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Nanopores pp 151–175Cite as

Simulation of Electronic Sensing of Biomolecules in Translocation Through a Nanopore in a Semiconductor Membrane

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Abstract

A two-level computational model for simulation of the electric signal detected on the electrodes of a Semiconductor-Oxide-Semiconductor (SOS) capacitor forming a nanoscale artificial membrane, and containing a nanopore with translocating DNA are presented. At the device level, a three-dimensional self-consistent scheme involving snapshots of the DNA charge distribution, as well as the electrolytic charge and the charge in the semiconductor membrane compute the electrostatic potential over the whole solid-liquid system. With this numerical approach we investigate the possibility of resolving individual nucleotides as well as their types in the absence of conformational disorder. At the system level, we develop a circuit-element model for the SOS semiconductor membrane where the membrane is discretized into interconnected elementary circuit elements to assess the response of the DNA away from the pore. The model is tested on the translocation of 11 base single-stranded C3AC7 DNA molecule, for which the electric signal shows good qualitative agreement with the multi-scale device approach of Gracheva et al. also described in the first part of this chapter (Gracheva et al., Nanotech. 17, 622–633, 2006), while quantifying the low-pass filtering in the membrane.

The material used in this chapter was in part published in the Nanotechnology Journal (Gracheva et al., Nanotech. 17, 622–633, 3160–3165, 2006). This material is reproduced with permission from the Publisher (Institute of Physics Publishing Limited).

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References

  1. Kasianowicz, J.J., Brandin, E., Branton, D., Deamer, D.W., Characterization of individual polynucleotide molecules using a membrane channel, PNAS 93, 13770–13773 (1996).

    Article  Google Scholar 

  2. Saenger, W. 1984. Principles of Nucleic Acid Structure. Springer Verlag, New York.

    Google Scholar 

  3. Song, L., Hobaugh, M.R., Shustak, C., Cheley, S., Bayley, H., Gouaux, J.E., Structure of staphylococcal alpha-hemolysin, a heptameric transmembrane pore, Science 274, 1859–1865 (1996).

    Article  Google Scholar 

  4. Akenson, M., Branton, D., Kasianowicz, J.J., Brandin, E., Deamer, D.W., Microsecond timescale discrimination among polycytidylic acid, polyadenylic acid, and polyuridylic acid as homopolymers or as segments within single RNA molecules, Biophys. J. 77, 3227–3233 (1999).

    Article  Google Scholar 

  5. Meller, A., Nivon, L., Brandin, E., Golovchenko, J., Branton, D., Rapid nanopore discrimination between single polynucleotide molecules, PNAS 97, 1079–1084 (2000).

    Article  Google Scholar 

  6. Deamer, D.W., Akeson, M., Nanopores and nucleic acids: prospects for ultrarapid sequencing, Trends in Biotech. 18, 147–151 (2000).

    Article  Google Scholar 

  7. Vercoutere, W., Winters-Hilt, S., Olsen, H., Deamer, D., Haussler, D., Akeson, M., Rapid discrimination among individual DNA hairpin molecules at single-nucleotide resolution using an ion channel, Nature Biotech. 19, 248–252 (2001).

    Article  Google Scholar 

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

    Article  Google Scholar 

  9. Meller, A., Branton, D., Single molecule measurements of DNA transport through a nanopore, Electrophoresis 23, 2583–2591 (2002).

    Article  Google Scholar 

  10. Deamer, D.W., Branton, D., Characterization of nucleic acids by nanopore analysis, Acc. Chem. Res. 35, 817–825 (2002).

    Article  Google Scholar 

  11. Li, J., Gershow, M., Stein, D., Brandin, E., Golovchenko, J.A., DNA molecules and configurations in a solid-state nanopore microscope, Nature materials 2, 611–615 (2003).

    Article  Google Scholar 

  12. Heng, J.B., Dimitrov, V., Grinkova, Y.V., Ho, C., Kim, T., Muller, D., Sligar, S., Sorsch, T., Twesten, R., Timp, R., Timp, G., The detection of DNA using a silicon nanopore, IEDM Tech. Digest 8, 767–770 (2003).

    Google Scholar 

  13. Heng, J.B., Ho, C., Kim, T., Timp, R., Aksimentiev, A., Grinkova, Y.V., Sligar, S., Schulten, K., Timp, G., Sizing DNA using an artificial nanopore, Biophys. J. 87, 2905–2911 (2004).

    Article  Google Scholar 

  14. Ho, C., Qiao, R., Heng, J.B., Chatterjee, A., Timp, R.J., Aluru, N.R., Timp, G., Electrolytic transport through a synthetic nanometer-diameter pore, PNAS 102, 10445–10450 (2005).

    Article  Google Scholar 

  15. Storm, A.J., Chen, J.H., Ling, X.S., Zandbergen, H.W., Dekker, C., Fabrication of solid-state nanopores with single-nanometer precision, Nature Materials 2, 537–540 (2003).

    Article  Google Scholar 

  16. Chang, H., Kosari, F., Andreadakis, G., Alam, M.A., Vasmatzis, G., Bashir, R., DNA-mediated fluctuations in ionic current through silicon oxide nanopore channels, Nano Lett. 4, 1551–1556 (2004).

    Article  Google Scholar 

  17. Aksimentiev, A., Heng, J.B., Timp, G., Schulten, K., Microscopic kinetics of DNA translocation through synthetic nanopores, Biophys. J. 87, 2086–2097 (2004).

    Article  Google Scholar 

  18. Heng, J.B., Aksimentiev, A., Ho, C., Dimitrov, V., Sorsch, T., Miner, J., Mansfield, W., Schulten, K., Timp, G., Beyond the gene chip, Bell Labs Tech. J. 10, 5–22 (2005).

    Article  Google Scholar 

  19. Gracheva, M. E., Xiong, A., Aksimentiev, A., Schulten, K., Timp, G., Leburton, J.-P., Simulation of the electric response of DNA translocation through a semiconductor nanopore-capacitor, Nanotech. 17, 622–633 (2006).

    Article  Google Scholar 

  20. King, G.M., Golovchenko, J.A., Probing nanotube-nanopore interactions, Phys. Rev. Lett. 95, 216103–216107 (2005).

    Article  Google Scholar 

  21. Fan, R., Karnik, R., Yue, M., Li, D., Majumdar, A., Yang, P., DNA translocation in inorganic nanotubes, Nano Lett. 5, 1633–1637 (2005).

    Article  Google Scholar 

  22. Fologea, D., Uplinger, J., Thomas, B., McNabb, D.S., Li, J., Slowing DNA translocation in a solid-state nanopore, Nano Lett. 5, 1734–1737 (2005).

    Article  Google Scholar 

  23. Zwolak, M., Ventra, M.D., Electronic Signature of DNA Nucleotides via Transverse Transport, Nano Lett. 5, 421–424 (2005); Lagerqvist, J., Zwolak, M., Di Ventra, M., arXiv:cond-mat/0601394 (2006).

    Google Scholar 

  24. Aksimentiev, A., Heng, J. B., Timp, G., Schulten, K., Microscopic kinetics of DNA translocation through synthetic nanopores, Biophysical Journal 87, 2086–2097 (2004).

    Article  Google Scholar 

  25. Heng, J.B., Aksimentiev, A., Ho, C., Marks, P., Grinkova, Y.V., Sligar, S., Schulten, K., Timp, G., The electromechanics of DNA in a synthetic nanopore, Biophys. J. 90, 1098–1106 (2006).

    Article  Google Scholar 

  26. Heng, J., Aksimentiev, A., Ho, C., Marks, P., Grinkova, Y., Sligar, S., Schulten, K., Timp, G., Stretching DNA using the electric field in a synthetic nanopore, Nano Lett. 5, 1883–1888 (2005).

    Article  Google Scholar 

  27. Phillips, J.C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., Chipote, C., Skeel, R.D., Kale, L., Schulten, K., Scalable molecular dynamics with NAMD, J. of Computational Chemistry 26, 1781–1802 (2005).

    Article  Google Scholar 

  28. Sze, S.M. (1981). Physics of semiconductor devices. Wiley-Interscience publication.

    Google Scholar 

  29. Sansom, M.S., Smith, G.R., Adcock, C., Biggin, P.C., The dielectric properties of water within model transbilayer pores, Biophys. J. 73, 2404–2415 (1997).

    Article  Google Scholar 

  30. Press, W.H., Teukolsky, S.A., Vetterling, W.T., Flannery, B.P. (2001). Numerical Recipes in Fortran 77. Cambridge University Press.

    Google Scholar 

  31. Gracheva, M.E., Aksimentiev, A., Leburton, J.-P., Electrical signatures of single-stranded DNA with single base mutations in a nanopore capacitor, Nanotechnology 17, 3160–3165 (2006).

    Article  Google Scholar 

  32. Vidal, J. , Gracheva, M.E., Leburton, J.-P., Electrically tunable solid-state silicon nanopore ion filter, Nanoscale Res. Lett. 2, 61–68 (2007).

