Triplex inducer-directed self-assembly of single-walled carbon nanotubes: A triplex DNA-based approach for controlled manipulation of nanostructures

Nucleic Acids Research

Volumn 39, Issue 9, 2011, Pages 3939-3948

  Zhao, Chao ^a,b   Qu, Konggang ^a,b   Xu, Can ^a,b   Ren, Jinsong ^a   Qu, Xiaogang ^a  

^a CHANGCHUN INSTITUTE OF APPLIED CHEMISTRY   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

Author keywords

[No Author keywords available]

Indexed keywords

CORALYNE; NANOMATERIAL; SINGLE WALLED NANOTUBE;

ARTICLE; ATOMIC FORCE MICROSCOPY; CIRCULAR DICHROISM; CONTROLLED STUDY; DNA DETERMINATION; DNA SEQUENCE; GEL MOBILITY SHIFT ASSAY; LIGHT SCATTERING; NANOANALYSIS; PRIORITY JOURNAL; SCANNING ELECTRON MICROSCOPY; STRUCTURE ANALYSIS;

BERBERINE ALKALOIDS; DNA; NANOTECHNOLOGY; NANOTUBES, CARBON;

EID: 79956003290     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq1347     Document Type: Article

References (60)

1. Dresselhaus, M.S., Dresselhaus, G. and Eklund, P.C. (1996) Science of Fullerenes and Carbon Nanotubes. Academic Press, San Diego, pp. 1-985.
2. Tasis, D., Tagmatarchis, N., Bianco, A. and Prato, M. (2006) Chemistry of carbon nanotubes. Chem. Rev., 106, 1105-1136.
3. Britz, D.A. and Khlobystov, A.N. (2006) Noncovalent interactions of molecules with single walled carbon nanotubes. Chem. Soc. Rev., 35, 637-659. (Pubitemid 43946042)
4. Valcarcel, M., Cardenas, S. and Simonet, B.M. (2007) Role of carbon nanotubes in analytical science. Anal. Chem., 79, 4788-4797. (Pubitemid 47051429)
5. Postma, H.W., Teepen, T., Yao, Z., Grifoni, M. and Dekker, C. (2001) Carbon nanotube single-electron transistors at room temperature. Science, 293, 76-79. (Pubitemid 32625496)
6. Tans, S.J., Verschueren, A.R.M. and Dekker, C. (1998) Room-temperature transistor based on a single carbon nanotube. Nature, 393, 49-52. (Pubitemid 28240249)
7. Bachtold, A., Hadley, P., Nakanishi, T. and Dekker, C. (2001) Logic circuits with carbon nanotube transistors. Science, 294, 1317-1320. (Pubitemid 33063092)
8. Javey, A., Wang, Q., Ural, A., Li, Y.M. and Dai, H.J. (2002) Carbon nanotube transistor arrays for multistage complementary logic and ring oscillators. Nano Lett., 2, 929-932. (Pubitemid 135708215)
9. Heath, J.R. and Ratner, M.A. (2003) Molecular electronics. Phys. Today, 56, 43-49.
10. Lund, K., Manzo, A.J., Dabby, N., Michelotti, N., Johnson-Buck, A., Nangreave, J., Taylor, S., Pei, R., Stojanovic, M.N., Walter, N.G. et al. (2010) Molecular robots guided by prescriptive landscapes. Nature, 465, 206-210.
11. Zheng, J., Birktoft, J.J., Chen, Y., Wang, T., Sha, R., Constantinou, P.E., Ginell, S.L., Mao, C. and Seeman, N.C. (2009) From molecular to macroscopic via the rational design of a self-assembled 3D DNA crystal. Nature, 461, 74-77.
12. Keren, K., Krueger, M., Gilad, R., Ben-Yoseph, G., Sivan, U. and Braun, E. (2002) Sequence-specific molecular lithography on single DNA molecules. Science, 297, 72-75. (Pubitemid 34743092)
13. Wang, X., Liu, F., Andavan, G.T., Jing, X., Singh, K., Yazdanpanah, V.R., Bruque, N., Pandey, R.R., Lake, R., Ozkan, M. et al. (2006) Carbon nanotube-DNA nanoarchitectures and electronic functionality. Small, 2, 1356-1365. (Pubitemid 44569182)
