Scanning tunneling spectroscopy of single DNA molecules

ACS Nano

Volumn 3, Issue 7, 2009, Pages 1651-1656

  Ryndyk, Dmitry A ^a   Shapir, Errez ^b   Porath, Danny ^b   Calzolari, Arrigo ^c   Felice, Rosa Di ^c   Cuniberti, Gianaurelio ^d  

^a UNIVERSITY OF REGENSBURG   (Germany)

^b HEBREW UNIVERSITY OF JERUSALEM   (Israel)

^c CNR   (Italy)

^d DRESDEN UNIVERSITY OF TECHNOLOGY   (Germany)

Author keywords

DNA; Molecular nanoelectronics; Scanning probe microscopy; Theoretical modeling

Indexed keywords

APPLIED VOLTAGES; CONDUCTANCE PEAKS; DNA MOLECULES; DOUBLE TUNNEL JUNCTIONS; METALLIC GOLD; MINIMAL MODEL; MOLECULAR NANOELECTRONICS; MOLECULE-ELECTRODE COUPLING; SCANNING TUNNELING SPECTROSCOPY; SEMI-EMPIRICAL; SINGLE DNA MOLECULES; THEORETICAL INVESTIGATIONS; THEORETICAL MODELING; THEORETICAL MODELS; TUNNELING CURRENT;

DNA; ELECTRIC POTENTIAL; GENES; MOLECULES; NANOELECTRONICS; NUCLEIC ACIDS; PROBES; SCANNING PROBE MICROSCOPY; SCANNING TUNNELING MICROSCOPY; SPECTROSCOPY; TUNNEL JUNCTIONS; WIND TUNNELS;

SCANNING;

EID: 68649111688     PISSN: 19360851     EISSN: 1936086X     Source Type: Journal    
DOI: 10.1021/nn800238g     Document Type: Article

References (28)

