Structure and electronic properties of "DNA-gold-nanotube" systems: A quantum chemical analysis

Journal of Molecular Graphics and Modelling

Volumn 26, Issue 7, 2008, Pages 1066-1075

  Pannopard, P ^a,b   Khongpracha, P ^a,b   Probst, M ^c   Limtrakul, J ^a,b  

^a Faculty of Engineering   (Thailand)

^b KASETSART UNIVERSITY   (Thailand)

^c UNIVERSITY OF INNSBRUCK   (Austria)

Author keywords

Adenine:thymine base pair (A:T); Density functional theory (DFT); DNA sensor; Gold atom; Single walled carbon nanotube (SWCNT)

Indexed keywords

DENSITY FUNCTIONAL THEORY; DNA SEQUENCES; ELECTRONIC PROPERTIES; GOLD; QUANTUM CHEMISTRY;

GOLD ATOM; GOLD NANOTUBES;

SINGLE-WALLED CARBON NANOTUBES (SWCN);

ADENINE; DNA HYBRID; GOLD; NANOMATERIAL; NANOTUBE; SINGLE WALLED NANOTUBE; THYMINE;

ARTICLE; CHEMICAL ANALYSIS; DENSITY FUNCTIONAL THEORY; DIPOLE; DNA HELIX; ELECTRON; HYBRIDIZATION; MODULATION; MOLECULAR RECOGNITION; PRIORITY JOURNAL; SENSITIVITY ANALYSIS; STRUCTURE ANALYSIS;

ADENINE; BASE PAIRING; BIOSENSING TECHNIQUES; COMPUTER SIMULATION; DNA; ELECTRONS; GOLD; MODELS, CHEMICAL; MODELS, MOLECULAR; MOLECULAR STRUCTURE; NANOTUBES, CARBON; NUCLEIC ACID CONFORMATION; QUANTUM THEORY; THYMINE;

EID: 40749151080     PISSN: 10933263     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmgm.2007.09.003     Document Type: Article

References (31)

