Interaction of DNA with CNTs: Properties and Prospects for Electronic Sequencing

Biosensing Using Nanomaterials

Volumn , Issue , 2009, Pages 67-96

  Meng, Sheng ^a   Kaxiras, Efthimios ^a  

^a HARVARD UNIVERSITY   (United States)

Author keywords

Combination of DNA and CNT structures and optical properties; Combined DNA CNT systems structural properties; Interaction between DNA and carbon nanotubes (CNTs)

Indexed keywords

EID: 79952012311     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9780470447734.ch3     Document Type: Chapter

References (58)

1. Zheng M, Jagota A, Semke ED, et al. DNA-assisted dispersion and separation of carbon nanotubes. Nat. Mater. 2003;2:338-342.
2. Zheng M, Jagota A, Strano MS, et al. Structure-based carbon nanotube sorting by sequence-dependent DNA assembly. Science. 2003;302:1545-1548.
3. Gigliotti B, Sakizzie B, Bethune DS, Shelby RM, Cha JN. Sequence-independent helical wrapping of single-walled carbon nanotubes by long genomic DNA. Nano Lett. 2006;6:159-164.
4. Heller DA, Jeng ES, Yeung TK, et al. Optical detection of DNA conformational polymorphism on single-walled carbon nanotubes. Science. 2006;311:508-511.
5. Xu Y, Pehrsson PE, Chen L, Zhang R, Zhao W. Double-stranded DNA single-walled carbon nanotube hybrids for optical hydrogen peroxide and glucose sensing. J. Phys. Chem. C. 2007;111:8638-8643.
6. Gladchenko GO, KarachevtsevMV, et al. Interaction of fragmented double-stranded DNA with carbon nanotubes in aqueous solution. Mol. Phys. 2006;104:3193-3201.
7. Gao HJ, Kong Y, Cui D, Ozkan CS. Spontaneous insertion of DNA oligonucleotides into carbon nanotubes. Nano Lett. 2003;3:471-473.
8. Gao HJ, Kong Y. Simulation of DNA-nanotube interactions. Annu. Rev. Mater. Res. 2004;34:123-150.
9. Okada T, Kaneko T, Hatakeyama R, Tohji K. Electrically triggered insertion of singlestrandedDNAinto single-walled carbon nanotubes. Chem. Phys. Lett. 2006;417:288-292.
10. Watson JD, Crick FHC. Molecular structure of nucleic acids: a structure for deoxyribose nucleic acid. Nature (London). 1953;171:737-738.
11. Iijima S. Helical microtubules of graphitic carbon. Nature (London). 1991;354:56-58.
12. Li J, Ng HT, Cassell A, et al. Carbon nanotube nanoelectrode array for ultrasensitive DNA detection. Nano Lett. 2003;3:597-602.
13. Kam NWS, Liu ZA, Dai HJ. Carbon nanotubes as intracellular transporters for proteins and DNA: an investigation of the uptake mechanism and pathway. Angew. Chem. Int. Ed. 2006;45:577-581.
14. Staii C, Johnson AT, Chen M, Gelperin A. DNA-decorated carbon nanotubes for chemical sensing. Nano Lett. 2005;5:1774-1778.
15. Lu G, Maragakis P, Kaxiras E. Carbon nanotube interaction with DNA. Nano Lett. 2005;5:897-900.
16. Star A, Tu E, Niemann J, Gabriel JP, Joiner CS, Valcke C. Label-free detection of DNA hybridization using carbon nanotube network field-effect transistors. Proc. Natl. Acad. Sci. USA. 2006;103:921-926.
17. Jeng ES, Moll AE, Roy AC, Gastala JB, Strano MS. Detection of DNA hybridization using the near-infrared band-gap fluorescence of single-walled carbon nanotubes. Nano Lett. 2006;6:371-375.
18. Nakashima N, OKuzono S, Murakami H, Nakai T, Yoshikawa K. DNA dissolves singlewalled carbon nanotubes in water. Chem. Lett. 2003;32:456-457.
19. Takahashi H, Numao S, Bandow S, Iijima S. AFM imaging of wrapped multiwall carbon nanotube in DNA. Chem. Phys. Lett. 2006;418:535-539.
20. Lu Y, Bangsaruntip S, Wang X, Zhang L, Nishi Y, Dai HJ. DNA functionalization of carbon nanotubes for ultrathin atomic layer deposition of high kappa dielectrics for nanotube transistors with 60mV/decade switching. J. Am. Chem. Soc. 2006;128:3518-3519.
21. Zhan XG, Krstic PS, Zikic R, Wells JC, Fuentes-Cabrera M. First-principles transversal DNA conductance deconstructed. Biophys. J. 2006;91:L4-L6.
22. Zwolak M, Di Ventra M. Electronic signature ofDNA nucleotides via transverse transport. Nano Lett. 2005;5:421-424.
23. Lagerqvist J, Zwolak M, Di Ventra M. Fast DNA sequencing via transverse electronic transport. Nano Lett. 2006;6:779-782.
24. Meng S, Maragakis P, Papaloukas C, Kaxiras E. DNA nucleoside interaction and identification with carbon nanotubes. Nano Lett. 2007;7:45-50.
25. Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M. CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J. Comp. Chem. 1983;4:187-217.
26. MacKerellADJr., Bashford D, Bellott RL,et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B. 1998;102:3586-3616.
27. Krivov SV, Chekmarev SF, Karplus M. Potential energy surfaces and conformational transitions in biomolecules: a successive confinement approach applied to a solvated tetrapeptide. Phys. Rev. Lett. 2002;88:038101.
