Theoretical study on the interaction of nucleotides on two-dimensional atomically thin graphene and molybdenum disulfide

FlatChem

Volumn 2, Issue , 2017, Pages 8-14

  Liang, Lijun ^a   Hu, Wei ^b   Xue, Zhengyang ^c   Shen, Jia Wei ^d  

^a HANGZHOU DIANZI UNIVERSITY   (China)

^b ROYAL INSTITUTE OF TECHNOLOGY   (Sweden)

^c ZHEJIANG UNIVERSITY   (China)

^d HANGZHOU NORMAL UNIVERSITY   (China)

Author keywords

Density functional theory; Free energy calculation; Graphene; MoS2; Two dimensional material

Indexed keywords

EID: 85019620591     PISSN: None     EISSN: 24522627     Source Type: Journal    
DOI: 10.1016/j.flatc.2017.02.001     Document Type: Article

References (47)

1. Laberty-Robert, C., Valle, K., Pereira, F., Sanchez, C., Design and properties of functional hybrid organic-inorganic membranes for fuel cells. Chem. Soc. Rev. 40:2 (2011), 961–1005.
2. Zhang, Z.-S., Kang, Y., Liang, L.-J., Liu, Y.-C., Wu, T., Wang, Q., Peptide encapsulation regulated by the geometry of carbon nanotubes. Biomaterials 35:5 (2014), 1771–1778.
3. Rao, C.N.R., Cheetham, A.K., Science and technology of nanomaterials: current status and future prospects. J. Mater. Chem. 11:12 (2001), 2887–2894.
4. Lim, E.-K., Kim, T., Paik, S., Haam, S., Huh, Y.-M., Lee, K., Nanomaterials for theranostics: recent advances and future challenges. Chem. Rev. 115:1 (2014), 327–394.
5. Jones, M.R., Seeman, N.C., Mirkin, C.A., Programmable materials and the nature of the DNA bond. Science, 347(6224), 2015, 1260901.
6. Yamada, M., Abe, K., Selective accumulation of rare earth metal and heavy metal ions by a DNA-inorganic hybrid material. Polym. J. 46:6 (2014), 366–371.
7. Li, J., Lu, Y., A highly sensitive and selective catalytic DNA biosensor for lead ions. J. Am. Chem. Soc. 122:42 (2000), 10466–10467.
8. Heller, M.J., DNA microarray technology: devices, systems, and applications. Annu. Rev. Biomed. Eng. 4:1 (2002), 129–153.
9. 3 nanopore sensors for sensitive detection of DNA and DNA–protein complexes. ACS nano 6:1 (2011), 441–450.
10. 2 transistors. Nat. Nanotechnol. 6:3 (2011), 147–150.
11. 2. ACS Nano 4:5 (2010), 2695–2700.
12. Novoselov, K.S.A., Geim, A.K., Morozov, S., Jiang, D., Katsnelson, M., Grigorieva, I., Dubonos, S., Firsov, A., Two-dimensional gas of massless dirac fermions in graphene. Nature 438:7065 (2005), 197–200.
13. Geim, A.K., Novoselov, K.S., The rise of graphene. Nat. Mater. 6:3 (2007), 183–191 14.
14. Britnell, L., Gorbachev, R.V., Jalil, R., Belle, B.D., Schedin, F., Mishchenko, A., Georgiou, T., Katsnelson, M.I., Eaves, L., Morozov, S.V., Field-effect tunneling transistor based on vertical graphene heterostructures. Science 335:6071 (2012), 947–950.
15. Liu, M., Zhang, Q., Zhao, H., Chen, S., Yu, H., Zhang, Y., Quan, X., Controllable oxidative DNA cleavage-dependent regulation of graphene/DNA interaction. Chem. Commun. 47:14 (2011), 4084–4086.
16. 2 crystals. Nat. Commun., 3, 2012, 1011.
17. He, S., Song, B., Li, D., Zhu, C., Qi, W., Wen, Y., Wang, L., Song, S., Fang, H., Fan, C., A graphene nanoprobe for rapid, sensitive, and multicolor fluorescent DNA analysis. Adv. Func. Mater. 20:3 (2010), 453–459.
18. Liang, L., Shen, J.-W., Zhang, Z., Wang, Q., DNA sequencing by two-dimensional materials: as theoretical modeling meets experiments. Biosens. Bioelectron., 2015.
19. Steinbock, L.J., Radenovic, A., The emergence of nanopores in next-generation sequencing. Nanotechnology, 26(7), 2015, 074003.
20. Iliafar, S., Mittal, J., Vezenov, D., Jagota, A., Interaction of single-stranded DNA with curved carbon nanotube is much stronger than with flat graphite. J. Am. Chem. Soc. 136:37 (2014), 12947–12957.
21. Varghese, N., Mogera, U., Govindaraj, A., Das, A., Maiti, P.K., Sood, A.K., Rao, C.N.R., Binding of DNA nucleobases and nucleosides with graphene. ChemPhysChem 10:1 (2009), 206–210.
22. Manna, A.K., Pati, S.K., Theoretical understanding of single-stranded DNA assisted dispersion of graphene. J. Mater. Chem. B 1:1 (2013), 91–100.
