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A patterned anisotropic nanofluidic sieving structure for continuous-flow separation of DNA and proteins

Nature Nanotechnology volume 2, pages 121–128 (2007)Cite this article

Abstract

Microfabricated regular sieving structures hold great promise as an alternative to gels to improve the speed and resolution of biomolecule separation. In contrast to disordered porous gel networks, these regular structures also provide well defined environments ideal for the study of molecular dynamics in confining spaces. However, the use of regular sieving structures has, to date, been limited to the separation of long DNA molecules, however separation of smaller, physiologically relevant macromolecules, such as proteins, still remains a challenge. Here we report a microfabricated anisotropic sieving structure consisting of a two-dimensional periodic nanofluidic filter array. The designed structural anisotropy causes different-sized or -charged biomolecules to follow distinct trajectories, leading to efficient separation. Continuous-flow size-based separation of DNA and proteins, as well as electrostatic separation of proteins, was achieved, demonstrating the potential use of this device as a generic molecular sieving structure for an integrated biomolecule sample preparation and analysis system.

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Figure 1: Schematic showing negatively charged macromolecules assuming bidirectional motion in the ANA under the influence of two orthogonal electric fields Ex and Ey.
Figure 2: Structure of the microfabricated device incorporating the ANA.
Figure 3: Ogston sieving of short DNA (the PCR marker) through the ANA.
Figure 4: Entropic trapping of long DNA (the λ DNA–Hind III digest) through the ANA.
Figure 5: Continuous-flow separation of proteins through the ANA.
Figure 6: Ogston sieving, entropic trapping and electrostatic sieving of DNA and proteins in the ANA.

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Acknowledgements

We acknowledge financial support from NIH (EB005743), the DuPont–MIT Alliance, NSF (CTS-0347348) and Singapore-MIT Alliance (SMA-II, CE Program). We thank P. Mao for helping take the scanning electron microscopy images and J. Yoo for contributing to the experimental setup. We acknowledge valuable comments on and suggestions for the manuscript by P. Doyle, H. Bow and C. Rothman. The MIT Microsystems Technology Laboratories are acknowledged for support in fabrication.

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Author notes

  1. Jianping Fu and Reto B. Schoch: These authors contributed equally to this work

Authors and Affiliations

  1. Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, 02139, Massachusetts, USA

    Jianping Fu

  2. Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, 02139, Massachusetts, USA

    Reto B. Schoch & Jongyoon Han

  3. Biological Engineering Division, Massachusetts Institute of Technology, Cambridge, 02139, Massachusetts, USA

    Reto B. Schoch, Anna L. Stevens, Steven R. Tannenbaum & Jongyoon Han

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  1. Jianping Fu
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  5. Jongyoon Han
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Contributions

J.F. and J.H. conceived and initiated the ANA concept and J.F. designed and fabricated the ANA device. J.F. conceived and performed experiments with short DNA, long DNA and denatured proteins. R.B.S. conceived and performed experiments with native proteins. J.F. and R.B.S. analysed the data. A.L.S. performed gel analysis and J.F. and J.H. developed the theoretical model. J.F. and R.B.S. wrote the manuscript and J.H. and S.R.T. supervized the project.

Corresponding authors

Correspondence to Jianping Fu, Reto B. Schoch or Jongyoon Han.

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The authors declare no competing financial interests.

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Fu, J., Schoch, R., Stevens, A. et al. A patterned anisotropic nanofluidic sieving structure for continuous-flow separation of DNA and proteins. Nature Nanotech 2, 121–128 (2007). https://doi.org/10.1038/nnano.2006.206

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