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Fast DNA sequencing with a graphene-based nanochannel device

Nature Nanotechnology volume 6, pages 162–165 (2011)Cite this article

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Abstract

Devices in which a single strand of DNA is threaded through a nanopore could be used to efficiently sequence DNA1,2,3,4,5,6,7,8,9. However, various issues will have to be resolved to make this approach practical, including controlling the DNA translocation rate, suppressing stochastic nucleobase motions, and resolving the signal overlap between different nucleobases4,7. Here, we demonstrate theoretically the feasibility of DNA sequencing using a fluidic nanochannel functionalized with a graphene nanoribbon. This approach involves deciphering the changes that occur in the conductance of the nanoribbon10,11 as a result of its interactions with the nucleobases via π–π stacking12,13. We show that as a DNA strand passes through the nanochannel14, the distinct conductance characteristics of the nanoribbon15,16,17 (calculated using a method based on density functional theory coupled to non-equilibrium Green function theory18–20) allow the different nucleobases to be distinguished using a data-mining technique and a two-dimensional transient autocorrelation analysis. This fast and reliable DNA sequencing device should be experimentally feasible in the near future.

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Figure 1: DNA base stacking on a graphene nanodevice during its passage through a fluidic nanochannel.
Figure 2: Electronic and transport properties of a GNR device stacked optimally with DNA bases.
Figure 3: Simulation results of the transport properties of 5′-GCATCGCT-3′.

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References

  1. Collins, F. S. et al. A vision for the future of genomics research. Nature 422, 835–847 (2003).

    Article  CAS  Google Scholar 

  2. Service, R. F. The race for the $1000 genome. Science 311, 1544–1546 (2006).

    Article  CAS  Google Scholar 

  3. Shendure, J. & Ji, H. Next-generation DNA sequencing. Nature Biotechnol. 26, 1135–1145 (2008).

    Article  CAS  Google Scholar 

  4. Branton, D. et al. The potential and challenges of nanopore sequencing. Nature Biotechnol. 26, 1146–1153 (2008).

    Article  CAS  Google Scholar 

  5. Garaj, S. et al. Graphene as a subnanometre trans-electrode membrane. Nature 467, 190–193 (2010).

    Article  CAS  Google Scholar 

  6. Meller, A., Nivon, L. & Branton, D. Voltage-driven DNA translocations through a nanopore. Phys. Rev. Lett. 86, 3435–3438 (2001).

    Article  CAS  Google Scholar 

  7. Zwolak, M. & Di Ventra, M. Colloquium: physical approaches to DNA sequencing and detection. Rev. Mod. Phys. 80, 141–165 (2008).

    Article  Google Scholar 

  8. Lagerqvist, J., Zwolak, M. & Di Ventra, M. Fast DNA sequencing via transverse electronic transport. Nano. Lett. 6, 779–782 (2006).

    Article  CAS  Google Scholar 

  9. Zwolak, M & Di Ventra, M. Electronic signature of DNA nucleotides via transverse transport. Nano. Lett. 5, 421–424 (2005).

    Article  CAS  Google Scholar 

  10. Novoselov, K. S. et al. Electric field effect in atomically thin carbon film. Science 306, 666–669 (2004).

    Article  CAS  Google Scholar 

  11. Kim, K. S. et al. Large-scale pattern growth of graphene films for stretchable transparent electrodes. Nature 457, 706–710 (2009).

    Article  CAS  Google Scholar 

  12. Kim, K. S., Tarakeshwar, P. & Lee, J. Y. Molecular clusters of π-systems: theoretical studies of structures, spectra and origin of interaction energies. Chem. Rev. 100, 4145–4185 (2000).

    Article  CAS  Google Scholar 

  13. Lee, E. C. et al. Understanding of assembly phenomena by aromatic–aromatic interactions: benzene dimer and the substituted systems. J. Phys. Chem. A 111, 3446–3457 (2007).

    Article  CAS  Google Scholar 

  14. Liang, X. & Chou, S. Y. Nanogap detector inside nanofluidic channel for fast real-time label-free DNA analysis. Nano Lett. 8, 1472–1476 (2008).

    Article  CAS  Google Scholar 

  15. Cai, J. et al. Atomically precise bottom-up fabrication of graphene nanoribbon. Nature 466, 470–473 (2010).

    Article  CAS  Google Scholar 

  16. Kosynkin, D. V. et al. Longitudinal unzipping of carbon nanotubes to form graphene nanoribbons. Nature 458, 872–876 (2009).

