Numerical investigation of molecular nano-array in potential-energy profile for a single dsDNA

Regular Article


A Rigorous numerical investigation on dsDNA translocation in quasi-2-dimensional nano-array filter is performed using Molecular Dynamics (MD) method. Various dsDNA molecules with different sizes are chosen in order to model Ogston sieving in a nano-array filter. The radius of gyration of dsDNA molecule is less than the characteristic length of the shallow region in nano-array. The dsDNA molecule is assumed to be in the 0.05M NaCl electrolyte. MD shows acceptable results for potential-energy profile for nano-array filter. According to the MD outcomes, the dsDNA electrophoretic mobility decreases almost linearly with dsDNA size and show the same trend as Ogston sieving for gel electrophoresis. In addition, different shapes for nano-array filter are studied for a unique dsDNA molecule. It is concluded that steeping the nano-array wall can cause the retardation of dsDNA translocation and decreases dsDNA electrophoretic mobility.

Graphical abstract


Flowing Matter: Liquids and Complex Fluids 


  1. 1.
    G.B. Smejkal, A. Lazarev, Separation Methods in Proteomics (CRC Press, 2005)Google Scholar
  2. 2.
    A.I. Lishanskaya, M.I. Mosevitsky, Biochem. Biophys. Res. Commun. 52, 1213 (1973)CrossRefGoogle Scholar
  3. 3.
    G.N. Fayad, Computational Modeling of Biological Molecule Separation in Nanofluidic Devices (Massachusetts Institute of Technology, USA, 2010)Google Scholar
  4. 4.
    Z.R. Li, G.R. Liu, J. Han, Y. Cheng, Y.Z. Chen, J.-S. Wang, N.G. Hadjiconstantinou, Phys. Rev. E 80, 041911 (2009)ADSCrossRefGoogle Scholar
  5. 5.
    J. Han, H.G. Craighead, Science 288, 1026 (2000)ADSCrossRefGoogle Scholar
  6. 6.
    J. Fu, P. Mao, J. Han, Appl. Phys. Lett. 87, 263902 (2005)ADSCrossRefGoogle Scholar
  7. 7.
    J. Fu, J. Yoo, J. Han, Phys. Rev. Lett. 97, 018103 (2006)ADSCrossRefGoogle Scholar
  8. 8.
    J. Han, J. Fu, R.B. Schoch, Lab on a Chip 8, 23 (2008)CrossRefGoogle Scholar
  9. 9.
    M. Muthukumar, Phys. Rev. Lett. 86, 3188 (2001)ADSCrossRefGoogle Scholar
  10. 10.
    C.Y. Kong, M. Muthukumar, J. Chem. Phys. 120, 3460 (2004)ADSCrossRefGoogle Scholar
  11. 11.
    R.B. Schoch, J. Han, P. Renaud, Rev. Mod. Phys. 80, 839 (2008)ADSCrossRefGoogle Scholar
  12. 12.
    A. Meller, J. Phys.: Condens. Matter 15, R581 (2003)ADSGoogle Scholar
  13. 13.
    J. Cebrián, M.J. Kadomatsu-Hermosa, A. Castán, V. Martínez, C. Parra, M.J. Fernández-Nestosa et al., Nucl. Acids Res. 1, gku1255 (2014)Google Scholar
  14. 14.
    H. Long, A. Kudlay, G. Schatz, J. Phys. Chem. B 110, 2918 (2006)CrossRefGoogle Scholar
  15. 15.
    J. Heng, A. Aksimentiev, C. Ho, P. Marks, Y. Grinkova, S. Sligar et al., Biophys. J. 90, 1098 (2006)CrossRefGoogle Scholar
  16. 16.
    M. Alishahi, K.R., O. Abouali, Russ. J. Electrochem. 51, 49 (2015)CrossRefGoogle Scholar
  17. 17.
    R. Carr, J. Comer, M. Ginsberg, A. Aksimentiev, IEEE Trans. Nanotechnol. 10, 75 (2011)ADSCrossRefGoogle Scholar
  18. 18.
    M. Alishahi, R. Kamali, O. Abouali, Eur. Phys. J. E 38, 1 (2015)CrossRefGoogle Scholar
  19. 19.
    J. Phillips, R. Braun, W. Wang, J. Gumbart, E. Tajkhorshid, E. Villa et al., J. Comput. Chem. 26, 1781 (2005)CrossRefGoogle Scholar
  20. 20.
    J. Li, Basic Molecular Dynamics (Springer, The Netherlands, 2005)Google Scholar
  21. 21.
    M. Bhandarkar, R. Brunner, C. Chipot, A. Dalke, S. Dixit, P. Grayson, J. Gullingsrud, NAMD User’s Guide, Urbana 51, 2003Google Scholar
  22. 22.
    A.D. MacKerell, D. Bashford, M.L.D.R. Bellott, R.L. Dunbrack, J.D. Evanseck, M.J. Field, S. Fischer et al., J. Phys. Chem. B 102, 3586 (1998)CrossRefGoogle Scholar
  23. 23.
    W. Humphrey, A. Dalke, K. Schulten, J. Mol. Graph. 14, 33 (1996)CrossRefGoogle Scholar
  24. 24.
    J.R. Comer, D.B. Wells, A. Aksimentiev, Modeling Nanopores for Sequencing DNA (Humana Press, 2011)Google Scholar
  25. 25.
    T.F. Soules, G.H. Gilmer, M.J. Matthews, J.S. Stolken, M.D. Feit, J. Non-Cryst. Solids. 6, 1564 (2011)ADSCrossRefGoogle Scholar
  26. 26.
    M. van Dijk, A.M. Bonvin, Nucl. Acids Res. 37, W235 (2009)CrossRefGoogle Scholar
  27. 27.
    A. Aksimentiev, R.K. Brunner, E. Cruz-Chú, J. Comer, IEEE Nanotechnol. Mag. 3, 20 (2009)CrossRefGoogle Scholar
  28. 28.
    N.C. Stellwagen, C. Gelfi, P.G. Righetti, Biopolymers 42, 687 (1997)CrossRefGoogle Scholar

Copyright information

© EDP Sciences, SIF, Springer-Verlag Berlin Heidelberg 2016

Authors and Affiliations

  1. 1.School of Mechanical EngineeringShiraz UniversityShirazIran

Personalised recommendations