Microchimica Acta

, Volume 183, Issue 3, pp 995–1002 | Cite as

Radial dependence of DNA translocation velocity in a solid-state nanopore

Original Paper

Abstract

The physical features (such as size and charge) of a molecule transiting a nanopore whose cross-section area is only slightly larger than that of the molecule can be inferred from the measured ion-current through the pore. The transport of DNA molecules through nanopores has been extensively studied in the hope to enable low-cost and high-throughput DNA sequencing. However, the experimentally measured velocities of DNA translocation have a wide distribution, and this compromises the sequencing. In order to better understand the origin of the wide distribution, I have carried out molecular dynamics simulations to study the radial dependence of the translocation velocity. The results suggest a stick-slip type of motion of the dsDNA near the pore surface and a smooth translocation of the dsDNA near the pore center. The smooth dsDNA translocation (with a constant velocity) is governed by the zeta-potential of the pore surface which can be modified by adjusting the pH value and/or the ion concentration of the bulk electrolyte. This enables the mean translocation velocity of the dsDNA to be tuned and reduced. In addition, simulation results suggest that the smooth transport of dsDNA can be achieved by minimizing the dsDNA’s interaction with the pore, for example by chemical modification of its surface.

Graphical Abstract

The smooth transport of DNA inside a solid-state nanopore can be achieved by repelling DNA away from the pore surface.

Keywords

DNA Nanopore Translocation velocity Radial dependence 

References

  1. 1.
    Sanger F, Nicklen S, Coulson A (1977) DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA 74(12):5463CrossRefGoogle Scholar
  2. 2.
    Branton D, Deamer D, Marziali A, Bayley H, Benner S, Butler T, Di Ventra M, Garaj S, Hibbs A, Huang X et al (1146) The potential and challenges of nanopore sequencing. Nat Biotech 26Google Scholar
  3. 3.
    Venkatesan B, Bashir R (2011) Nanopore sensors for nucleic acid analysis. Nat Nanotech 6(10):615–624CrossRefGoogle Scholar
  4. 4.
    Kasianowicz JJ, Brandin E, Branton D, Deamer DW (1996) Characterization of individual polynucleotide molecules using a membrane channel. Proc Natl Acad Sci USA 93:13,770CrossRefGoogle Scholar
  5. 5.
    Dekker C (2007) Solid-state nanopores. Nat Nanotech 2:209–215CrossRefGoogle Scholar
  6. 6.
    Li J, Stein D, McMullan C, Branton D, Aziz MJ, Golovchenko JA (2001) Ion-beam sculpting at nanometre length scales. Nature 412:166–169CrossRefGoogle Scholar
  7. 7.
    Luan B (2015) Numerically testing phenomenological models for conductance of a solid-state nanopore. Nanotechnology 055(5):502Google Scholar
  8. 8.
    Zhang S, Sun T, Wang J (2015) Biomimetic phosphate assay based on nanopores obtained by immobilization of zirconium (iv) on a film of polyethyleneimine. Microchim Acta 182(7-8):1387CrossRefGoogle Scholar
  9. 9.
    Meller A, Nivon L, Brandin E, Golovchenko J, Branton D (2000) Rapid nanopore discrimination between single polynucleotide molecules. Proc Natl Acad Sci USA 97:1079CrossRefGoogle Scholar
  10. 10.
    Fologea D, Uplinger J, Thomas B, McNabb D S, Li J (2005) Slowing DNA translocation in a solid-state nanopore. Nano Lett 5:1734–1737CrossRefGoogle Scholar
  11. 11.
    Anderson BN, Muthukumar M, Meller A (2013) pH tuning of DNA translocation time through organically functionalized nanopores. ACS nano 7(2):1408CrossRefGoogle Scholar
  12. 12.
    Peng H, Ling X (2009) Reverse DNA translocation through a solid-state nanopore by magnetic tweezers. Nanotechnology 20:185,101CrossRefGoogle Scholar
  13. 13.
    Hyun C, Kaur H, Rollings R, Xiao M, Li J (2013) Threading immobilized dna molecules through a solid-state nanopore at > 100 μs per base rate. Acs Nano 7(7):5892CrossRefGoogle Scholar
  14. 14.
    Van Dorp S, Keyser U, Dekker N, Dekker C, Lemay S (2009) Origin of the electrophoretic force on DNA in solid-state nanopores. Nat Phys 5:347CrossRefGoogle Scholar
  15. 15.
    Polonsky S, Rossnagel S, Stolovitzky G (2007) Nanopore in metal-dielectric sandwich for DNA position control. Appl Phys Lett 91:153, 103CrossRefGoogle Scholar
  16. 16.
    Luan B, Peng H, Polonsky S, Rossnagel S, Stolovitzky G, Martyna G (2010) Base-by-base ratcheting of single stranded DNA through a solid-state nanopore. Phys Rev Lett 104(23):238,103CrossRefGoogle Scholar
  17. 17.
    Luan BQ, Aksimentiev A (2008) Electro-osmotic screening of the DNA charge in a nanopore. Phys Rev E 78:021,912CrossRefGoogle Scholar
  18. 18.
    He Y, Tsutsui M, Fan C, Taniguchi M, Kawai T (2011) Controlling dna translocation through gate modulation of nanopore wall surface charges. ACS nano 5(7):5509CrossRefGoogle Scholar
  19. 19.
    Yeh L H, Zhang M, Qian S, Hsu JP (2012) Regulating dna translocation through functionalized soft nanopores. Nanoscale 4(8):2685CrossRefGoogle Scholar
  20. 20.
    Carson S, Wilson J, Aksimentiev A, Wanunu M (2014) Smooth dna transport through a narrowed pore geometry. Biophys J 107(10):2381CrossRefGoogle Scholar
  21. 21.
    Van Beest B, Kramer G, Van Santen R (1990) Force fields for silicas and aluminophosphates based on ab initio calculations. Phys Rev Lett 64(16):1955–1958CrossRefGoogle Scholar
  22. 22.
    Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, Chipot C, Skeel RD, Kale L, Schulten K (2005) Scalable molecular dynamics with NAMD. J Comp Chem 26:1781CrossRefGoogle Scholar
  23. 23.
    Perez A, Marchan I, Svozil D, Sponer J, Cheatham TE, Laughton CA, Orozco M (2007) Refinement of the AMBER force field for nucleic acids: Improving the description of α/ γ conformers. Biophys J 92:3817CrossRefGoogle Scholar
  24. 24.
    Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML (1983) Comparison of simple potential functions for simulating liquid water. J Chem Phys 79:926CrossRefGoogle Scholar
  25. 25.
    Beglov D, Roux B (1994) Finite representation of an infinite bulk system: Solvent boundary potential for computer simulations. J Chem Phys 100:9050CrossRefGoogle Scholar
  26. 26.
    Cruz-Chu ER, Aksimentiev A, Schulten K (2006) Water-silica force field for simulating nanodevices. J Phys Chem B 110 :21, 497CrossRefGoogle Scholar
  27. 27.
    Brünger AT (1992) X-PLOR, Version 3.1: A System for X-ray Crystallography and NMR, The Howard Hughes Medical Institute and Department of Molecular Biophysics and Biochemistry. Yale UniversityGoogle Scholar
  28. 28.
    Wanunu M, Sutin J, McNally B, Chow A, Meller A (2008) DNA translocation governed by interactions with solid-state nanopores. Biophys J 95(10):4716CrossRefGoogle Scholar
  29. 29.
    Maffeo C, Yoo J, Comer J, Wells D, Luan B, Aksimentiev A (2014) Close encounters with DNA. J Phys: Condens Matter 413(41):101Google Scholar
  30. 30.
    Ghosal S (2007) Effect of salt concentration on the electrophoretic speed of a polyelectrolyte through a nanopore. Phys Rev Lett 98:238,104CrossRefGoogle Scholar
  31. 31.
    Luan B, Stolovitzky G (2013) An electro-hydrodynamics-based model for the ionic conductivity of solid-state nanopores during DNA translocation. Nanotechnology 195(19):702Google Scholar
  32. 32.
    Luan B, Wang C, Royyuru A, Stolovitzky G (2014) Controlling the motion of DNA in a nanochannel with transversal alternating electric voltages. Nanotechnology 265(26):101Google Scholar

Copyright information

© Springer-Verlag Wien 2015

Authors and Affiliations

  1. 1.IBM T J Watson Research CenterYorktown HeightsUSA

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