    Article  CAS  Google Scholar 

  17. Jiao, L., Zhang, L., Wang, X., Diankov, G. & Dai, H. Narrow graphene nanoribbons from carbon nanotubes. Nature 458, 877–880 (2009).

    Article  CAS  Google Scholar 

  18. Kim, W. Y. & Kim, K. S. Tuning molecular orbitals in molecular electronics and spintronics. Acc. Chem. Res. 43, 111–120 (2010).

    Article  CAS  Google Scholar 

  19. Kim, W. Y. & Kim, K. S. Prediction of very large values of magnetoresistance in a graphene nanoribbon device. Nature Nanotech. 3, 408–412 (2008).

    Article  CAS  Google Scholar 

  20. Kim, W. Y. & Kim, K. S. Carbon nanotube, graphene, nanowire, and molecule based electron and spin transport phenomena using the nonequilibrium Green's function method at the level of first principles theory. J. Comput. Chem. 29, 1073–1083 (2008).

    Article  CAS  Google Scholar 

  21. Lee, J. Y. et al. Near-field focusing and magnification through self-assembled nanoscale spherical lenses. Nature 460, 498–501 (2009).

    Article  CAS  Google Scholar 

  22. Fano, U. Effects of configuration interaction on intensities and phase shifts. Phys. Rev. 124, 1866–1878 (1961).

    Article  CAS  Google Scholar 

  23. Schedin, F. et al. Detection of individual gas molecules adsorbed on graphene. Nature Mater. 6, 652–655 (2007).

    Article  CAS  Google Scholar 

  24. Novoselov, K. S. et al. Room-temperature quantum hall effect in graphene, Science 315, 1329 (2007).

    Article  Google Scholar 

  25. Meng, S. et al. DNA nucleoside interaction and identification with carbon nanotubes. Nano Lett. 7, 45–50 (2007).

    Article  CAS  Google Scholar 

  26. Phillips, J. C. et al. Scalable molecular dynamics with NAMD. J. Comput. Chem. 26, 1781–1802 (2005).

    Article  CAS  Google Scholar 

  27. Antony, J. & Grimme, S. Structures and interaction energies of stacked graphene–nucleobase complexes. Phys. Chem. Chem. Phys. 10, 2722–2729 (2008).

    Article  CAS  Google Scholar 

  28. Cummings, J. & Zettl, A. Low-friction nanoscale linear bearing realized from multiwall carbon nanotubes. Science 289, 602–605 (2000).

    Article  Google Scholar 

  29. Hong, B. H. et al. Extracting subnanometer single shells from ultralong multi-walled carbon nanotubes. Proc. Natl Acad. Sci. USA 102, 14155–14158 (2005).

    Article  CAS  Google Scholar 

  30. Mo, Y., Turner, K. T. & Szlufarska, I. Friction laws at the nanoscale. Nature 457, 1116–1119 (2009).

    Article  CAS  Google Scholar 

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Acknowledgements

This work was supported by the National Research Foundation (National Honor Scientist program: 2010-0020414, WCU:R32-2008-000-10180-0, EPB Center: 2009-0063312, GRL) and KISTI (KSC-2008-K08-0002). The authors thank D. R. Mason and N. Kim for discussions.

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Author notes

  1. Woo Youn Kim

    Present address: Present address: Department of Chemistry, KAIST, Daejeon 305-701, Korea,

  2. Seung Kyu Min and Woo Youn Kim: These authors contributed equally to this work

Authors and Affiliations

  1. Department of Chemistry and Department of Physics, Center for Superfunctional Materials, Pohang University of Science and Technology, Hyojadong, Namgu, 790-784, Pohang, Korea

    Seung Kyu Min, Woo Youn Kim, Yeonchoo Cho & Kwang S. Kim

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  1. Seung Kyu Min
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Contributions

S.K.M. and W.Y.K. worked together. Y.C. assisted in the calculations and analysis. K.S.K. supervised the project. S.K.M., W.Y.K. and K.S.K. wrote the paper together.

Corresponding author

Correspondence to Kwang S. Kim.

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The authors declare no competing financial interests.

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Min, S., Kim, W., Cho, Y. et al. Fast DNA sequencing with a graphene-based nanochannel device. Nature Nanotech 6, 162–165 (2011). https://doi.org/10.1038/nnano.2010.283

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