Transverse electronic transport in double-stranded DNA nucleotides

Journal of Physical Chemistry B

Volumn 113, Issue 18, 2009, Pages 6230-6239

  Jauregui, Luis A ^a,b   Salazar Salinas, Karim ^a   Seminario, Jorge M ^a  

^a Texas AandM University   (United States)

^b UNIVERSIDAD NACIONAL DE INGENIERÍA   (Peru)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; GENES; NUCLEOTIDES;

AB INITIO TECHNIQUES; COUNTERIONS; CURRENT VOLTAGE; DOUBLE STRANDED DNA; ELECTRON TRANSPORT; ELECTRONIC TRANSPORT; GOLD ELECTRODES; ORDERS OF MAGNITUDE; SIGNAL LEVEL; SODIUM CATIONS; TRANSVERSE CURRENTS;

NUCLEIC ACIDS;

EID: 66349121401     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp808790j     Document Type: Article

References (61)

1. Porath, D.; Bezryadin, A.; de Vries, S.; Dekker, C. Direct measurement of electrical transport through DNA molecules. Nature (London) 2000, 403, 635-638.
2. Fink, H. W.; Schonenberger, C. Electrical conduction through DNA molecules. Nature (London) 1999, 398, 407-410.
3. Cohen, H.; Nogues, C.; Naaman, R.; Porath, D. Direct measurement of electrical transport through single DNA molecules of complex sequence. Proc. Natl. Acad. Sci. U.S.A. 2005, 702, 11589-11593.
4. Tanaka, H.; Kawai, T. Visualization of detailed structures within DNA. Surf. Sci. 2003, 539, L531-L536.
5. Xu, M. S.; Endres, R. G.; Tsukamoto, S.; Kitamura, M.; Ishida, S.; Arakawa, Y. Conformation and local environment dependent conductance of DNA molecules. Small 2005, 7, 1168-1172.
6. Shapir, E.; Cohen, H.; Calzolari, A.; Cavazzoni, C.; Ryndyk, D. A.; Cuniberti, G.; Kotlyar, A.; Di Felice, R.; Porath, D. Electronic structure of single DNA molecules resolved by transverse scanning tunnelling spec-troscopy. Nat. Mater. 2008, 7, 68-74.
7. Xu, M.; Endres, R. G.; Arakawa, Y. The electronic properties of DNA bases. Small 2007, 3, 1539-1543.
8. Meller, A.; Nivon, L.; Branton, D. Voltage-driven DNA translo-cations through a nanopore. Phys. Rev. Lett. 2001, 86, 3435-3438.
9. Kasianowicz, J. J.; Brandin, E.; Branton, D.; Deamer, D. W. Characterization of individual polynucleotide molecules using a membrane channel. Proc. Natl. Acad. Sci. U.S.A. 1996, 93, 13770-13773.
10. Li, J. L.; Gershow, M.; Stein, D.; Brandin, E.; Golovchenko, J. A. DNA molecules and configurations in a solid-state nanopore microscope. Nat. Mater. 2003, 2, 611-615.
11. Dekker, C. Solid-state nanopores. Nat. Nanotechnol. 2007, 2, 209-215.
12. Fologea, D.; Gershow, M.; Ledden, B.; McNabb, D. S.; Golovchenko, J. A.; Li, J. L. Detecting single stranded DNA with a solid state nanopore. Nano Lett. 2005, 5, 1905-1909.
13. Gracheva, M. E.; Vidal, J.; Leburton, J. P. p-n semiconductor membrane for electrically tunable ion current rectification and filtering. Nano Lett. 2007, 7, 1717-1722.
14. Muthukumar, M. Mechanism of DNA transport through pores. Annu. Rev. Biophys. Biomol. Struct. 2007, 36, 435-450.
15. Pope, K. J.; Smith, J. L. P.; Shapter, J. G. Imaging molecular adsorbates using scanning tunnelling microscopy and image processing. Smart Mater. Struct. 2002, 77, 679-685.
16. Gierhart, B. C.; Howitt, D. G.; Chen, S. J.; Zhu, Z.; Kotecki, D. E.; Smith, R. L.; Collins, S. D. Nanopore with Transverse Nanoelectrodes for Electrical Characterization and Sequencing of DNA. Sens. Actuators B 2008, 132, 593-600.
17. Yan, L. M.; Seminario, J. M. Electron transport in nano-gold-silicon interfaces. Int. J. Quantum Chem. 2007, 107, 440-450.
18. Seminario, J. M.; Yan, L. Ab initio analysis of electron currents in thioalkanes. Int. J. Quantum Chem. 2005, 102, 711-723.
19. Yan, L. M.; Seminario, J. M. Electronic structure and electron transport characteristics of a cobalt complex. J. Phys. Chem. A 2005, 109, 6628-6633.
