Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

Electronic structure of single DNA molecules resolved by transverse scanning tunnelling spectroscopy

Nature Materials volume 7, pages 68–74 (2008)Cite this article

Abstract

Attempts to resolve the energy-level structure of single DNA molecules by scanning tunnelling spectroscopy span over the past two decades, owing to the unique ability of this technique to probe the local density of states of objects deposited on a surface. Nevertheless, success was hindered by extreme technical difficulties in stable deposition and reproducibility. Here, by using scanning tunnelling spectroscopy at cryogenic temperature, we disclose the energy spectrum of poly(G)–poly(C) DNA molecules deposited on gold. The tunnelling current–voltage (I–V) characteristics and their derivative (dI/dV–V) curves at 78 K exhibit a clear gap and a peak structure around the gap. Limited fluctuations in the I–V curves are observed and statistically characterized. By means of ab initio density functional theory calculations, the character of the observed peaks is generally assigned to groups of orbitals originating from the different molecular components, namely the nucleobases, the backbone and the counterions.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: The measurement scheme, DNA STM image and STS on bare gold.
Figure 2: Current–voltage and conductance curves from the STS measurements.
Figure 3: Statistical analysis of the experimental STS results.
Figure 4: Simulated structures and computed DOS.
Figure 5: Reproducibility of the experimental STS curves over ‘time’.

Similar content being viewed by others

References

  1. Ratner, M. A. Photochemistry: Electronic motion in DNA. Nature 397, 480–481 (1999).

    Article  CAS  Google Scholar 

  2. Taubes, G. Biophysics: Double helix does chemistry at a distance—But how? Science 275, 1420–1421 (1997).

    Article  CAS  Google Scholar 

  3. Porath, D., Bezryadin, A., de Vries, S. & Dekker, C. Direct measurement of electrical transport through DNA molecules. Nature 403, 635–638 (2000).

    Article  CAS  Google Scholar 

  4. Porath, D., Cuniberti, G. & Di Felice, R. Charge transport in DNA-based devices. Topics Curr. Chem. 237, 183–227 (2004).

    Article  CAS  Google Scholar 

  5. Endres, R. G., Cox, D. L. & Singh, R. R. P. Colloquium: The quest for high-conductance DNA. Rev. Mod. Phys. 76, 195–214 (2004).

    Article  CAS  Google Scholar 

  6. Wiesendanger, R. Scanning Probe Microscopy and Spectroscopy (Cambridge Univ. Press, Cambridge, 1994).

    Book  Google Scholar 

  7. Porath, D. & Millo, O. Single electron tunneling and level spectroscopy of isolated C60 molecules. J. Appl. Phys. 81, 2241–2244 (1997).

    Article  CAS  Google Scholar 

  8. Porath, D., Levi, Y., Tarabiah, M. & Millo, O. Tunneling spectroscopy of isolated C60 molecules in the presence of charging effects. Phys. Rev. B 56, 9829–9833 (1997).

    Article  CAS  Google Scholar 

  9. Huo, J. G. & Wang, K. D. Study of single molecules and their assemblies by scanning tunneling microscopy. Pure Appl. Chem. 78, 905–933 (2006).

    Article  Google Scholar 

  10. Banin, U. & Millo, O. Tunneling and optical spectroscopy of semiconductor nanocrystals. Annu. Rev. Phys. Chem. 54, 465–492 (2003).

    Article  CAS  Google Scholar 

  11. Binnig, G. & Rohrer, H. in Proc. 6th General Conf. of the European Physical Society, Trends in Physics Vol. 1 (eds Janta, J. & Pantoflicek, J.) 38 (European Physical Society, Prague, 1984).

    Google Scholar 

  12. Binnig, G. & Rohrer, H. Scanning tunneling microscopy—from birth to adolescence. Rev. Mod. Phys. 59, 615–625 (1987).

    Article  CAS  Google Scholar 

  13. Shapir, E. et al. High-resolution STM imaging of novel poly(dG)-poly(dC) DNA. J. Phys. Chem. B 110, 4430–4433 (2006).

    Article  CAS  Google Scholar 

  14. Lindsay, S. M., Thundat, T. & Nagahara, L. A. Adsorbate deformation as a contrast mechanism in STM images of bio-polymers in an aqueous environment: Images of the unstained, hydrated DNA double helix. J. Microsc. 152, 213–220 (1988).

