Controlling DNA translocation speed through graphene nanopore via plasmonic fields

Document Type : Article


Department of Electrical & Computer Engineering, Tarbiat Modares University, Tehran, Iran


We propose a novel plasmonic-based method for controlling translocation speed of DNA molecule through graphene nanopore. Dynamic properties of a double-stranded DNA molecule passage through a graphene nanopore are investigated by employing molecular dynamics simulation. Also, the effect of plasmonic fields parallel to the graphene plane on the translocation speed of the DNA molecule is studied. The DNA translocation speed is calculated for different values of confinement, spectral width, and power of the plasmonic field. Results show the potential of the method for controlling translocation speed of DNA via surface plasmons in graphene nanopore. The plasmon field power, confinement depth, and spectral width can increase translocation time of DNA up to 107, 62 and 15 %. Also, strong plasmon field can trap the DNA molecule in the nanopore. The suggested method can be utilized to solve the fast-translocation challenge of the nanopore DNA sequencers.


Main Subjects

1. Branton, D., Deamer, D., Marziali, A., Bayley, H.,
Benner, S., Butler, T., Di Ventra, M., Garaj, S.,
Hibbs, A., Huang, X., and Jovanovich, S.B. The
potential and challenges of nanopore sequencing", Nat.
Biotechnol, 26, pp. 1146-1153 (2008).
2. Schneider, G.F., Kowalczyk, S.W., Calado, V.E.,
Pandraud, G., Zandbergen, H.W., Vandersypen, L.M.,
and Dekker, C. DNA translocation through graphene
nanopores", Nano Lett., 10, pp. 3163-316(2010).
3. Arjmandi-Tash, H., Belyaeva, L.A., and Schneider,
G.F. Single molecule detection with graphene and
other two-dimensional materials: nanopores and beyond",
Chem. Soc. Rev., 45, pp. 476-493 (2016).
4. Pud, S., Verschueren, D., Vukovic, N., Plesa, C.,
Jonsson, M.P., Dekker, C. Self-aligned plasmonic
nanopores by optically controlled dielectric breakdown",
Nano Lett., 15, pp. 7112-711(2015).
5. Sathe, C., Zou, X., Leburton, J.P., and Schulten, K.
Computational investigation of DNA detection using
graphene nanopores", ACS Nano, 5, pp. 8842-8851
6. Fotouhi, B., Ahmadi, V., Abasifard, M., and Roohi,
R. Interband  plasmon of graphene nanopores: a
potential sensing mechanism for DNA nucleotides", J.
Phys. Chem. C., 120, pp. 13693-13700 (2016).
7. Fotouhi, B., Ahmadi, V., and Faramarzi, V. Nanoplasmonic-
based structures for DNA sequencing", Opt.
Lett., 41, pp. 4229-4232 (2016).
8. Nam, S., Choi, I., Fu, C.C., Kim, K., Hong, S., Choi,
Y., Zettl, A., and Lee, L.P. Graphene nanopore with
a self-integrated optical antenna", Nano Lett., 14, pp.
5584-5589 (2014).
9. Belkin, M., Chao, S.H., Jonsson, M.P., Dekker, C., and
Aksimentiev, A. Plasmonic nanopores for trapping,
controlling displacement, and sequencing of DNA",
ACS Nano, 9, pp. 10598-10611 (2015).
10. Qiu, H. and Guo, W. Detecting ssDNA at singlenucleotide
resolution by sub-2-nanometer pore in
1856 B. Fotouhi et al./Scientia Iranica, Transactions F: Nanotechnology 25 (2018) 1849{1856
monoatomic graphene: a molecular dynamics study",
App. Phys. Lett., 100, 083106 (2012).
11. Keyser, U.F. Controlling molecular transport through
nanopores", J. R. Soc. Interface, rsif2011022 (2011).
12. Ghorbanzadeh, M., Moravvej-Farshi, M.K., Darbari,
S. Designing a plasmonic optophoresis system for
trapping and simultaneous sorting/counting of microand
nano-particles", J. Lightwave Technol, 33, pp.
3453-3460 (2015).
13. Plimpton, S. Fast parallel algorithms for short-range
molecular dynamics", J. Comp. Phys., 117, pp. 1-19
14. MacKerell, Jr. A.D., Bashford, D., Bellott, M., Dunbrack,
Jr. R.L., Evanseck, J.D., Field, M.J., Fischer,
S., Gao, J., Guo, H., Ha, S., Joseph-McCarthy, D.,
Kuchnir, L., Kuczera, K., Lau, F.T.K., Mattos, C.,
Michnick, S., Ngo, T., Nguyen, D.T., Prodhom, B.,
Reiher, W.E., Roux, B., Schlenkrich, M., Smith, J.C.,
Stote, R., Straub, J., Watanabe, M., Wiorkiewicz-
Kuczera, J., Yin, D., and Karplus, M. All-atom empirical
potential for molecular modeling and dynamics
studies of proteins", J. Phys. Chem. B., 102, pp. 3586-
3616 (1998).
15. Jorgensen, W.L., Chandrasekhar, J., Madura, J.D.,
Impey, R.W., and Klein, M.L. Comparison of simple
potential functions for simulating liquid water", J.
Chem. Phys., 79, pp. 926-935 (1983).
16. Ewald, P.P. The calculation of optical and electrostatic
grid potential", Ann. Phys., 369, pp. 253-
17. Humphrey, W., Dalke, A., and Schulten, K. VMD:
visual molecular dynamics", J. Molec. Graphics, 14,
pp. 33-38 (1996).
18. Li, L., Zhang, Y., Yang, J., Bi, K., Ni, Z., Li, D., and
Chen, Y. Molecular dynamics study of DNA translocation
through graphene nanopores", Phys. Rev. E.,
87, 06270(2013).
19. Belkin, M. and Aksimentiev, A. Molecular dynamics
simulation of DNA capture and transport in heated
nanopores", ACS Appl. Mater. Interfaces, 8, pp.
12599-12608 (2016).
20. Zhang, Z., Shen, J., Wang, H., Wang, Q., Zhang, J.,
Liang, L., Agren, H., and Tu, Y. E ects of graphene
nanopore geometry on DNA sequencing", J. Phys.
Chem. Lett., 5, pp. 1602-160(2014).
21. Zhou, W., Lee, J., Nanda, J., Pantelides, S.T., Pennycook,
S.J., and Idrobo, J.C. Atomically localized
plasmon enhancement in monolayer graphene", Nat.
Nanotechnol., 7, pp. 161-165 (2012).
22. Ghorbanzadeh, M., Darbari, S., and Moravvej-Farshi,
M.K. Graphene-based plasmonic force switch", App.
Phys. Lett., 108, 111105 (2016).
23. Rajeshwar, P.S. and Donat, P.H. UV-induced DNA
damage and repair: a review", Photochem. Photobiol.
Sci., 1, pp. 225-236 (2002).
24. Fotouhi, B., Ahmadi, V., Abasifard, M., and Faramarzi,
V. Petahertz-frequency plasmons in graphene
nanopore and their application to nanoparticle sensing",
Sci. Iran. Trans. F., 24, pp. 1669-1677 (2017).
25. Seyedfaraji, A. and Ahmadi, V. New design of ringbased
Raman ampli er using opto
uidic materials",
Opt. Eng., 52, 097103 (2013).
26. Saveleva, M.S., Lengert, E.V., Gorin, D.A., Parakhonskiy,
B.V., and Skirtach, A.G. Polymeric and lipid
membranes from spheres to
at membranes and vice
versa", Membranes, 7, p. 44 (2017).
27. Alizadeh, A., Parsafar, G.A., and Ejtehadi, M.R.
Mechanism of water permeation through modi ed
carbon nanotubes as a model for peptide nanotube
channels", Int. J. Nanotechnol., 6, pp. 926-941 (2009).