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RNA aptasensor based on gold nanoparticles for selective detection of neomycin B, molecular approach

  • Mohammad Khavani
  • Mohammad IzadyarEmail author
  • Mohammad Reza Housaindokht
Original Paper
  • 10 Downloads

Abstract

In this article, immobilized RNA aptamer on the gold nanoparticle surface was theoretically designed for selective detection of the neomycin B, neomycin C and paromomycin. Several molecular dynamic simulations on the pure aptamer, aptamer with –S(CH2)6– linker and immobilized aptamer on the gold nanoparticles surface were performed in the presence of different analytes. The obtained results indicate that the linker does not perturb the structure of the RNA aptamer. Also, full atomistic MD simulations on the immobilized RNA aptamer, as a biosensor, reveal a good sensing ability toward neomycin B in the presence of paromomycin and neomycin C. Due to complex formation, the distance of the aptamer and gold nanoparticles decreases. Moreover, the analysis of the electrostatic interactions between the aptamer and neomycin B shows a reduction in the tendency of the aptamer to interact with the gold nanoparticles, significantly. On the basis of the DFT-D3 calculations, neomycin B forms the most stable complex with the aptamer binding site, due to the strong hydrogen bond formation. Moreover, the obtained results indicate that electrostatic interactions are the driving forces of complex formation. On the basis of QM/MD results, the proposed aptasensor is a good candidate for the detection of neomycin B.

Keywords

RNA aptasensor Neomycin B MD simulation Theoretical design Electrostatic interaction 

Notes

Acknowledgements

The Research Council of Ferdowsi University of Mashhad is acknowledged for financial support (Grant No. 3/44401). We hereby acknowledge that part of this computation was performed at the HPC center of Ferdowsi University of Mashhad.

Supplementary material

13738_2019_1708_MOESM1_ESM.docx (1.2 mb)
Supplementary material 1 (DOCX 1177 kb)

References

  1. 1.
    M.G. Wallis, U. von Ahsen, R. Schroeder, M. Famulok, Chem. Biol. 2, 543 (1995)CrossRefGoogle Scholar
  2. 2.
    M.G. Wallis, R. Schroeder, Prog. Biophys. Mol. Biol. 67, 141 (1997)CrossRefGoogle Scholar
  3. 3.
    T. Hermann, E. Westhof, Curr. Opin. Biotechnol. 9, 66 (1998)CrossRefGoogle Scholar
  4. 4.
    M.L. Zapp, S. Stern, M.R. Green, Cell 74, 969 (1993)CrossRefGoogle Scholar
  5. 5.
    J. Rogers, A.H. Chang, U. von Ahsen, R. Schroeder, J. Davies, J. Mol. Biol. 259, 916 (1996)CrossRefGoogle Scholar
  6. 6.
    A. Bini, S. Centi, S. Tombelli, M. Minunni, M. Mascini, Anal. Bioanal. Chem. 390, 1077 (2008)CrossRefGoogle Scholar
  7. 7.
    J.A. Cowan, T. Ohyama, D. Wang, K. Natarajan, Nucleic Acids Res. 28, 2935 (2000)CrossRefGoogle Scholar
  8. 8.
    S. Tombelli, M. Minunni, M. Mascini, Biosens. Bioelectron. 20, 2424 (2005)CrossRefGoogle Scholar
  9. 9.
    A.-E. Radi, J.L. Acero Sánchez, E. Baldrich, C.K. O’Sullivan, J. Am. Chem. Soc. 128, 117 (2006)CrossRefGoogle Scholar
  10. 10.
    W.J. Parak, T. Pellegrino, C.M. Micheel, D. Gerion, S.C. Williams, A.P. Alivisatos, Nano Lett. 3, 33 (2003)CrossRefGoogle Scholar
  11. 11.
    J.-S. Lee, D.S. Seferos, D.A. Giljohann, C.A. Mirkin, J. Am. Chem. Soc. 130, 5430 (2008)CrossRefGoogle Scholar
  12. 12.
    S.J. Hurst, A.K. Lytton-Jean, C.A. Mirkin, Anal. Chem. 78, 8313 (2006)CrossRefGoogle Scholar
  13. 13.
    J. Zhang, L. Wang, H. Zhang, F. Boey, S. Song, C. Fan, Small 6, 201 (2010)CrossRefGoogle Scholar
  14. 14.
    I. Palchetti, M. Mascini, Analyst 133, 846 (2008)CrossRefGoogle Scholar
  15. 15.
    Z. Jiang, Y. Fan, M. Chen, A. Liang, X. Liao, G. Wen, X. Shen, X. He, H. Pan, H. Jiang, Anal. Chem. 81, 5439 (2009)CrossRefGoogle Scholar
  16. 16.
    B. Li, Y. Du, S. Dong, Anal. Chim. Acta 644, 78 (2009)CrossRefGoogle Scholar
  17. 17.
    N.L. Rosi, D.A. Giljohann, C.S. Thaxton, A.K. Lytton-Jean, M.S. Han, C.A. Mirkin, Science 312, 1027 (2006)CrossRefGoogle Scholar
  18. 18.
    C.-C. Chen, Y.-P. Lin, C.-W. Wang, H.-C. Tzeng, C.-H. Wu, Y.-C. Chen, C.-P. Chen, L.-C. Chen, Y.-C. Wu, J. Am. Chem. Soc. 128, 3709 (2006)CrossRefGoogle Scholar
  19. 19.
    CYuH Nakshatri, J. Irudayaraj, Nano Lett. 7, 2300 (2007)CrossRefGoogle Scholar
  20. 20.
    S. Balamurugan, A. Obubuafo, S.A. Soper, R.L. McCarley, D.A. Spivak, Langmuir 22, 6446 (2006)CrossRefGoogle Scholar
  21. 21.
    O.-S. Lee, V.Y. Cho, G.C. Schatz, J. Phys. Chem. B 116, 7000 (2012)CrossRefGoogle Scholar
  22. 22.
    J. Lin, H. Zhang, Z. Chen, Y. Zheng, ACS Nano 4, 5421 (2010)CrossRefGoogle Scholar
  23. 23.
    O.S. Lee, G.C. Schatz, J. Phys. Chem. C 113, 2316 (2009)CrossRefGoogle Scholar
  24. 24.
    M. Ruan, M. Seydou, V. Noel, B. Piro, F. Maurel, F. Barbault, J. Phys. Chem. B 121, 4071 (2017)CrossRefGoogle Scholar
  25. 25.
    L. Jiang, A. Majumdar, W. Hu, T. Jaishree, W. Xu, D.J. Patel, Structure 7, 817 (1999)CrossRefGoogle Scholar
  26. 26.
    C.J. Dickson, L. Rosso, R.M. Betz, R.C. Walker, I.R. Gould, Soft Matter 8, 9617 (2012)CrossRefGoogle Scholar
  27. 27.
    J. Wang, R.M. Wolf, J.W. Caldwell, P.A. Kollman, D.A. Case, J. Comput. Chem. 25, 1157 (2004)CrossRefGoogle Scholar
  28. 28.
    S. Grimme, J. Antony, S. Ehrlich, H. Krieg, J. Chem. Phys 132, 154104 (2010)CrossRefGoogle Scholar
  29. 29.
    R.J. Bartlett, G.D. Purvis, Int. J. Quantum Chem. 14, 561 (1978)CrossRefGoogle Scholar
  30. 30.
    S.M. Tschampel, M.R. Kennerty, R.J. Woods, J. Chem. Theory Comput. 3, 1721 (2007)CrossRefGoogle Scholar
  31. 31.
    H. Heinz, T. J. Lin, R. Kishore Mishra, F.S. Emami, Langmuir 29, 1754 (2013)CrossRefGoogle Scholar
  32. 32.
    E. Pohjolainen, X. Chen, S. Malola, G. Groenhof, H. Häkkinen, J. Chem. Theory Comput. 12, 1342 (2016)CrossRefGoogle Scholar
  33. 33.
    R.A. Lippert, K.J. Bowers, R.O. Dror, M.P. Eastwood, B.A. Gregersen, J.L. Klepeis, I. Kolossvary, D.E. Shaw, J. Chem. Phys 126, 046101 (2007)CrossRefGoogle Scholar
  34. 34.
    J.-P. Ryckaert, G. Ciccotti, H.J. Berendsen, J. Comput. Phys. 23, 327 (1977)CrossRefGoogle Scholar
  35. 35.
    B.P. Uberuaga, M. Anghel, A.F. Voter, J. Chem. Phys 120, 6363 (2004)CrossRefGoogle Scholar
  36. 36.
    B.R. Miller III, T.D. McGee Jr., J.M. Swails, N. Homeyer, H. Gohlke, A.E. Roitberg, J. Chem. Theory Comput. 8, 3314 (2012)CrossRefGoogle Scholar
  37. 37.
    H. Gohlke, C. Kiel, D.A. Case, J. Mol. Biol. 330, 891 (2003)CrossRefGoogle Scholar
  38. 38.
    A.E. Reed, L.A. Curtiss, F. Weinhold, Chem. Rev. 88, 899 (1988)CrossRefGoogle Scholar
  39. 39.
    M. Cossi, N. Rega, G. Scalmani, V. Barone, J. Comput. Chem. 24, 669 (2003)CrossRefGoogle Scholar
  40. 40.
    M.J. Frisch, G.W. Trucks, H.B. Schlegel, G.E. Scuseria, M.A. Robb, J.R. Cheeseman, J.A. Montgomery, T. Vreven, K.N. Kudin, J.C. Burant, J.M. Millam, S.S. Iyengar, J. Tomasi, V. Barone, B. Mennucci, M. Cossi, G. Scalmani, N. Rega, G.A. Petersson, H. Nakatsuji, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, M. Klene, X. Li, J.E. Knox, H.P. Hratchian, J.B. Cross, V. Bakken, C. Adamo, J. Jaramillo, R. Gomperts, R.E. Stratmann, O. Yazyev, A.J. Austin, R. Cammi, C. Pomelli, J.W. Ochterski, P.Y. Ayala, K. Morokuma, G.A. Voth, P. Salvador, J.J. Dannenberg, V.G. Zakrzewski, S. Dapprich, A.D. Daniels, M.C. Strain, O. Farkas, D.K. Malick, A.D. Rabuck, K. Raghavachari, J.B. Foresman, J.V. Ortiz, Q. Cui, A.G. Baboul, S. Clifford, J. Cioslowski, B.B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, I. Komaromi, R.L. Martin, D.J. Fox, T. Keith, M.A. Al-Laham, C.Y. Peng, A. Nanayakkara, M. Challacombe, P.M.W. Gill, B. Johnson, W. Chen, M.W. Wong, C. Gonzalez, J.A. Pople, Gaussian 09, Revision D.01 (Gaussian Inc., Wallingford, CT, 2009)Google Scholar
  41. 41.
    R.F.W. Bader, Atoms in Molecules, a Quantum Theory (Oxford University Press, New York, 1990)Google Scholar
  42. 42.
    W. Scherer, P. Sirsch, D. Shorokhov, M. Tafipolsky, G.S. McGrady, E. Gullo, Chem. Eur. J. 9, 6057 (2003)CrossRefGoogle Scholar
  43. 43.
    H. Schmider, A. Becke, J. Mol. Struct. THEOCHEM 527, 51 (2000)CrossRefGoogle Scholar
  44. 44.
    R. Chaudret, B. De Courcy, J. Contreras-Garcia, E. Gloaguen, A. Zehnacker-Rentien, M. Mons, J.-P. Piquemal, Phys. Chem. Chem. Phys. 16, 9876 (2014)CrossRefGoogle Scholar
  45. 45.
    T. Lu, F. Chen, J. Comput. Chem. 33, 580 (2012)CrossRefGoogle Scholar
  46. 46.
    Y. Liu, W.D. Wilson, Drug-DNA Interaction Protocols (Humana Press, New York, 2010), p. 1CrossRefGoogle Scholar

Copyright information

© Iranian Chemical Society 2019

Authors and Affiliations

  1. 1.Department of Chemistry, Faculty of ScienceFerdowsi University of MashhadMashhadIran

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