    Article  CAS  Google Scholar 

  15. Wilson, T. E. et al. Scanning tunneling microscopy at high gap resistances and on chemically modified silicon surfaces. J. Vac. Sci. Technol. B 9, 1171–1176 (1991).

    Article  CAS  Google Scholar 

  16. Youngquist, M. G., Driscoll, R. J., Coley, T. R., Goddard, W. A. & Baldeschwieler, J. D. Scanning tunneling microscopy of DNA: Atom-resolved imaging, general observations and possible contrast mechanism. J. Vac. Sci. Technol. B 9, 1304–1308 (1991).

    Article  CAS  Google Scholar 

  17. Tanaka, H. & Kawai, T. Visualization of detailed structures within DNA. Surf. Sci. 539, L531–L536 (2003).

    Article  CAS  Google Scholar 

  18. Iijima, M. et al. STM/STS study of electron density of states at the bases sites in the DNA alternating copolymers. Chem. Lett. 34, 1084–1085 (2005).

    Article  CAS  Google Scholar 

  19. Lindsay, S. M. et al. Studies of the electrical properties of large molecular adsorbates. J. Vac. Sci. Technol. B 9, 1096–1101 (1991).

    Article  CAS  Google Scholar 

  20. Xu, M. S. et al. Conformation and local environment dependent conductance of DNA molecules. Small 1, 1–4 (2005).

    Article  Google Scholar 

  21. Xu, M. S. et al. Conductance of single thiolated poly(GC)-poly(GC) DNA molecules. Appl. Phys. Lett. 87, 083902 (2005).

    Article  Google Scholar 

  22. Clemmer, C. & Beebe, T. P. Graphite: A mimic for DNA and other biomolecules in scanning tunneling microscope studies. Science 251, 640–642 (1991).

    Article  CAS  Google Scholar 

  23. de Pablo, P. J. et al. Absence of dc-conductivity in λ-DNA. Phys. Rev. Lett. 85, 4992–4995 (2000).

    Article  CAS  Google Scholar 

  24. Gervasio, F. L., Carloni, P. & Parrinello, M. Electronic structure of wet DNA. Phys. Rev. Lett. 89, 108102 (2002).

    Article  Google Scholar 

  25. York, D. M., Lee, T.-S. & Yang, W. Quantum mechanical treatment of biological macromolecules in solution using linear-scaling electronic structure methods. Phys. Rev. Lett. 80, 5011–5014 (1998).

    Article  CAS  Google Scholar 

  26. Elhadj, S., Singh, G. & Saraf, R. F. Optical properties of an immobilized DNA monolayer from 255 to 700 nm. Langmuir 20, 5539–5543 (2004).

    Article  CAS  Google Scholar 

  27. Barnes, N. R., Schreiner, A. F., Finnegan, M. G. & Johnson, M. K. Insight into externally bound 5,10,15,20-tetrakis(2-N-methylpyridyl)porphyrinatopalladium(II), PdP(2), with B-form DNA duplexes poly(G-C)2, poly(A-T)2, and CT DNA by using combined MCD, CD, and optical data. Biospectroscopy 4, 341–352 (1998).

    Article  CAS  Google Scholar 

  28. Kotlyar, A. B., Borovok, N., Molotsky, T., Fadeev, L. & Gozin, M. In vitro synthesis of uniform poly(dG)–poly(dC) by Klenow exo- fragment of polymerase I. Nucleic Acids Res. 33, 525–535 (2005).

    Article  CAS  Google Scholar 

  29. Cuniberti, G., Craco, L., Porath, D. & Dekker, C. Backbone-induced semiconducting behavior in short DNA wires. Phys. Rev. B 65, R241314 (2002).

    Article  Google Scholar 

  30. Mehrez, H. & Anantram, M. P. Interbase electronic coupling for transport through DNA. Phys. Rev. B 71, 115405 (2005).

    Article  Google Scholar 

  31. Hübsch, A., Endres, R. G., Cox, D. L. & Singh, R. R. P. Optical conductivity of wet DNA. Phys. Rev. Lett. 94, 178102 (2005).

    Article  Google Scholar 

  32. Barnett, R. N. et al. Effect of base sequence and hydration on the electronic and hole transport properties of duplex DNA: Theory and experiment. J. Phys. Chem. A 107, 3525–3537 (2003).