20. Derosa, P. A.; Guda, S.; Seminario, J. M. A programmable molecular diode driven by charge-induced conformational changes. J. Am. Chem. Soc. 2003, 125, 14240-14241.
21. Sotelo, J. C.; Seminario, J. M. Local reactivity of 02 with Pt3 on Co3Pt and related backgrounds. J. Chem. Phys. 2008, 128, p. 204701,.
22. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Montgomery, J. A., Jr.; Vreven, T.; Kudin, K. N.; Burant, J. C.; Millam, J. M.; Iyengar, S. S.; Tomasi, J.; Barone, V.; Mennucci, B.; Cossi, M.; Scalmani, G.; Rega, N.; Petersson, G. A.; Nakatsuji, H.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Klene, M.; Li, X.; Knox, J. E.; Hratchian, H. P.; Cross, J. B.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C.; Ochterski, J. W.; Ayala, P. Y.; Morokuma, K.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Zakrzewski, V. G.; Dapprich, S.; Daniels, A. D.; Strain, M. C.; Farkas, O.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Ortiz, J. V.; Cui, Q.; Baboul, A. G.; Clifford, S.; Cioslowski, J. B. B.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Gonzalez, C.; Pople, J. A. Gaussian 03, revision C.2 or D.01; Gaussian, Inc.: Pittsburgh, PA, 2003.
23. Hohenberg, P.; Kohn, W. Inhomogeneous electron gas. Phys. Rev. B 1964, 136, 864-871.
24. Kohn, W.; Sham, L. J. Self-consistent equations including exchange and con-elation effects. Phys. Rev. A 1965, 140, 1133-1138.
25. Becke, A. D. Density-functional thermochemistry III. The role of exact exchange. J. Chem. Phys. 1993, 98, 5648-5652.
26. Perdew, J. P. Unified Theory of Exchange and Correlation beyond the Local Density Approximation. In Electronic Structure of Solids; Ziesche, P., Eschrig, H., Eds.; Akademie Verlag: Berlin, 1991; pp 11-20.
27. Perdew, J. P. Nonlocal Density Functionals for Exchange and Correlation: Theory and Applications. In Density Functional Theory of Molecules, Clusters, and Solids; Ellis, D. E., Ed.; Kluwer: New York, 1995; pp 47-66.
28. Wadt, W. R.; Hay, P. J. Ab initio effective core potentials for molecular calculations. Potentials for main group elements Na to Bi. J. Chem. Phys. 1985, 82, 284-298.
29. Hay, P. J.; Wadt, W. R. Ab initio effective core potentials for molecular calculations. Potentials for K to Au including the outermost core orbitals. J. Chem. Phys. 1985, 82, 299-310.
30. Hay, P. J.; Wadt, W. R. Ab initio effective core potentials for molecular calculations. Potentials for the transition metal atoms Sc to Hg. J. Chem. Phys. 1985, 82, 270-283.
31. Roetti, C. The CRYSTAL Code. In Quantum-Mechanical Ab-initio Calculation of the properties of Crystalline Materials; Pisani, C. Ed.; Springer-Verlag: Berlin, 1996; Vol. 67, pp 125-137.
32. O'Boyle, N. M. GaussSum 2.1; 2007; http://gausssum.sf.net.
33. Salazar, P. F.; Seminario, J. M. Identifying Receptor-Ligand Interactions through an ab Initio Approach. J. Phys. Chem. B 2008, 112, 1290,.
34. Sotelo, J. C.; Seminario, J. M. Biatomic substrates for bulk-molecule interfaces: The PtCo-oxygen interface. J. Chem. Phys. 2007, 727, 244706.
35. Tovar, R. M.; Johnson, K. P.; Ashline, K.; Seminario, J. M. Effects of Substituents on Molecular Devices. Int. J. Quantum Chem. 2008, 708, 1546-1554.
36. Juarregui, L. A.; Seminario, J. M. A DNA sensor for sequencing and mismatches based on electron transport through Watson-Crick and non-Watson-Crick base pairs. IEEE Sens. 2008, 8, 803-814.
37. Salazar-Salinas, K.; Jauregui, L. A.; Kubli-Garfias, C.; Seminario, J. M. Molecular biosensor based on a coordinated iron complex. J. Chem. Phys. 2009, 130, 105101-1-9.
38. Lagerqvist, J.; Zwolak, M.; Di Ventra, M. Fast DNA sequencing via transverse electronic transport. Nano Lett. 2006, 6, 779-782.
39. Zwolak, M.; Di Ventra, M. Electronic signature of DNA nucleotides via transverse transport. Nano Lett. 2005, 5, 421-424.
