Molecular dynamics simulations of the adsorption of DNA segments onto graphene oxide

Journal of Physics D: Applied Physics

Volumn 47, Issue 50, 2014, Pages

  Chen, Junlang ^a,b   Chen, Liang ^b   Wang, Yu ^b   Chen, Shude ^a  

^a EAST CHINA NORMAL UNIVERSITY   (China)

^b ZHEJIANG A F UNIVERSITY   (China)

Author keywords

Adsorption; DNA segments; Graphene oxide

Indexed keywords

ADSORPTION; BINDING ENERGY; DNA; ELECTROSTATICS; GRAPHENE; MOLECULAR DYNAMICS;

BINDING AFFINITIES; DNA SEGMENTS; DYNAMIC PROCESS; ELECTROSTATIC REPULSION; ENERGY PENALTIES; GRAPHENE OXIDES; MOLECULAR DYNAMICS SIMULATIONS;

BIOINFORMATICS;

EID: 84913588720     PISSN: 00223727     EISSN: 13616463     Source Type: Journal    
DOI: 10.1088/0022-3727/47/50/505401     Document Type: Article

References (41)

1. Li H and Rothberg L 2004 Colorimetric detection of DNA sequences based on electrostatic interactions with unmodified gold nanoparticles Proc. Natl Acad. Sci. USA 101 14036
2. Zhao W, Brook M A and Li Y 2008 Design of gold nanoparticle-based colorimetric biosensing assays ChemBioChem 9 2363
3. Wang H, Yang R, Yang L and Tan W 2009 Nucleic acid conjugated nanomaterials for enhanced molecular recognition ACS Nano 3 2451
4. Abouzar M H, Poghossian A, Cherstvy A G, Pedraza A M, Ingebrandt S and Schöning M J 2012 Label-free electrical detection of DNA by means of field-effect nanoplate capacitors: Experiments and modeling Phys. Status Solidi A 209 925
5. Lerf A, He H, Forster M and Klinowski J 1998 Structure of graphite oxide revisited J. Phys. Chem. B 102 4477
6. Dreyer D R, Park S, Bielawski C W and Ruoff R S 2010 The chemistry of graphene oxide Chem. Soc. Rev. 39 228
7. Mkhoyan K A, Contryman A W, Silcox J, Stewart D A, Eda G, Mattevi C, Miller S and Chhowalla M 2009 Atomic and electronic structure of graphene-oxide Nano Lett. 9 1058
8. Li S, Aphale A N, Macwan I G, Patra P K, Gonzalez W G, Miksovska J and Leblanc R M 2012 Graphene oxide as a quencher for fluorescent assay of amino acids, peptides, and proteins ACS Appl. Mater. Interfaces 4 7069
9. Lu C H, Li J, Zhang X L, Zheng A X, Yang H H, Chen X and Chen G N 2011 General approach for monitoring peptide-protein interactions based on graphene-peptide complex Anal. Chem. 83 7276
10. Pu Y, Zhu Z, Han D, Liu H, Liu J, Liao J, Zhang K and Tan W 2011 Insulin-binding aptamer-conjugated graphene oxide for insulin detection Analyst 136 4138
11. Chou S S, De M, Luo J, Rotello V M, Huang J and Dravid V P 2012 Nanoscale graphene oxide (nGO) as artificial receptors: implications for biomolecular interactions and sensing J. Am. Chem. Soc. 134 16725
12. Wang Y, Li Z, Hu D, Lin C-T, Li J and Lin Y 2010 Aptamer/graphene oxide nanocomplex for in situ molecular probing in living cells J. Am. Chem. Soc. 132 9274
13. He S, Song B, Li D, Zhu C, Qi W, Wen Y, Wang L, Song S, Fang H and Fan C 2010 A graphene nanoprobe for rapid, sensitive, and multicolor fluorescent DNA analysis Adv. Funct. Mater. 20 453
14. Liu Z, Robinson J T, Sun X and Dai H 2008 PEGylated nanographene oxide for delivery of water-insoluble cancer drugs J. Am. Chem. Soc. 130 10876
15. Kumar R V, Cheon C M, Yeon K J, Yeon K G, Ju K M, Hee K S, Satyendra M, Pal S R and Sik H C 2011 Synthesis and drug-delivery behavior of chitosan-functionalized graphene oxide hybrid nanosheets Macromol. Mater. Eng. 296 131
16. Sun X, Liu Z, Welsher K, Robinson J T, Goodwin A, Zaric S and Dai H 2008 Nano-graphene oxide for cellular imaging and drug delivery Nano Res. 1 203
17. Tang L, Wang Y, Liu Y and Li J 2011 DNA-directed self-assembly of graphene oxide with applications to ultrasensitive oligonucleotide assay ACS Nano 5 3817
