the symbols. FIG. 4. Electropherograms of the XhoI λ -DNA mixture in a 1   μ m diameter micropost array (lower curve) and a 360 nm nanopost array (upper curve) measured 12.5 mm away from the shifted- T injection under 10 V/cm. FIG. 5. (Color online) Relative mobility of the three species of DNA in post arrays of 360 nm, 460 nm, and 1   μ m diameter posts at 10 V/cm.


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