40. Zwolak, M.; Lagerqvist, J.; Di Ventra, M. Influence of the environment and probes on rapid DNA sequencing via transverse electronic transport. Biophys. J. 2007, 93, 2384-2390.
41. Zhang, X. G.; Krstic, P. S.; Zikic, R.; Wells, J. C.; Fuentes-Cabrera, M. First-principles transversal DNA conductance deconstructed. Biophys. J. 2006, 91, L4-L6.
42. Bamett, R. N.; Cleveland, C. L.; Landman, U.; Boone, E.; Kanvah, S.; Schuster, G. B. Effect of base sequence and hydration on the electronic and hole transport properties of duplex DNA: Theory and experiment. J. Phys. Chem. A 2003, 707, 3525-3537.
43. Hiibsch, A.; Endres, R. G.; Cox, D. L.; Singh, R. R. P. Optical conductivity of wet DNA. Phys. Rev. Lett. 2005, 94, 178102.
44. Coutinho, K.; Ludwig, V.; Canuto, S. Combined Monte Carlo and quantum mechanics study of the hydration of the guanine-cytosine base pair. Phys. Rev. E 2004, 69, 061902.
45. Kabelac, M.; Hobza, P. Potential energy and free energy surfaces of all ten canonical and methylated nucleic acid base pairs: Molecular dynamics and quantum chemical ab initio studies. J. Phys. Chem. B 2001, 705, 5804-5817.
46. Shimizu, N.; Kawano, S.; Tachikawa, M. Electron-correlated and density functional studies on hydrogen-bonded proton transfer in adenine-thymine base pair of DNA. J. Mol. Struct. 2005, 735-36, 243-248.
47. Maruyama, Y.; Tachikawa, M.; Kawano, S. Ab initio study of DNA double-strand breaks by hydroxyl radical. Jpn. Soc. Mech. Eng. Int. J. Ser. B: Fluids Therm. Eng. 2005, 48, 196-201.
48. Seminario, J. M.; Tour, J. M. Systematic Study of the Lowest Energy States of Aun (n=l-4) Using DFT. Int. J. Quantum Chem. 1997, 65, 749-758.
49. Seminario, J. M.; Zacarias, A. G.; Castro, M. Systematic Study of the Lowest Energy States of Pd, Pd2, and Pd3. Int. J. Quantum Chem. 1997, 61, 515-523.
50. Derosa, P. A.; Seminario, J. M.; Balbuena, P. B. Properties of Small Bimetallic Ni-Cu Clusters. J. Phys. Chem. A 2001, 105, 7917-7925.
51. Seminario, J. M.; De La Cruz, C.; Derosa, P. A.; Yan, L. Nanometer-Size Conducting and Insulating Molecular Devices. J. Phys. Chem. B 2004, 708, 17879-17885.
52. Di Felice, R.; Calzolari, A.; Molinari, E.; Garbesi, A. Ab initio study of model guanine assemblies: The role of pi-pi coupling and band transport. Phys. Rev. B 2001, 65, 045104.
53. Seminario, J. M.; Araujo, R. A.; Yan, L. Negative Differential Resistance in Metallic and Semiconducting Clusters. J. Phys. Chem. B 2004, 708, 6915-6918.
54. Rangel, N. L.; Seminario, J. M. Nanomicrointerface to read molecular potentials into current-voltage based electronics. J. Chem. Phys. 2008, 728, 114711.
55. Rangel, N. L.; Seminario, J. M. Graphene Terahertz Generators for Molecular Circuits and Sensors. J. Phys. Chem. A 2008, 772, 13699.
56. Tovar, R. M.; Johnson, K. P.; Ashline, K.; Seminario, J. M. Effects of Substituents on Molecular Devices. Int. J. Quantum Chem. 2008, 708, 1546.
57. Agapito, L. A.; Bautista, E. J.; Seminario, J. M. Conductance model of gold-molecule-silicon and carbon nanotube-molecule-silicon junctions. Phys. Rev. B 2007, 76, 115316.
58. Bautista, E. J.; Yan, L.; Seminario, J. M. Ab initio analysis of electron transport in oligoglycines. J. Phys. Chem. C 2007, 777, 14552-14559.
59. Seminario, J. M. Quantum Current-Voltage relation for a single electron. J. Phys. B 2007, 40, F275-276.
60. Yan, L.; Bautista, E. J.; Seminario, J. M. Ab initio analysis of electron currents through benzene, napthalene, and anthracene. Nanotech-nology 2007, 78, 485701.
61. Seminario, J. M.; Zacarias, A. G.; Tour, J. M. Molecular Alligator Clips for Single Molecule Electronics. Studies of Group 16 and Isonitriles Interfaced with Au Contacts. J. Am. Chem. Soc. 1999, 727, 411-416.