    Article  CAS  Google Scholar 

  33. Hanna, A. E. & Tinkham, M. Variation of the Coulomb staircase in a two-junction system by fractional electron charge. Phys. Rev. B 44, 5919–5922 (1991).

    Article  CAS  Google Scholar 

  34. Millo, O. et al. Charging and quantum size effects in tunnelling and optical spectroscopy of CdSe nanorods. Nanotechnology 15, R1–R6 (2004).

    Article  CAS  Google Scholar 

  35. Cavazzoni, C. & Chiarotti, G. L. A parallel and modular Car-Parrinello code. Comput. Phys. Commun. 123, 56–76 (1999).

    Article  CAS  Google Scholar 

  36. Giannozzi, P., de Angelis, F. & Car, R. First-principle molecular dynamics with ultrasoft pseudopotentials: Parallel implementation and application to extended bioinorganic systems. J. Chem. Phys. 120, 5903–5915 (2004).

    Article  CAS  Google Scholar 

  37. Perdew, J. P., Burke, K. & Ernzerhof, M. Generalized gradient approximation made simple. Phys. Rev. Lett. 77, 3865–3868 (1996).

    Article  CAS  Google Scholar 

  38. Vanderbilt, D. Soft self-consistent pseudopotentials in a generalized eigenvalue formalism. Phys. Rev. B 41, 7892–7895 (1990).

    Article  CAS  Google Scholar 

  39. Lu, X.-J. & Olson, W. K. 3DNA: A software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. Nucleic Acids Res. 311, 5108–5121 (2003).

    Article  Google Scholar 

Download references

Acknowledgements

We thank I. Brodsky, A. Migliore, M. Cavallari and O. Millo for fruitful discussions, and laboratory and computational help. Funding was provided by the EC through contracts IST-2001-38951 (‘DNA-Based Nanowires’) and FP6-029192 (‘DNA-Based Nanodevices’). Computer time was provided by CINECA (Bologna) and by INFM-CNR through National Supercomputing Projects.

Author information

Author notes

  1. Gianaurelio Cuniberti

    Present address: Present address: Institute for Materials Science and Max Bergmann Center for Biomaterials, Dresden University of Technology, D-01069 Dresden, Germany,

Authors and Affiliations

  1. Physical Chemistry Department and Center for Nanoscience and Nanotechnology, The Hebrew University, Jerusalem 91904, Israel

    Errez Shapir, Hezy Cohen & Danny Porath

  2. National Center on nanoStructures and bioSystems at Surfaces (S3) of INFM-CNR, Via Campi 213/A, 41100 Modena, Italy

    Arrigo Calzolari, Carlo Cavazzoni & Rosa Di Felice

  3. CINECA, Via Magnanelli 6/3, 40033 Casalecchio di Reno Bologna, Italy

    Carlo Cavazzoni

  4. Institute for Theoretical Physics, University of Regensburg, D-93040 Regensburg, Germany

    Dmitry A. Ryndyk & Gianaurelio Cuniberti

  5. Department of Biochemistry George S. Wise Faculty of Life Sciences and Nanotechnology Center Tel Aviv University, Ramat Aviv 69978, Israel

    Alexander Kotlyar

Authors
  1. Errez Shapir
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Hezy Cohen
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Arrigo Calzolari
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Carlo Cavazzoni
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Dmitry A. Ryndyk
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Gianaurelio Cuniberti
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Alexander Kotlyar
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Rosa Di Felice
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Danny Porath
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

E.S. carried out all of the measurements, analysed the data and participated in writing the experimental paragraphs of the paper. H.C. collaborated in the set-up of the experiments and in the development of sample preparation. A.C. and C.C. carried out the calculations. A.C. participated in the analysis of the computational results. D.A.R. and G.C. participated in the theoretical interpretation. A.K. produced the poly(dG)–poly(dC) molecules. R.D.F. designed and guided the theoretical part and carried out the computational analysis and interpretation. D.P. designed and guided the whole work and in particular the experimental part and its analysis. R.D.F. and D.P. wrote the paper.

Corresponding authors

Correspondence to Rosa Di Felice or Danny Porath.

Supplementary information

Supplementary Information

Supplementary information (PDF 67 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Shapir, E., Cohen, H., Calzolari, A. et al. Electronic structure of single DNA molecules resolved by transverse scanning tunnelling spectroscopy. Nature Mater 7, 68–74 (2008). https://doi.org/10.1038/nmat2060

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nmat2060

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing