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Steric Modulation of Ionic Currents in DNA Translocation Through Nanopores

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Abstract

Ionic currents accompanying DNA translocation strongly depend on molarity of the electrolyte solution and the shape and surface charge of the nanopore. By means of the Poisson–Nernst–Planck equations it is shown how conductance is modulated by the presence of the DNA intruder and as a result of competing electrostatic and confinement factors. The theoretical results reproduce quantitatively the experimental ones and are summarized in a conductance diagram that allows distinguishing the region of reduced conductivity from the region of enhanced conductivity as a function of molarity and the pore dimension.

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References

  1. Lodish, H., Baltimore, D., Berk, A., Zipursky, L., Matsudaira, P., Darnell, J.: Cell-to-Cell Signaling: Hormones and Receptors, Molecular Cell Biology. Vol. 1, W. H. Freeman, New York (1996)

  2. Dekker, C.: Solid-state nanopores. Nat. Nanotechnol. 2, 209–215 (2007)

    Article  ADS  Google Scholar 

  3. Venkatesan, B.M., Bashir, R.: Nanopore sensors for nucleic acid analysis. Nat. Nanotechnol. 6, 615–624 (2011)

    Article  ADS  Google Scholar 

  4. Vlassiouk, I., Smirnov, S., Siwy, Z.: Ionic selectivity of single nanochannels. Nano lett. 8, 1978–1985 (2008)

    Article  ADS  Google Scholar 

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

    Article  Google Scholar 

  6. Marconi, U.M.B., Melchionna, S., Pagonabarraga, I.: Effective electrodiffusion equation for non-uniform nanochannels. J. Chem. Phys. 138, 244107 (2013)

    Article  ADS  Google Scholar 

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

    Article  ADS  Google Scholar 

  8. Fologea, D., Gershow, M., Ledden, B., McNabb, D.S., Golovchenko, J.A., Li, J.: Detecting single stranded DNA with a solid state nanopore. Nano lett. 5, 1905–1909 (2005)

    Article  ADS  Google Scholar 

  9. Mara, A., Siwy, Z., Trautmann, C., Wan, J., Kamme, F.: An asymmetric polymer nanopore for single molecule detection. Nano Lett. 4, 497–501 (2004)

    Article  ADS  Google Scholar 

  10. Storm, A.J., Storm, C., Chen, J., Zandbergen, H., Joanny, J.-F., Dekker, C.: Fast DNA translocation through a solid-state nanopore. Nano Lett. 5, 1193–1197 (2005)

    Article  ADS  Google Scholar 

  11. Cao, Q., Zuo, C., Li, L., Li, Y., Yang, Y.: Translocation of nanoparticles through a polymer brush-modified nanochannel. Biomicrofluidics 6, 034101 (2012)

    Article  Google Scholar 

  12. Gupta, C., Liao, W.-C., Gallego-Perez, D., Castro, C., Lee, L.: DNA translocation through short nanofluidic channels under asymmetric pulsed electric field. Biomicrofluidics 8, 024114 (2014)

    Article  Google Scholar 

  13. Luan, B., Stolovitzky, G.: An electro-hydrodynamics-based model for the ionic conductivity of solid-state nanopores during DNA translocation. Nanotechnology 24, 195702 (2013)

    Article  ADS  Google Scholar 

  14. Zheng, Q., Wei, G.-W.: Poisson-Boltzmann-Nernst-Planck model. J. Chem. Phys. 134, 194101 (2011)

    Article  ADS  Google Scholar 

  15. Marconi, U.M.B., Melchionna, S.: Ionic conduction in non-uniform nanopores and DNA translocation: a Nernst-Planck-Jacobs one-dimensional description. Mol. Phys. 111, 3493–3501 (2013)

  16. Vlassiouk, I., Smirnov, S., Siwy, Z.: Nanofluidic ionic diodes. Comparison of analytical and numerical solutions. ACS Nano 2, 1589–1602 (2008)

    Article  Google Scholar 

  17. Schuss, Z., Nadler, B., Eisenberg, R.S.: Derivation of Poisson and Nernst-Planck equations in a bath and channel from a molecular model. Phys. Rev. E 64, 036116 (2001)

    Article  ADS  Google Scholar 

  18. Cervera, J., Schiedt, B., Ramirez, P.: A Poisson/Nernst-Planck model for ionic transport through synthetic conical nanopores. EPL (Europhys. Lett.) 71, 35 (2005)

    Article  ADS  Google Scholar 

  19. Jacobs, M.: Diffusion Processes. Springer-Verlag, New York (1967)

    Book  Google Scholar 

  20. Zwanzig, R.: Diffusion past an entropy barrier. J. Phys. Chem. 96, 3926–3930 (1992)

    Article  Google Scholar 

  21. Reguera, D., Rubi, J.: Kinetic equations for diffusion in the presence of entropic barriers. Phys. Rev. E 64, 061106 (2001)

    Article  ADS  Google Scholar 

  22. Gillespie, D., Nonner, W., Eisenberg, R.S.: Coupling Poisson-Nernst-Planck and density functional theory to calculate ion flux. J. Phys. Condens. Matter 14, 12129 (2002)

    Article  ADS  Google Scholar 

  23. Kontturi, K., Murtomäki, L., Manzanares, J.A.: Ionic Transport Processes: In Electrochemistry and Membrane Science. OUP, Oxford (2008)

    Book  Google Scholar 

  24. Dickinson, E.J., Limon-Petersen, J.G., Compton, R.G.: The electroneutrality approximation in electrochemistry. J. Solid State Electrochem. 15, 1335–1345 (2011)

    Article  Google Scholar 

  25. Ghosal, S.: Effect of salt concentration on the electrophoretic speed of a polyelectrolyte through a nanopore. Phys. Rev. lett. 98, 238104 (2007)

    Article  ADS  Google Scholar 

  26. Ghosal, S.: Electrokinetic-flow-induced viscous drag on a tethered DNA inside a nanopore”, arXiv preprint arXiv:1203.1945 (2012)

  27. Ghosal, S.: Electrophoresis of a polyelectrolyte through a nanopore. Phys. Rev. E 74, 041901 (2006)

    Article  ADS  Google Scholar 

  28. Bocquet, L., Charlaix, E.: Nanofluidics, from bulk to interfaces. Chem. Soc. Rev. 39, 1073–1095 (2010)

    Article  Google Scholar 

  29. Lyklema, J., Minor, M.: On surface conduction and its role in electrokinetics. Colloids Surf. A Physicochem. Eng. Asp. 140, 33–41 (1998)

    Article  Google Scholar 

  30. Smeets, R.M., Keyser, U.F., Krapf, D., Wu, M.-Y., Dekker, N.H., Dekker, C.: Salt dependence of ion transport and DNA translocation through solid-state nanopores. Nano Lett. 6, 89–95 (2006)

    Article  ADS  Google Scholar 

  31. Melchionna, S., Marini Bettolo Marconi, U.: Electro-osmotic flows under nanoconfinement: a self-consistent approach. EPL (EuroPhys. Lett.) 95, 44002 (2011)

    Article  ADS  Google Scholar 

  32. Marini Bettolo Marconi, U., Melchionna, S.: Charge transport in nanochannels: a molecular theory. Langmuir 28, 13727–13740 (2012)

    Article  Google Scholar 

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Authors and Affiliations

  1. Dipartimento di Fisica, Università La Sapienza, P.le A. Moro 2, 00185, Rome, Italy

    Valerio Mazzone

  2. Istituto Processi Chimico-Fisici, Consiglio Nazionale delle Ricerche (IPCF-CNR), Rome, Italy

    Simone Melchionna

  3. Scuola di Scienze e Tecnologie, Università di Camerino, INFN Perugia, Via Madonna delle Carceri, 62032, Camerino, Italy

    Umberto Marini Bettolo Marconi

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  1. Valerio Mazzone
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  2. Simone Melchionna
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  3. Umberto Marini Bettolo Marconi
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Correspondence to Simone Melchionna.

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Mazzone, V., Melchionna, S. & Marconi, U.M.B. Steric Modulation of Ionic Currents in DNA Translocation Through Nanopores. J Stat Phys 158, 1181–1194 (2015). https://doi.org/10.1007/s10955-014-1159-8

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  • DOI: https://doi.org/10.1007/s10955-014-1159-8

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