28. Elber R Karplus M Multiple conformational states of proteins: a molecular-dynamics analysis of myoglobin Science 1987;235:318-321.
29. Wales DJ Scheraga HA. Review: Chemistry-global optimization of clusters, crystals, and biomolecules Science 1999;285:1368-1372. (c) Wales DJ A microscopic basis for the global appearance of energy landscapes. Science 2001;293:2067-2070.
30. Wales DJ A microscopic basis for the global appearance of energy landscapes. Science 2001;293:2067-2070.
31. Ortmann F, Schmidt WG, Bechstedt F. Attracted by long-range electron correlation: adenine on graphite. Phys. Rev. Lett. 2005;95:186101.
32. Gowtham S, Scheicher RH, Ahuja R, Pandey R, Karna SP. Physisorption of nucleobases on graphene: density-functional calculations. Phys. Rev. B. 2007;76:033401.
33. For these calculations we employed a periodic supercell with dimensions of 20å × 20å ×12.78å . Larger supercells show minor differences in the structural and electronic features: a sampling of a 1×1×3 k-point mesh in reciprocal space is used to generate the charge density and the density of states. Gaussian smearing of electronic eigenvalues with a width of 0.1 eV is employed.
34. Freund JE.Ph.D. dissertation. Ludwig-Maximilians Universit€at M€unchen, 1998.
35. Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 1983;79:926-935.
36. Berendsen HJC, Postma JPM, Nola AD, Haak JR. Molecular-dynamics with coupling to an external bath. J. Chem. Phys. 1984;81:3684-3690.
37. Darden T,York D, Pedersen L. Particle mesh Ewald: anN log(N) method for Ewald sums in large systems. J. Chem. Phys. 1993;98:10089-10092.
38. Johnson RR, Johnson ATC, Klein ML. Probing the structure of DNA-carbon nanotube hybrids with molecular dynamics. Nano Lett. 2008;8:69-75.
39. Cathcart H, Quinn S, Nicolosi V, Kelly JM, Blau WJ, Coleman JN. Spontaneous debundling of single-walled carbon nanotubes in DNA-based dispersions. J. Phys. Chem. C. 2007;111:66-74.
40. Ishibashi A, Yamaguchi Y, Murakami H, Nakashima N. Layer-by-layer assembly of RNA/single-walled carbon nanotube nanocomposites. Chem. Phys. Lett. 2006;419:574-577.
41. Zhao XC, Johnson JK. Simulation of adsorption of DNA on carbon nanotubes. J. Am. Chem. Soc. 2007;129:10438-10445.
42. Li JL, Gershow M, Stein D, Brandin E, Golovchenko JA. DNA molecules and configurations in a solid-state nanopore microscope. Nat. Mater. 2003;2:611-615.
43. Zimmerli U, Koumoutsakos P. Simulations of electrophoretic RNA transport through transmembrane carbon nanotubes. Biophys. J. 2008;94:2546-2557.
44. Enyashin AN, Gemming S, Seifert G. DNA-wrapped carbon nanotubes. Nanotechnology. 2007;18:245702.
45. Fantini C, Jorio A, Santos AP, Peressinotto VST, Pimenta MA. Characterization of DNAwrapped carbon nanotubes by resonance Raman and optical absorption spectroscopies. Chem. Phys. Lett. 2007;439:138-142.
46. Preuss M, Schmidt WG, Bechstedt F. Coulombic amino group-metal bonding: adsorption of adenine on Cu(110). Phys. Rev. Lett. 2005;94:236102.
47. Ebbsen TW. Carbon Nanotubes: Preparation and Properties. CRCPress, Boca Raton, FL, 1997.
48. Tersoff J, Hamann DR. Theory of the scanning tunneling microscope. Phys. Rev. B. 1985;31:805-813.
49. Hughes ME, Brandin E, Golovchenko JA. Optical absorption of DNA-carbon nanotube structures. Nano Lett. 2007;7:1191-1194.
50. Meng S, Wang WL, Maragakis P, Kaxiras E. Determination of DNA-base orientation on carbon nanotubes through directional optical absorbance. Nano Lett. 2007;7:2312-2316.
51. Murakami Y, Einarsson E, Edamura T, Maruyama S. Polarization dependence of the optical absorption of single-walled carbon nanotubes. Phys. Rev. Lett. 2005;94:087402.
52. Rajendra J, Rodger A. The binding of single-stranded DNA and PNA to single-walled carbon nanotubes probed by flow linear dichroism. Chem. Eur. J. 2005;11:4841-4847.
53. Daniel S, Rao TP, Rao KS, et al.AreviewofDNAfunctionalized/grafted carbon nanotubes and their characterization. Sens. Actuators B. 2007;122:672-682.
54. Chu S. Laser manipulation of atoms and particles. Science. 1991;253:861-866.
55. Smith SB, Finzi L, Bustamante C. Direct mechanical measurements of the elasticity of single dna-molecules by using magnetic beads. Science. 1992;258:1122-1126.
56. Kong J, LeRoy BJ, Lemay SG, Dekker C. Integration of a gate electrode into carbon nanotube devices for scanning tunneling microscopy. Appl. Phys. Lett. 2005;86:112106.
57. Rummel RM, Ziegler C. Room temperature adsorption of aniline (C6H5NH2) on Si(100) (2×1) observed with scanning tunneling microscopy. Surf. Sci. 1998;418:303-313.
58. Rumelhart DE, Hinton GE, Williams RJ. Learning representations by back-propagating errors. Nature. 1986;323:533-536.