23. Hu, Y., Wang, K., Zhang, Q., Li, F., Wu, T., Niu, L., Decorated graphene sheets for label-free DNA impedance biosensing. Biomaterials 33:4 (2012), 1097–1106.
24. Lv, W., Guo, M., Liang, M.-H., Jin, F.-M., Cui, L., Zhi, L., Yang, Q.-H., Graphene-DNA hybrids: self-assembly and electrochemical detection performance. J. Mater. Chem. 20:32 (2010), 6668–6673.
25. Liang, L.J., Wu, T., Kang, Y., Wang, Q., Dispersion of graphene sheets in aqueous solution by oligodeoxynucleotides. ChemPhysChem 14:8 (2013), 1626–1632.
26. Kong, Z., Zheng, W., Wang, Q., Wang, H., Xi, F., Liang, L., Shen, J.-W., Charge-tunable absorption behavior of DNA on graphene. J. Mater. Chem. B 3:24 (2015), 4814–4820.
27. Shankla, M., Aksimentiev, A., Conformational transitions and stop-and-go nanopore transport of single-stranded DNA on charged graphene. Nat. Commun., 5, 2014.
28. Banerjee, S., Wilson, J., Shim, J., Shankla, M., Corbin, E.A., Aksimentiev, A., Bashir, R., Slowing DNA transport using graphene–DNA interactions. Adv. Func. Mater. 25:6 (2015), 936–946.
29. Shen, J.-W., Wu, T., Wang, Q., Pan, H.-H., Molecular simulation of protein adsorption and desorption on hydroxyapatite surfaces. Biomaterials 29:5 (2008), 513–532.
30. Jeon, S.I., Lee, J.H., Andrade, J.D., De Gennes, P., Protein—surface interactions in the presence of polyethylene oxide: I. Simplified Theory. J. Colloid Interface Sci. 142:1 (1991), 149–158.
31. Jimenez-Cruz, C.A., Kang, S.G., Zhou, R., Large scale molecular simulations of nanotoxicity. Wiley Interdiscip Rev. Syst. Biol. Med. 6:4 (2014), 329–343.
32. Zhou, R., Gao, H., Cytotoxicity of graphene: recent advances and future perspective. Wiley Interdiscip Rev. Nanomed. Nanobiotechnol. 6:5 (2014), 452–474.
33. Souaille, M., Roux, B.T., Extension to the weighted histogram analysis method: combining umbrella sampling with free energy calculations. Comput. Phys. Commun. 135:1 (2001), 40–57.
34. Liang, L., Cui, P., Wang, Q., Wu, T., Ågren, H., Tu, Y., Theoretical study on key factors in DNA sequencing with graphene nanopores. RSC Adv. 3:7 (2013), 2445–2453.
35. Berendsen, H.J.C., van der Spoel, D., van Drunen, R., GROMACS: a message-passing parallel molecular dynamics implementation. Comput. Phys. Commun. 91:1 (1995), 43–56.
36. Zhang, Z., Shen, J., Wang, H., Wang, Q., Zhang, J., Liang, L., Ågren, H., Tu, Y., Effects of graphene nanopore geometry on DNA sequencing. J. Phys. Chem. Lett. 5:9 (2014), 1602–1607.
37. 2. ACS Nano 8:8 (2014), 7914–7922.
38. 2). Model. Simul. Mater. Sci., 21(4), 2013, 045003.
39. Kumar, S., Rosenberg, J.M., Bouzida, D., Swendsen, R.H., Kollman, P.A., The weighted histogram analysis method for free-energy calculations on biomolecules. I. The method. J. Comput. Chem. 13:8 (1992), 1011–1021.
40. Kresse, G., Furthmüller, J., Efficiency of ab-initio total energy calculations for metals and semiconductors using a plane-wave basis set. Comput. Mater. Sci. 6:1 (1996), 15–50.
41. Gowtham, S., Scheicher, R.H., Ahuja, R., Pandey, R., Karna, S.P., Physisorption of nucleobases on graphene: density-functional calculations. Phys. Rev. B, 76(3), 2007, 033401.
42. Blöchl, P.E., Projector augmented-wave method. Phys. Rev. B, 50(24), 1994, 17953.
43. Perdew, J.P., Burke, K., Ernzerhof, M., Generalized gradient approximation made simple. Phys. Rev. Lett., 77(18), 1996, 3865.
44. Henkelman, G., Uberuaga, B.P., Jónsson, H., A climbing image nudged elastic band method for finding saddle points and minimum energy paths. J. Chem. Phys. 113:22 (2000), 9901–9904.
45. Neugebauer, J., Hess, B.A., Fundamental vibrational frequencies of small polyatomic molecules from density-functional calculations and vibrational perturbation theory. J. Chem. Phys. 118:16 (2003), 7215–7225.
46. Jacquemin, D., Preat, J., Wathelet, V., Perpète, E.A., Substitution and chemical environment effects on the absorption spectrum of indigo. J. Chem. Phys., 124(7), 2006, 074104.
47. Shen, J.-W., Tang, T., Wei, X.-H., Zheng, W., Sun, T.-Y., Zhang, Z., Liang, L., Wang, Q., On the loading mechanism of ssDNA into carbon nanotubes. RSC Adv. 5:70 (2015), 56896–56903.