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Solid-state nanopore channels with DNA selectivity

Nature Nanotechnology volume 2, pages 243248 (2007) | Download Citation

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Abstract

Solid-state nanopores have emerged as possible candidates for next-generation DNA sequencing devices. In such a device, the DNA sequence would be determined by measuring how the forces on the DNA molecules, and also the ion currents through the nanopore, change as the molecules pass through the nanopore. Unlike their biological counterparts, solid-state nanopores have the advantage that they can withstand a wide range of analyte solutions and environments. Here we report solid-state nanopore channels that are selective towards single-stranded DNA (ssDNA). Nanopores functionalized with a ‘probe’ of hair-pin loop DNA can, under an applied electrical field, selectively transport short lengths of ‘target’ ssDNA that are complementary to the probe. Even a single base mismatch between the probe and the target results in longer translocation pulses and a significantly reduced number of translocation events. Our single-molecule measurements allow us to measure separately the molecular flux and the pulse duration, providing a tool to gain fundamental insight into the channel–molecule interactions. The results can be explained in the conceptual framework of diffusive molecular transport with particle–channel interactions.

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Acknowledgements

We acknowledge very useful discussions with M.A. Alam, D.E. Bergstrom and G. Balasundaram (Purdue University), P. Kohli (Southern Illinois University, Carbondale), and also C. Martin (University of Florida) for providing critical input to the conceptual discussion. We are thankful to B.M.K. Venkatesan, H. Chang, E.P. Judokusumo, R. Qaseem and P. Bajaj for help in data analysis. We also thank E.J. Basgall at PSU for electron-beam lithography through the NSF-funded National Nanotechnology Infrastructure Network. Partial wafer fabrication was performed in the Nanotechnology Core Facility at University of Illinois at Chicago. This work was initiated with support from NIH/NIBIB Award No. R21RR15118-01, and subsequently supported by the NASA Institute for Nanoelectronics and Computing at Purdue under Award No. NCC 2–1363.

Author information

Affiliations

  1. Birck Nanotechnology Center, School of Electrical and Computer Engineering, Purdue University, West Lafayette, Indiana 47907, USA

    • Samir M. Iqbal
    • , Demir Akin
    •  & Rashid Bashir
  2. Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana 47907, USA

    • Demir Akin
    •  & Rashid Bashir

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Contributions

S.M.I. developed the DNA attachment protocols, fabricated the devices, carried out the DNA functionalization and characterization of the devices, and led the measurement and analysis of the data. D.A. identified the DNA probe sequence and helped in developing experiments for the optical characterization of the DNA attachment chemistries. S.M.I. and R.B. designed the experiments and developed the conceptual framework and wrote the paper. R.B. supervised all aspects of the project described above.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Demir Akin or Rashid Bashir.

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    Supplementary Information

    Supplementary figures S1—S6, Tables S1 and S2

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DOI

https://doi.org/10.1038/nnano.2007.78

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