Journal of Structural Chemistry

, Volume 59, Issue 5, pp 1228–1235 | Cite as

Biosensor Properties of DA-DA Dinucleotide in the Presence of DI-L-Lysine and Single Carbon Nanotubes: Molecular Dynamics Simulation and Density Functional Theory Approach

  • F. Bagherolhashemi
  • M. R. BozorgmehrEmail author
  • M. Momen-Heravi


In this work, the biosensor behavior of the DA-DA dinucleotide (DA2N) in the presence of DL-lysine (DLL) and three different single carbon nanotubes (SWNT), i.e., (5-5), (6-6), and (7-7), is studied by molecular dynamics (MD) simulation and density functional theory (DFT) approaches. The MD simulation of the system of DA2N with DLL and various nanotubes was performed. The obtained results for the RMSD values reveal that the simulated systems are in the equilibrium. The single point energy calculations of the DA2N structure in various simulations are performed. The HOMO-LUMO gap and their corresponding orbitals are obtained for DA2N. The results indicate that the adenine ring is responsible for the charge transfer in DA2N. The calculated Fukui indices show that the nitrogen atom of the five-membered adenine ring plays a more active role in the DA2N reactivity.


diffusion coefficient carbon nanotube Fukui indices HOMO LUMO 


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. 1.
    J. Lv, Y. Miao, J. Yang, J. Qin, D. Li, and G. Yan. Biosens. Bioelectron., 2017, 91, 560.CrossRefGoogle Scholar
  2. 2.
    W. Sun, Y. Lu, Y. Wu, Y. Zhang, P. Wang, Y. Chen, and G. Li. Sens. Actuators, B, 2014, 202, 160.CrossRefGoogle Scholar
  3. 3.
    X. Wang, C. Jiao, and Z. Yu. Sens. Actuators, B, 2014, 192, 628.CrossRefGoogle Scholar
  4. 4.
    S. C. Kogan, M. Doherty, and J. Gitschier. N. Engl. J. Med., 1987, 317, 985.CrossRefGoogle Scholar
  5. 5.
    A. Rasooly and J. Jacobson. Biosens. Bioelectron., 2006, 21, 1851.CrossRefGoogle Scholar
  6. 6.
    C. Jiang, T. Yang, K. Jiao, and H. Gao. Electrochim. Acta, 2008, 53, 2917.CrossRefGoogle Scholar
  7. 7.
    Y. Sun, J. Li, Y. Wang, C. Ding, Y. Li. Lin, W. Sun, and C. Luo. Spectrochim. Acta, Part A, 2017, 178, 1.CrossRefGoogle Scholar
  8. 8.
    J. Wang, S. Zhang, and Y. Zhang. Analyt. Biochem., 2010, 396, 304.CrossRefGoogle Scholar
  9. 9.
    B. Dribinskii and N. Kasyanenko. J. Struct. Chem., 2011, 52(6), 1202.Google Scholar
  10. 10.
    C. M. Ward, M. L. Read, and L. W. Seymour. Blood, 2001, 97, 2221.CrossRefGoogle Scholar
  11. 11.
    H. Cai, X. Cao, Y. Jiang, P. He, and Y. Fang. Anal. Bioanal. Chem., 2003, 375, 287.CrossRefGoogle Scholar
  12. 12.
    G. Dovbeshko, O. Fesenko, E. Obraztsova, K. Allakhverdiev, and A. Kaja. J. Struct. Chem., 2009, 50(5), 954.Google Scholar
  13. 13.
    R. L. Rich and D. G. Myszka. J. Mol. Recognit., 2006, 19, 478.CrossRefGoogle Scholar
  14. 14.
    T. Bogdan and E. Alekseev. J. Struct. Chem., 2017, 58(2), 384.Google Scholar
  15. 15.
    Z. Qiu, H. Cai, H. Wang, Y. Xia, and H. Wang. J. Struct. Chem., 2012, 53, 1037.CrossRefGoogle Scholar
  16. 16.
    F. Mohammadi, M. Sahihi, and A. K. Bordbar. Spectrochim. Acta, Part A, 2015, 140, 274.CrossRefGoogle Scholar
  17. 17.
    H. R. Drew, R. M. Wing, T. Takano, C. Broka, S. Tanaka, K. Itakura, and R. E. Dickerson. Proc. Natl. Acad. Sci., 1981, 78, 2179.CrossRefGoogle Scholar
  18. 18.
    W. L. Delano. 2002, DOIGoogle Scholar
  19. 19.
    D. J. Price and C. L. Brook. Iii. J. Chem. Phys., 2004, 121, 10096.CrossRefGoogle Scholar
  20. 20.
    V. Zoete, M. A. Cuendet, A. Grosdidier, and O. Michielin. J. Comput. Chem., 2011, 32, 2359.CrossRefGoogle Scholar
  21. 21.
    G. Bussi, D. Donadio, and M. Parrinello. J. Chem. Phys., 2007, 126.Google Scholar
  22. 22.
    T. Darden, D. York, and L. Pedersen. J. Chem. Phys., 1993, 98, 10089.CrossRefGoogle Scholar
  23. 23.
    B. Hess, H. Bekker, H. J. C. Berendsen, and J. G. E. M. Fraaije. J. Comput. Chem., 1997, 18, 1463.CrossRefGoogle Scholar
  24. 24.
    S. Miyamoto and P. A. Kollman. J. Comput. Chem., 1992, 13, 952.CrossRefGoogle Scholar
  25. 25.
    E. Lindahl, B. Hess, and D. Va. Der Spoel. J. Mol. Model., 2001, 7, 306.CrossRefGoogle Scholar
  26. 26.
    C. Lee, W. Yang, and R. G. Parr. Phys. Rev. B, 1988, 37, 785.CrossRefGoogle Scholar
  27. 27.
    M. Frisch, G. Trucks, H. Schlegel, G. Scuseria, M. Robb, J. Cheeseman, J. Montgomery Jr, T. Vreven, K. Kudin, and J. Burant. Inc., Pittsburgh, PA, 2003. DOI P.12478.Google Scholar
  28. 28.
    G. Zhurko and D. Zhurko. Available on line, 2004. DOIGoogle Scholar
  29. 29.
    T. Lu and F. Chen. J. Comput. Chem., 2012, 33, 580.CrossRefGoogle Scholar
  30. 30.
    D. Brune and S. Kim. Proc. Natl. Acad. Sci., 1993, 90, 3835.CrossRefGoogle Scholar
  31. 31.
    D. Frenkel and B. Smit. Understanding molecular simulation: from algorithms to applications. Academic press, 2001.Google Scholar
  32. 32.
    K. Fukui, T. Yonezawa, and H. Shingu. J. Chem. Phys., 1952, 20, 722.CrossRefGoogle Scholar
  33. 33.
    R. G. Parr and W. Yang. J. Am. Chem. Soc., 1984, 106, 4049.CrossRefGoogle Scholar
  34. 34.
    A. Bunev, V. Statsyuk, and Y. A. Tudakova. J. Struct. Chem., 2011, 52(2), 428.Google Scholar
  35. 35.
    M. Landau, V. Sheluchenko, and S. Dubov. J. Struct. Chem., 1970, 11(3), 467.Google Scholar
  36. 36.
    B. Meric, K. Kerman, D. Ozkan, P. Kara, A. Erdem, O. Kucukoglu, E. Erciyas, and M. Ozsoz. J. Pharm. Biomed. Anal., 2002, 30, 1339.CrossRefGoogle Scholar
  37. 37.
    S. C. B. Oliveira, O. Corduneanu, and A. M. Oliveira–Brett. Bioelectrochemistry, 2008, 72, 53.CrossRefGoogle Scholar

Copyright information

© Pleiades Publishing, Ltd. 2018

Authors and Affiliations

  • F. Bagherolhashemi
    • 1
  • M. R. Bozorgmehr
    • 1
    Email author
  • M. Momen-Heravi
    • 1
  1. 1.Department of Chemistry, Mashhad BranchIslamic Azad UniversityMashhadIran

Personalised recommendations