14. Katz, E. and Willner, I. (2004) Biomolecule-functionalized carbon nanotubes: applications in nanobioelectronics. Chemphyschem, 5, 1084-1104.
15. Dwyer, C., Guthold, M., Falvo, M., Washburn, S., Superfine, R. and Erie, D. (2002) DNA-functionalized single-walled carbon nanotubes. Nanotechnology, 13, 601-604. (Pubitemid 35263787)
16. Hazani, M., Naaman, R., Hennrich, F. and Kappes, M.M. (2003) Confocal fluorescence imaging of DNA-functionalized carbon nanotubes. Nano Lett., 3, 153-155. (Pubitemid 37130528)
17. Zheng, M., Jagota, A., Semke, E.D., Diner, B.A., McLean, R.S., Lustig, S.R., Richardson, R.E. and Tassi, N.G. (2003) DNA-assisted dispersion and separation of carbon nanotubes. Nat. Mater., 2, 338-342.
18. Singh, R., Pantarotto, D., McCarthy, D., Chaloin, O., Hoebeke, J., Partidos, C.D., Briand, J.P., Prato, M., Bianco, A. and Kostarelos, K. (2005) Binding and condensation of plasmid DNA onto functionalized carbon nanotubes: toward the construction of nanotube-based gene delivery vectors. J. Am. Chem. Soc., 127, 4388-4396. (Pubitemid 40463064)
19. Li, S., He, P., Dong, J., Guo, Z. and Dai, L. (2005) DNA-directed self-assembling of carbon nanotubes. J. Am. Chem. Soc., 127, 14-15. (Pubitemid 40094341)
20. Hazani, M., Hennrich, F., Kappes, M., Naaman, R., Peled, D., Sidorov, V. and Shvarts, D. (2004) DNA-mediated self-assembly of carbon nanotube-based electronic devices. Chem. Phys. Lett., 391, 389-392.
21. Lu, Y.H., Yang, X.Y., Ma, Y.F., Du, F., Liu, Z.F. and Chen, Y.S. (2006) Self-assembled branched nanostructures of single-walled carbon nanotubes with DNA as linkers. Chem. Phys. Lett., 419, 390-393. (Pubitemid 43220499)
22. Li, Y.L., Han, X.G. and Deng, Z.X. (2007) Grafting single-walled carbon nanotubes with highly hybridizable DNA sequences: potential building blocks for DNA-programmed material assembly. Angew. Chem. Int. Ed., 46, 7481-7484.
23. Feng, L., Li, X., Peng, Y., Geng, J., Ren, J. and Qu, X. (2009) Spectral and electrochemical detection of protonated triplex formation by a small-molecule anticancer agent. Chem. Phys. Lett., 480, 309-312.
24. Helene, C. (1991) The anti-gene strategy: control of gene expression by triplex-forming-oligonucleotides. Anticancer Drug Des., 6, 569-584.
25. Maher, L.J. 3rd (1992) DNA triple-helix formation: an approach to artificial gene repressors? Bioessays, 14, 807-815.
26. Duval-Valentin, G., de Bizemont, T., Takasugi, M., Mergny, J.L., Bisagni, E. and Helene, C. (1995) Triple-helix specific ligands stabilize H-DNA conformation. J. Mol. Biol., 247, 847-858.
27. Maher, L.J. 3rd (1996) Prospects for the therapeutic use of antigene oligonucleotides. Cancer Invest., 14, 66-82.
28. Jung, Y.H., Lee, K.B., Kim, Y.G. and Choi, I.S. (2006) Proton-fueled, reversible assembly of gold nanoparticles by controlled triplex formation. Angew. Chem. Int. Ed., 45, 5960-5963. (Pubitemid 44408677)
29. Han, M.S., Lytton-Jean, A.K. and Mirkin, C.A. (2006) A gold nanoparticle based approach for screening triplex DNA binders. J. Am. Chem. Soc., 128, 4954-4955.
