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Wang C, Nam SW, Cotte JM, Jahnes CV, Colgan EG, Bruce RL, Brink M, Lofaro MF, Patel JV, Gignac LM, Joseph EA, Rao SP, Stolovitzky G, Polonsky S, Lin Q. Wafer-scale integration of sacrificial nanofluidic chips for detecting and manipulating single DNA molecules. Nat Commun 2017; 8:14243. [PMID: 28112157 PMCID: PMC5264239 DOI: 10.1038/ncomms14243] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 12/12/2016] [Indexed: 12/18/2022] Open
Abstract
Wafer-scale fabrication of complex nanofluidic systems with integrated electronics is essential to realizing ubiquitous, compact, reliable, high-sensitivity and low-cost biomolecular sensors. Here we report a scalable fabrication strategy capable of producing nanofluidic chips with complex designs and down to single-digit nanometre dimensions over 200 mm wafer scale. Compatible with semiconductor industry standard complementary metal-oxide semiconductor logic circuit fabrication processes, this strategy extracts a patterned sacrificial silicon layer through hundreds of millions of nanoscale vent holes on each chip by gas-phase Xenon difluoride etching. Using single-molecule fluorescence imaging, we demonstrate these sacrificial nanofluidic chips can function to controllably and completely stretch lambda DNA in a two-dimensional nanofluidic network comprising channels and pillars. The flexible nanofluidic structure design, wafer-scale fabrication, single-digit nanometre channels, reliable fluidic sealing and low thermal budget make our strategy a potentially universal approach to integrating functional planar nanofluidic systems with logic circuits for lab-on-a-chip applications. The wide use of microfluidics for biological analysis demands scalable preparation methods, yet in practice it is very challenging. Here, Wang et al. show a wafer-scale fabrication of nanofluidic chips with single-digit nanometre dimension, which is compatible with standard semiconductor processing.
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Affiliation(s)
- Chao Wang
- IBM T.J. Watson Research Center, 1101 Kitchawan Road, PO Box 218, Yorktown Heights, New York 10598, USA.,School of Electrical, Computer and Energy Engineering, and Biodesign Center for Molecular Design &Biomimetics, Arizona State University, Tempe, Arizona 85287, USA
| | - Sung-Wook Nam
- IBM T.J. Watson Research Center, 1101 Kitchawan Road, PO Box 218, Yorktown Heights, New York 10598, USA
| | - John M Cotte
- IBM T.J. Watson Research Center, 1101 Kitchawan Road, PO Box 218, Yorktown Heights, New York 10598, USA
| | - Christopher V Jahnes
- IBM T.J. Watson Research Center, 1101 Kitchawan Road, PO Box 218, Yorktown Heights, New York 10598, USA
| | - Evan G Colgan
- IBM T.J. Watson Research Center, 1101 Kitchawan Road, PO Box 218, Yorktown Heights, New York 10598, USA
| | - Robert L Bruce
- IBM T.J. Watson Research Center, 1101 Kitchawan Road, PO Box 218, Yorktown Heights, New York 10598, USA
| | - Markus Brink
- IBM T.J. Watson Research Center, 1101 Kitchawan Road, PO Box 218, Yorktown Heights, New York 10598, USA
| | - Michael F Lofaro
- IBM T.J. Watson Research Center, 1101 Kitchawan Road, PO Box 218, Yorktown Heights, New York 10598, USA
| | - Jyotica V Patel
- IBM T.J. Watson Research Center, 1101 Kitchawan Road, PO Box 218, Yorktown Heights, New York 10598, USA
| | - Lynne M Gignac
- IBM T.J. Watson Research Center, 1101 Kitchawan Road, PO Box 218, Yorktown Heights, New York 10598, USA
| | - Eric A Joseph
- IBM T.J. Watson Research Center, 1101 Kitchawan Road, PO Box 218, Yorktown Heights, New York 10598, USA
| | - Satyavolu Papa Rao
- IBM T.J. Watson Research Center, 1101 Kitchawan Road, PO Box 218, Yorktown Heights, New York 10598, USA
| | - Gustavo Stolovitzky
- IBM T.J. Watson Research Center, 1101 Kitchawan Road, PO Box 218, Yorktown Heights, New York 10598, USA.,Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Stanislav Polonsky
- IBM T.J. Watson Research Center, 1101 Kitchawan Road, PO Box 218, Yorktown Heights, New York 10598, USA
| | - Qinghuang Lin
- IBM T.J. Watson Research Center, 1101 Kitchawan Road, PO Box 218, Yorktown Heights, New York 10598, USA
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Abstract
Here, we present an experimental demonstration of slowing DNA translocation across a nanochannel by modulating the channel surface charge through an externally applied gate bias. The experiments were performed on a nanofluidic field-effect transistor, which is a monolithic integrated platform featuring a 50 nm-diameter in-plane alumina nanocapillary whose entire length is surrounded by a gate electrode. The field-effect transistor behavior was validated on the gating of ionic conductance and protein transport. The gating of DNA translocation was subsequently studied by measuring discrete current dips associated with single λ-DNA translocation events under a source-to-drain bias of 1 V. The translocation speeds under various gate bias conditions were extracted by fitting event histograms of the measured translocation time to the first passage time distributions obtained from a simple 1D biased diffusion model. A positive gate bias was observed to slow the translocation of single λ-DNA chains markedly; the translocation speed was reduced by an order of magnitude from 18.4 mm/s obtained under a floating gate down to 1.33 mm/s under a positive gate bias of 9 V. Therefore, a dynamic and flexible regulation of the DNA translocation speed, which is vital for single-molecule sequencing, can be achieved on this device by simply tuning the gate bias. The device is realized in a conventional semiconductor microfabrication process without the requirement of advanced lithography, and can be potentially further developed into a compact electronic single-molecule sequencer.
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Affiliation(s)
- Yifan Liu
- Department of Electronic and Computer Engineering, ‡Division of Biomedical Engineering, The Hong Kong University of Science and Technology , Clear Water Bay, Kowloon, Hong Kong S. A. R
| | - Levent Yobas
- Department of Electronic and Computer Engineering, ‡Division of Biomedical Engineering, The Hong Kong University of Science and Technology , Clear Water Bay, Kowloon, Hong Kong S. A. R
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