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DNA translocation through an array of kinked nanopores

Nature Materials volume 9, pages 667–675 (2010)Cite this article

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Abstract

Synthetic solid-state nanopores are being intensively investigated as single-molecule sensors for detection and characterization of DNA, RNA and proteins. This field has been inspired by the exquisite selectivity and flux demonstrated by natural biological channels and the dream of emulating these behaviours in more robust synthetic materials that are more readily integrated into practical devices. So far, the guided etching of polymer films, focused ion-beam sculpting, and electron-beam lithography and tuning of silicon nitride membranes have emerged as three promising approaches to define synthetic solid-state pores with sub-nanometre resolution. These procedures have in common the formation of nominally cylindrical or conical pores aligned normal to the membrane surface. Here we report the formation of ‘kinked’ silica nanopores, using evaporation-induced self-assembly, and their further tuning and chemical derivatization using atomic-layer deposition. Compared with ‘straight through’ proteinaceous nanopores of comparable dimensions, kinked nanopores exhibit up to fivefold reduction in translocation velocity, which has been identified as one of the critical issues in DNA sequencing. Additionally, we demonstrate an efficient two-step approach to create a nanopore array exhibiting nearly perfect selectivity for ssDNA over dsDNA. We show that a coarse-grained drift–diffusion theory with a sawtooth-like potential can reasonably describe the velocity and translocation time of DNA through the pore. By control of pore size, length and shape, we capture the main functional behaviours of protein pores in our solid-state nanopore system.

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Figure 1: TEM images of porous and Pt pore-filled thin-film mesophases.
Figure 2: X-ray scattering analyses and corresponding structure of the ordered, porous, silica thin-film mesophase membrane used for the DNA-translocation experiments.
Figure 3: Experimental platform for monitoring DNA translocation through a freely suspended kinked nanopore membrane.
Figure 4: Analysis of DNA translocation through a kinked-nanopore array.
Figure 5: Dynamics of dsDNA translocation through a kinked-nanopore array.
Figure 6: Analysis of ssDNA translocation through a kinked-nanopore array after APTMS ALD treatment.

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Acknowledgements

This work is supported by the Air Force Office of Scientific Research grant FA 9550-10-1-0054, DOE Basic Energy Sciences grant DE-FG02-02-ER15368, US Department of Energy, Office of Basic Energy Sciences, Division of Materials Sciences and Engineering, and Sandia National Laboratories’ LDRD program. Z.C. acknowledges DOE Basic Energy Sciences grant DE-FG02-02-ER15368 for carrying out nanopore-array fabrication and DNA translocation. D.R.D. acknowledges support from DOE Basic Energy Science grant DE-FG02-02-ER15368 and the Air Force Office of Scientific Research grant FA 9550-10-1-0054 for carrying out GISAXS and electrochemical deposition experiments. C.J.B. acknowledges the US Department of Energy, Office of Basic Energy Sciences, Division of Materials Sciences and Engineering and Sandia National Laboratories’ LDRD program for conceiving the experiments and writing the paper. Y.J. acknowledges Sandia National Laboratories’ LDRD program for carrying out ALD experiments. GISAXS experiments in this paper were conducted at the Advanced Photon Source at Argonne National Laboratory. Use of this facility is supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences, under contract DE-AC02-06CH11357.

Sandia National Laboratories is a multiprogramme laboratory operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin company, for the US Department of Energy’s National Nuclear Security Administration under contract DE-AC04-94AL85000.

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Authors and Affiliations

  1. Department of Chemical & Nuclear Engineering and Center for Micro-Engineered Materials, University of New Mexico, 87131, USA

    Zhu Chen, Darren R. Dunphy, Nanguo Liu, George Xomeritakis & C. Jeffrey Brinker

  2. Sandia National Laboratories, 87185, USA

    Yingbing Jiang, David P. Adams, Carter Hodges & C. Jeffrey Brinker

  3. School of Pharmacy, University of New Mexico, 87131, USA

    Nan Zhang

  4. Department of Mechanical Science and Engineering and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 61801, USA

    Xiaozhong Jin & N. R. Aluru

  5. School of Chemical Engineering, Purdue University, 47907, USA

    Steven J. Gaik & Hugh W. Hillhouse

  6. Department of Molecular Genetics and Microbiology, The University of New Mexico, 87131, USA

    C. Jeffrey Brinker

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Contributions

Z.C., C.J.B. and D.R.D. wrote the paper. C.J.B. conceived and directed the research. Z.C. carried out nanopore-array fabrication, DNA translocation and Fourier-transform infrared and N2 adsorption experiments. Z.C. and Y.J. carried out TEM characterization and ALD experiments. D.R.D., H.W.H. and S.J.G. carried out GISAXS experiments. D.P.A. and C.H. carried out FIB lithography experiments. N.L. contributed to the DNA translocation set-up. D.R.D. carried out electrochemical-deposition experiments. N.R.A. and X.J. developed the transport model and carried out the simulations. Z.C. and N.Z. carried out PCR experiments.

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Correspondence to C. Jeffrey Brinker.

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Chen, Z., Jiang, Y., Dunphy, D. et al. DNA translocation through an array of kinked nanopores. Nature Mater 9, 667–675 (2010). https://doi.org/10.1038/nmat2805

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