18. Zhou X, Zhang Y, Wang C and Zhang J 2012 Photo-fenton reaction of graphene oxide: a new strategy to prepare graphene quantum dots for DNA cleavage ACS Nano 6 6592
19. Wu M, Kempaiah R, Huang P J, Maheshwari V and Liu J 2011 Adsorption and desorption of DNA on graphene oxide studied by fluorescently labeled oligonucleotides Langmuir 27 2731
20. Zhang X, Huang P J, Servos M R and Liu J 2012 Effects of polyethylene glycol on DNA adsorption and hybridization on gold nanoparticles and graphene oxide Langmuir 28 14330
21. Liu B, Sun Z, Zhang X and Liu J 2013 Mechanisms of DNA sensing on graphene oxide Anal. Chem. 85 7987
22. Georgakilas V, Otyepka M, Bourlinos A B, Chandra V, Kim N, Kemp K C, Hobza P, Zboril R and Kim K S 2012 Functionalization of graphene: covalent and non-covalent approaches, derivatives and applications Chem. Rev. 112 6156
23. Balapanuru J, Yang J-X, Xiao S, Bao Q, Jahan M, Polavarapu L, Wei J, Xu Q-H and Loh K-P 2009 A graphene platform for sensing biomolecules Angew. Chem. 121 4879
24. Zhao X and Johnson J K 2007 Simulation of adsorption of DNA on carbon nanotubes J. Am. Chem. Soc. 129 10438
25. Zhao X 2011 Self-assembly of DNA segments on graphene and carbon nanotube arrays in aqueous solution: a molecular simulation study J. Phys. Chem. C 115 6181
26. Case D A, Darden T A, Cheatham T E, Simmering C L I, Wang J, Duke R E, Luo R, Merz K M, Wang B and Pearlman D A 2004 Amber 8.0
27. Shih C J, Lin S, Sharma R, Strano M S and Blankschtein D 2012 Understanding the pH-dependent behavior of graphene oxide aqueous solutions: a comparative experimental and molecular dynamics simulation study Langmuir 28 235
28. Tu Y et al 2013 Destructive extraction of phospholipids from Escherichia coli membranes by graphene nanosheets Nature Nanotechnol. 8 594
29. Chen J, Wang X, Dai C, Chen S and Tu Y 2014 Adsorption of GA module onto graphene and graphene oxide: a molecular dynamics simulation study Phys. E 62 59
30. Hummer G, Rasaiah J C and Noworyta J P 2001 Water conduction through the hydrophobic channel of a carbon nanotube Nature 414 188
31. Patra N, Wang B and Král P 2009 Nanodroplet activated and guided folding of graphene nanostructures Nano Lett. 9 3766
32. Berendsen H J C, Spoel D V D and Drunen R V 1995 GROMACS: a message-passing parallel molecular dynamics implementation Comput. Phys. Commun. 91 43
33. Jorgensen W L, Chandrasekhar J, Madura J D, Impey R W and Klein M L 1983 Comparison of simple potential functions for simulating liquid water J. Phys. Chem. 79 926
34. Hess B, Bekker H, Berendsen H J C and Fraaije J G E M 1997 LINCS: a linear constraint solver for molecular simulations J. Comput. Chem. 18 1463
35. Miyamoto S and Kollman P A 1992 SETTLE: an analytical version of the SHAKE and RATTLE algorithm for rigid water models J. Comput. Chem. 13 952
36. Darden T, York D and Pedersen L 1993 Particle mesh Ewald: an Nlog(N) method for Ewald sums in large systems J. Phys. Chem. 98 10089
37. Essmann U, Perera L, Berkowitz M L, Darden T, Lee H and Pedersen L G 1995 A smooth particle mesh Ewald method J. Phys. Chem. 103 8577
38. Berendsen H J C, Postma J P M, van Gunsteren W F, DiNola A and Haak J R 1984 Molecular dynamics with coupling to an external bath J. Phys. Chem. 81 3684
39. Cherstvy A G and Teif V B 2014 Electrostatic effect of H1-histone protein binding on nucleosome repeat length Phys. Biol. 11 044001
40. Winkler R G and Cherstvy A G 2013 Strong and weak polyelectrolyte adsorption onto oppositely charged curved surfaces Adv. Polym. Sci. 255 1
41. Cherstvy A G and Winkler R G 2012 Polyelectrolyte adsorption onto oppositely charged interfaces: image-charge repulsion and surface curvature J. Phys. Chem. B 116 9838