    Article  Google Scholar 

  33. Geddes, L.A., Baker, L.E., Principles of Applied Biomedical Instrumentation, 3rd ed. New York, USA, Willey - Interscience Publication (1989).

    Google Scholar 

  34. Bard, A.J., Faulkner, L.R., Electrochem. Meth., New York, USA, John Wiley & sons - Inter-science Publication (1980).

    Google Scholar 

  35. Martinoia, S., Massobrio, G., A behaviorial macromodel ofthe ISFET in Spice, Sensors and Actuators 62, 182–189 (2000).

    Article  Google Scholar 

  36. Leroux, A., Destine, J., Vanderheyden, B., Gracheva, M.E., Leburton, J.-P., SPICE-circuit simulation of the electrical response of semiconductor membrane to a single-stranded DNA translocating through a nanopore, to be published in the IEEE Transactions on Nanotechnology (2010).

    Google Scholar 

  37. Kasianowicz, J.J., Nanopores: flossing with DNA, Nature Materials 3, 355–356 (2004).

    Article  Google Scholar 

  38. Muller, R.S., Kamins, T.I., Chan, M. (2003). Device electronics for integrated circuits. John Wiley and sons Inc.

    Google Scholar 

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Acknowledgments

This work was funded by NIRT-NSF grant #NSFCCR02-10843, DARPA grant #392FA9550-04-1-0214, NIH grants ROI-HG003713-01 and P41-PR05969. The authors gratefully acknowledge the use of the supercomputer time at the National Center for Supercomputer Applications provided through Large Resource Allocation Committee grant MCA05S028. We are grateful to Dr. G. Timp for useful discussion and to Dr. A. Aksimentiev for supplying NAMD data.

Author information

Authors and Affiliations

  1. Department of Electrical and Computer Engineering and Department of Physics, Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA

    Jean-Pierre Leburton

Authors
  1. Maria E. Gracheva
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  2. Amandine Leroux
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  3. Jacques Destiné
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  4. Jean-Pierre Leburton
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Corresponding author

Correspondence to Jean-Pierre Leburton .

Editor information

Editors and Affiliations

  1. Department of Electrical Engineering, Nanotechnology Research and Teaching Fac, University of Texas at Arlington, S. Cooper Street, Arlington, 76019-0119, Texas, USA

    Samir M. Iqbal

  2. Department of Electrical and Computer En, University of Illinois at Urbana-Champai, N. Wright Street 208, Urbana, 61820, Illinois, USA

    Rashid Bashir

Appendix

Appendix

7.1.1 Ionic Concentrations

The ionic concentrations in KCl electrolyte solution are similar to electron and hole concentrations in an intrinsic semiconductor. Because of this similarity, we can consider the K + Cl – electrolytic solution as an intrinsic semiconductor and introduce virtual semiconductor parameters, i.e. a virtual energy band gap E geff , virtual density states of K + ions and Cl – ions, \( {N_{{K^{+} }}} \) and \( {N_{C{l^{-} }}} \), and virtual effective masses, \( m_{{K^{+} }}^* \) and \( m_{C{l^{-} }}^* \) for potassium and chlorine ions, respectively [38]. With these virtual parameters, we can calculate the ion concentrations of the electrolytic solution as follows:

$$ {[{K^{+} }]_0} = {[C{l^{-} }]_0} = \sqrt {{{N_{{K^{+} }}}{N_{C{l^{-} }}}}} \exp \,\left(\! { - \frac{{{E_{geff}}}}{{2kT}}} \right), $$
(7.20)

where [K +]0 and [Cl –]0 are the bulk ion concentration, and the virtual density of states \( {N_{{K^{+} }}} \) and \( {N_{C{l^{-} }}} \) are given by

$$ {N_{{K^{+} }}} = 2\left( {\frac{{m_{{K^{+} }}^*kT}}{{2\pi {\hbar^2}}}} \right),\,\,{N_{C{l^{-}}}}\! = 2\left( {\frac{{m_{C{l^{-} }}^*kT}}{{2\pi {\hbar^2}}}} \right). $$
(7.21)

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Gracheva, M.E., Leroux, A., Destiné, J., Leburton, JP. (2011). Simulation of Electronic Sensing of Biomolecules in Translocation Through a Nanopore in a Semiconductor Membrane. In: Iqbal, S., Bashir, R. (eds) Nanopores. Springer, Boston, MA. https://doi.org/10.1007/978-1-4419-8252-0_7

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  • DOI: https://doi.org/10.1007/978-1-4419-8252-0_7

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