1. Drummond T.G., Hill M.G., and Barton J.K. Electrochemical DNA sensors. Nat. Biotechnol. 21 10 (2003) 1192-1199
2. Vercoutere W., and Akeson M. Biosensors for DNA sequence detection. Curr. Opin. Chem. Biol. 6 6 (2002) 816-822
3. Wang J. Electrochemical nucleic acid biosensors. Anal. Chim. Acta 469 1 (2002) 63-71
4. Zhai J., Hong C., and Yang R. DNA based biosensors. Biotechnol. Adv. 15 1 (1997) 43-58
5. Daniel M.-C., and Astruc D. Gold nanoparticles: assembly, supramolecular chemistry, quantum-size-related properties, and applications toward biology, catalysis, and nanotechnology. Chem. Rev. 104 1 (2004) 293-346 (Washington, DC, United States)
6. Tansil N.C., and Gao Z. Nanoparticles in biomolecular detection. Nanotoday 1 1 (2006) 28-37
7. Thaxton C.S., Georganopoulou D.G., and Mirkin C.A. Gold nanoparticle probes for the detection of nucleic acid targets. Clin. Chim. Acta 363 1-2 (2006) 120-126
8. Zhang Z.-L., Pang D.-W., Yuan H., Cai R.-X., and Abruna H.D. Electrochemical DNA sensing based on gold nanoparticle amplification. Anal. Bioanal. Chem. 381 4 (2005) 833-838
9. Kimura-Suda H., Petrovykh D.Y., Tarlov M.J., and Whitman L.J. Base-dependent competitive adsorption of single-stranded DNA on gold. J. Am. Chem. Soc. 125 30 (2003) 9014-9015
10. Kryachko E.S., and Remacle F. Complexes of DNA bases and Watson-Crick base pairs with small neutral gold clusters. J. Phys. Chem. B 109 48 (2005) 22746-22757
11. Cai H., Cao X., Jiang Y., He P., and Fang Y. Carbon nanotube-enhanced electrochemical DNA biosensor for DNA hybridization detection. Anal. Bioanal. Chem. 375 2 (2003) 287-293
12. Gruner G. Carbon nanotube transistors for biosensing applications. Anal. Bioanal. Chem. 384 2 (2006) 322-335
13. Merkoci A. Micro. Chim. Acta 152 3-4 (2006) 157-174
14. Merkoci A., Pumera M., Llopis X., Perez B., del Valle M., and Alegret S. New materials for electrochemical sensing VI: carbon nanotubes. TrAC Trends Anal. Chem. 24 9 (2005) 826-838
15. Valcarcel M., Simonet B.M., Cardenas S., and Suarez B. Present and future applications of carbon nanotubes to analytical science. Anal. Bioanal. Chem. 382 8 (2005) 1783-1790
16. Jiang L., and Gao L. Modified carbon nanotubes: an effective way to selective attachment of gold nanoparticles. Carbon 41 15 (2003) 2923-2929
17. Liu L., Wang T., Li J., Guo Z.-X., Dai L., Zhang D., and Zhu D. Self-assembly of gold nanoparticles to carbon nanotubes using a thiol-terminated pyrene as interlinker. Chem. Phys. Lett. 367 5-6 (2002) 747-752
18. Ma X., Li X., Lun N., and Wen S. Synthesis of gold nano-catalysts supported on carbon nanotubes by using electroless plating technique. Mater. Chem. Phys. 97 2-3 (2006) 351-356
19. Zhang Y., Franklin N.W., Chen R.J., and Dai H. Metal coating on suspended carbon nanotubes and its implication to metal-tube interaction. Chem. Phys. Lett. 331 (2000) 35-41
20. Lim S.H., Wei J., and Lin J. Electrochemical genosensing properties of gold nanoparticle-carbon nanotube hybrid. Chem. Phys. Lett. 400 4-6 (2004) 578-582
21. Perdew J.P., Burke K., and Ernzerhof M. Generalized gradient approximation made simple. Phys. Rev. Lett. 77 18 (1996) 3865-3868
22. Andrae D., Haeussermann U., Dolg M., Stoll H., and Preuss H. Energy-adjusted ab initio pseudopotentials for the second and third row transition elements. Theor. Chem. Acc. 77 2 (1990) 123-141
23. M.J. Frisch, G.W. Trucks, H.B. Schlegel, G.E. Scuseria, M.A. Robb, J.R. Cheeseman, J.A.Jr. Montgomery, T. Vreven, K.N. Kudin, J.C. Burant, J.M. Millam, S.S. Iyengar, J. Tomasi, V. Barone, M. Mennucci, B. Cossi, G. Scalmani, N. Rega, G.A. Petersson, H. Nakatsuji, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, M. Klene, X. Li, J.E. Knox, H.P. Hratchian, J.B. Cross, C. Adamo, J. Jaramillo, R. Gomperts, R.E. Stratmann, O. Yazyev, A.J. Austin, R. Cammi, C. Pomelli, J.W. Ochterski, P.Y. Ayala, K. Morokuma, G.A. Voth, P. Salvador, J.J. Dannenberg, V.G. Zakrzewski, S. Dapprich, A.D. Daniels, M.C. Strain, O. Farkas, D.K. Malick, A.D. Rabuck, K. Raghavachari, J.B. Foresman, J.V. Ortiz, Q. Cui, A.G. Baboul, S. Clifford, J. Cioslowski, B.B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, I.L. Komaromi, R. Martin, D.J. Fox, T. Keith, M.A. Al-Laham, C.Y. Peng, A. Nanayakkara, M. Challacombe, P.M.W. Gill, B. Johnson, W. Chen, M.W. Wong, C. Gonzalez, J.A. Pople, Gaussian 03, Revision B.05, Gaussian, Inc., Wallingford CT, 2004.
24. Ahlrichs R., Baer M., Haeser M., Horn H., and Koelmel C. Electronic structure calculations on workstation computers: the program system TURBOMOLE. Chem. Phys. Lett. 162 3 (1989) 165-169
25. Eichkorn K., Treutler O., Oehm H., Haeser M., and Ahlrichs R. Auxiliary basis sets to approximate Coulomb potentials. Chem. Phys. Lett. 240 4 (1995) 283-290
26. Eichkorn K., Treutler O., Oehm H., Haeser M., and Ahlrichs R. Auxiliary basis sets to approximate Coulomb potentials [Erratum]. Chem. Phys. Lett. 242 6 (1995) 652-660
27. Seeman N.C., Rosenberg J.M., Suddath F.L., Kim J.J., and Rich A. RNA double-helical fragments at atomic resolution: I. The crystal and molecular structure of sodium adenylyl-3′,5′-uridine hexahydrate. J. Mol. Biol. 104 1 (1976) 109-144
28. Yanson I.K., Teplitskii A.B., and Sukhodub L.F. Experimental studies of molecular interactions between nitrogen bases of nucleic acids. Biopolymers 18 5 (1979) 1149-1170
29. Durgun E., Dag S., Bagci V.M.K., Gulseren O., Yildirim T., and Ciraci S. Systematic study of adsorption of single atoms on a carbon nanotube. Phys. Rev. B: Condensed Matter Mater. Phys. 67 20 (2003) 201401/201401-201401/201404
30. E.D. Glendening, J.K. Badenhoop, A.E. Reed, J.E. Carpenter, J.A. Bohmann, C.M. Morales, F. Weinhold, NBO 5.0, Theoretical Chemistry Institute, University of Wisconsin, Madison, WI, 2001, http://www.chem.wisc.edu/∼nbo5.
31. Hay P.J., and Wadt W.R. Ab initio effective core potentials for molecular calculations. Potentials for the transition metal atoms scandium to mercury. J. Chem. Phys. 82 1 (1985) 270-283