30. Helene, C. (1998) DNA recognition. Reading the minor groove. Nature, 391, 436-438.
31. Chan, P.P. and Glazer, P.M. (1997) Triplex DNA: fundamentals, advances, and potential applications for gene therapy. J. Mol. Med., 75, 267-282. (Pubitemid 27209976)
32. Faria, M. and Giovannangeli, C. (2001) Triplex-forming molecules: from concepts to applications. J. Gene Med., 3, 299-310. (Pubitemid 33691769)
33. Niemeyer, C.M. (2000) Self-assembled nanostructures based on DNA: towards the development of nanobiotechnology. Curr. Opin. Chem. Biol., 4, 609-618.
34. Brucale, M., Zuccheri, G. and Samori, B. (2005) The dynamic properties of an intramolecular transition from DNA duplex to cytosine-thymine motif triplex. Org. Biomol. Chem., 3, 575-577. (Pubitemid 40296607)
35. Plum, G.E. (1997) Thermodynamics of oligonucleotide triple helices. Biopolymers, 44, 241-256.
36. Xing, F., Song, G., Ren, J., Chaires, J.B. and Qu, X. (2005) Molecular recognition of nucleic acids: coralyne binds strongly to poly(A). FEBS Lett., 579, 5035-5039. (Pubitemid 41242849)
37. Polak, M. and Hud, N.V. (2002) Complete disproportionation of duplex poly(dT)·poly(dA) into triplex poly(dT)·poly(dA) ·poly(dT) and poly(dA) by coralyne. Nucleic Acids Res., 30, 983-992. (Pubitemid 34679667)
38. Persil, O., Santai, C.T., Jain, S.S. and Hud, N.V. (2004) Assembly of an antiparallel homo-adenine DNA duplex by small-molecule binding. J. Am. Chem. Soc., 126, 8644-8645. (Pubitemid 38955716)
39. Li, X., Peng, Y., Ren, J. and Qu, X. (2006) Carboxyl-modified single-walled carbon nanotubes selectively induce human telomeric i-motif formation. Proc. Natl Acad. Sci. USA, 103, 19658-19663. (Pubitemid 46037487)
40. Li, X., Peng, Y. and Qu, X. (2006) Carbon nanotubes selective destabilization of duplex and triplex DNA and inducing B-A transition in solution. Nucleic Acids Res., 34, 3670-3676. (Pubitemid 44400416)
41. Zhao, C., Ren, J. and Qu, X. (2008) Single-walled carbon nanotubes binding to human telomeric i-motif DNA under molecular-crowding conditions: more water molecules released. Chem. Eur. J., 14, 5435-5439.
42. Zhao, C., Peng, Y., Song, Y., Ren, J. and Qu, X. (2008) Self-assembly of single-stranded RNA on carbon nanotube: polyadenylic acid to form a duplex structure. Small, 4, 656-661. (Pubitemid 351808065)
43. Zhao, C., Song, Y., Ren, J. and Qu, X. (2009) A DNA nanomachine induced by single-walled carbon nanotubes on gold surface. Biomaterials, 30, 1739-1745.
44. Baker, S.E., Cai, W., Lasseter, T.L., Weidkamp, K.P. and Hamers, R.J. (2002) Covalently bonded adducts of deoxyribonucleic acid (DNA) oligonucleotides with single-wall carbon nanotubes: Synthesis and hybridization. Nano Lett., 2, 1413-1417. (Pubitemid 135706538)
45. Wong, S.S., Woolley, A.T., Joselevich, E., Cheung, C.L. and Lieber, C.M. (1998) Covalently-functionalized single-walled carbon nanotube probe tips for chemical force microscopy. J. Am. Chem. Soc., 120, 8557-8558. (Pubitemid 28420496)
46. Huang, W.J., Taylor, S., Fu, K.F., Lin, Y., Zhang, D.H., Hanks, T.W., Rao, A.M. and Sun, Y.P. (2002) Attaching proteins to carbon nanotubes via diimide-activated amidation. Nano Lett., 2, 311-314. (Pubitemid 135706313)