1. Porath, D.; Cuniberti, G.; Di Felice, R. Charge Transport in DNA-based Devices. In Topics in Current Chemistry; Schuster, G., Ed.; Springer: Berlin, 2004; pp 183-227.
2. Gutierrez, R.; Porath, D.; Cuniberti, G. DNA Conduction: The Issue of Static Disorder, Dynamic Fluctuations and Environmental Effects. In Charge Transport in Disordered Solids with Applications in Electronics; Baranowski, S., Ed.; John Wiley & Sons Inc.: 2006; pp 433-464.
3. Porath, D.; Bezryadin, A.; de Vries, S.; Dekker, C. Direct Measurement of Electrical Transport through DNA Molecules. Nature 2000, 403, 635-638.
4. Xu, B.; Zhang, P.; Li, X.; Tao, N. Direct Conductance Measurements of Single DNA Molecules in Aqueous Solution. Nano Lett. 2004, 4, 1105-1108.
5. Cohen, H.; Nogues, C.; Naaman, R.; Porath, D. Direct Measurement of Electric Transport through Single DNA Molecules of Complex Sequence. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 11589-11593.
6. Cohen, H.; Nogues, C.; Ullien, D.; Daube, S.; Naaman, R.; Porath, D. Electrical Characterization of Self-Assembled Single-and Double-Stranded DNA Monolayers Using Conductive AFM. Faraday Discuss. 2006, 131, 367-376. (Pubitemid 44421998)
7. Shapir, E.; Cohen, H; Calzolari, A.; Cavazzoni, C.; Ryndyk, D. A.; Cuniberti, G.; Kotlyar, A. B.; Di Felice, R; Porath, D. Electronic Structure of Single DNA Molecules Resolved by Transverse Scanning Tunnelling Spectroscopy. Nat. Mater. 2008, 7, 68-74.
8. Cuniberti, G.; Craco, L.; Porath, D.; Dekker, C. Backbone-Induced Semiconducting Behavior in Short DNA Wires. Phys. Rev. B 2002, 65, 241314.
9. Jones, M. L.; Kurnikov, I. V.; Beratan, D. N. The Nature of Tunneling Pathway and Average Packing Density Modelsfor Protein-Mediated Electron Transfer. J. Phys. Chem. A 2002, 106, 2002-2006.
10. Modern Methods for Theoretical Physical Chemistry of Biopolymers Starikov, E. B., Lewis, J. P., Tanaka, S., Eds.; Elsevier: New York, 2006.
11. Gervasio, F. L.; Carloni, P.; Parrinello, M. Electronic Structure of Wet DNA. Phys. Rev. Lett. 2002, 89, 108102.
12. de Pablo, P. J.; Moreno-Herrero, F.; Colchero, J.; Gómez Herrero, J.; Herrero, P.; Baró , A. M.; Ordejón, P.; Soler, J. M.; Artacho, E. Absence of dc-Conductivity in λ-DNA. Phys. Rev. Lett. 2000, 85, 4992-4995.
13. Barnett, R. N.; Cleveland, C. L.; Joy, A.; Landmann, U.; Schuster, G. Charge Migration in DNA: Ion-Gated Transport. Science 2001, 294, 567-571.
14. Lagerqvist, J.; Zwolak, M.; Di Ventra, M. Fast DNA Sequencing via Transverse Electronic Transport. Nano Lett. 2006, 6, 779-782.
15. Rink, G.; Kong, Y.; Koslowski, T. Theory and Simulation of Charge Transfer through DNAONanotube Contacts. Chem. Phys. 2006, 327, 98-104.
16. Starikov, E. B.; Tanaka, S.; Kurita, N.; Sengoku, Y.; Natsume, T.; Wenzel, W. Investigation of a Kubo-Formula-Based Approach to Estimate DNA Conductance in an Atomistic Model. Eur. Phys. J. E. 2005, 18, 437-445.
17. Van Zalinge, H.; Bates, A.; Schiffrin, D. J.; Starikov, E.; Wenzel, W.; Nichols, R. J. Variable-Temperature Measurements of the Single-Molecule Conductance of Double-Stranded DNA. Angew. Chem., Int. Ed. 2006, 45, 5499-5502.
18. Mehrez, N.; Anantram, M. P. Interbase Electronic Coupling for Transport through DNA. Phys. Rev. B 2005, 71, 115405.
19. Shapir, E.; Yi, J.; Cohen, H.; Kotlyar, A. B.; Cuniberti, G.; Porath, D. The Puzzle of Contrast Inversion in DNA STM Imaging. J. Phys. Chem. B 2005, 109, 14270-14274.
20. Shapir, E.; Cohen, H.; Sapir, T.; Borovok, N.; Kotlyar, A. B.; Porath, D. High-Resolution STM Imaging of Novel Poly(G)-poly(C) DNA Molecules. J. Phys. Chem. B 2006, 110, 4430-4433.
21. Gutiérrez, R.; Mandal, S.; Cuniberti, G. Quantum Transport through a DNA Wire in a Dissipative Environment. Nano Lett. 2005, 5, 1093-1097. (Pubitemid 40940591)
22. Gutiérrez, R.; Mohapatra, S.; Cohen, H.; Porath, D.; Cuniberti, G. Inelastic Quantum Transport in a Ladder Model: Implications for DNA Conduction and Comparison to Experiments on Suspended DNA Oligomers. Phys. Rev. B 2006, 74, 235105.
23. Note that the DFT-B3LYP calculations18 that generated the tight-binding parameters employed in our model were done for short poly(G)-poly(C) segments including only the nucleobases, without backbone and counterions. We can only compute with our model electronic features that pertain to the structural elements that we insert; therefore, by construction we only compute features due to guanine and cytosine. How these features vary upon changing the measurement geometry is instead a genuine unbiased result of our theory.
24. Hobza, P.; Sponer, J. Structure, Energetics, and Dynamics of the Nucleic Acid Base Pairs: Nonempirical ab Initio Calculations. Chem. Rev. 1999, 99, 3247-3276.
25. Zwolak, M.; Di Ventra, M. Electronic Signature of DNA Nucleotides via Transverse Transport. Nano Lett. 2005, 5, 421-424.
26. Semenov, M.; Bolbukh, T.; Maleev, V. Infrared Study of the Influence of Water on DNA Stability in the Dependence on AT/GC Composition. J. Mol. Struct. 1997, 408/409, 213-217.
27. Maleev, V.; Semenov, M.; Kashpur, V.; Bolbukh, T.; Shestopalova, A.; Anishchenko, D. Structure and Hydration of Polycytidylic Acid from the Data of Infrared Spectroscopy, EHF Dielectrometry and Computer Modeling. J. Mol. Struct. 2002, 605, 51-61.
28. Gutiérrez-Laliga, R.; Caetano, R.; Woiczikowski, P. B.; Kubar, T.; Elstner, M.; Cuniberti, G. Charge Transport through Biomolecular Wires in a Solvent: Bridging Molecular Dynamics and Model Hamiltonian Approaches. Phys. Rev. Let. 2009, 102, 208102.