47. Arya, D.P., Coffee, R.L. Jr, Willis, B. and Abramovitch, A.I. (2001) Aminoglycoside-nucleic acid interactions: remarkable stabilization of DNA and RNA triple helices by neomycin. J. Am. Chem. Soc., 123, 5385-5395. (Pubitemid 32888504)
48. Arya, D.P., Micovic, L., Charles, I., Coffee, R.L. Jr, Willis, B. and Xue, L. (2003) Neomycin Binding to Watson-Hoogsteen (W-H) DNA Triplex Groove: a Model. J. Am. Chem. Soc., 125, 3733-3744. (Pubitemid 36512360)
49. Jain, S.S., Polak, M. and Hud, N.V. (2003) Controlling nucleic acid secondary structure by intercalation: effects of DNA strand length on coralyne-driven duplex disproportionation. Nucleic Acids Res., 31, 4608-4615. (Pubitemid 37441820)
50. Vetcher, A.A., Srinivasan, S., Vetcher, I.A., Abramov, S.M., Kozlov, M., Baughman, R.H. and Levene, S.D. (2006) Fractionation of SWNT/nucleic acid complexes by agarose gel electrophoresis. Nanotechnology, 17, 4263-4269. (Pubitemid 44424381)
51. Lee, J.S., Latimer, L.J.P. and Hampel, K.J. (1993) Coralyne binds tightly to both T·A·T-containing and C·G·C+-containing DNA triplexes. Biochemistry, 32, 5591-5597. (Pubitemid 23178524)
52. Wilson, W.D., Tanious, F.A., Mizan, S., Yao, S.J., Kiselyov, A.S., Zon, G. and Strekowski, L. (1993) DNA triple-helix specific intercalators as antigene enhancers: unfused aromatic cations. Biochemistry, 32, 10614-10621. (Pubitemid 23327793)
53. Wilson, W.D., Mizan, S., Tanious, F.A., Yao, S. and Zon, G. (1994) The interaction of intercalators and groove-binding agents with DNA triple-helical structures: the influence of ligand structure, DNA backbone modifications and sequence. J. Mol. Recogit., 7, 89-98. (Pubitemid 2126195)
54. Latimer, L.J.P., Payton, N., Forsyth, G. and Lee, J.S. (1995) The binding of analogs of coralyne and related heterocyclics to DNA triplexes. Biochem. Cell Biol., 73, 11-18.
55. Ren, J.S. and Chaires, J.B. (1999) Sequence and structural selectivity of nucleic acid binding ligands. Biochemistry, 38, 16067-16075. (Pubitemid 129520527)
56. Larsen, T.A., Goodsell, D.S., Cascio, D., Grzeskowiak, K. and Dickerson, R.E. (1989) The structure of DAPI bound to DNA. J. Biomol. Struct. Dyn., 7, 477-491. (Pubitemid 20032405)
57. Tanious, F.A., Veal, J.M., Buczak, H., Ratmeyer, L.S. and Wilson, W.D. (1992) DAPI (40,6-diamidino-2-phenylindole) binds differently to DNA and RNA: minor-groove binding at AT sites and intercalation at AU sites. Biochemistry, 31, 3103-3112.
58. Wilson, W.D., Tanious, F.A., Barton, H.J., Jones, R.L., Fox, K.R., Wydra, R.L. and Strekowski, L. (1990) DNA sequence dependent binding modes of 40,6-diamidino-2-phenylindole (DAPI). Biochemistry, 29, 8452-8461. (Pubitemid 20307826)
59. Kim, S.K., Eriksson, S., Kubista, M. and Norden, B. (1993) Interaction of 40,6-diamidino-2-phenylindole (DAPI) with poly[d(G-C)2] and poly[d(G-m5C)2]: evidence for major groove binding of a DNA probe. J. Am. Chem. Soc., 115, 3441-3447.
60. Sehlstedt, U., Kim, S.K. and Norden, B. (1993) Binding of 40,6-diamidino-2-phenylindole to [poly(dI-dC)]2 and [poly(dG-dC)]2: the exocyclic amino group of guanine prevents minor groove binding. J. Am. Chem. Soc., 115, 12258-12263. (Pubitemid 24077501)