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:

Detection and identification of genetic material via single-molecule conductance

Nature Nanotechnology volume 13, pages 1167–1173 (2018)Cite this article

Subjects

Abstract

The ongoing discoveries of RNA modalities (for example, non-coding, micro and enhancer) have resulted in an increased desire for detecting, sequencing and identifying RNA segments for applications in food safety, water and environmental protection, plant and animal pathology, clinical diagnosis and research, and bio-security. Here, we demonstrate that single-molecule conductance techniques can be used to extract biologically relevant information from short RNA oligonucleotides, that these measurements are sensitive to attomolar target concentrations, that they are capable of being multiplexed, and that they can detect targets of interest in the presence of other, possibly interfering, RNA sequences. We also demonstrate that the charge transport properties of RNA:DNA hybrids are sensitive to single-nucleotide polymorphisms, thus enabling differentiation between specific serotypes of Escherichia coli. Using a combination of spectroscopic and computational approaches, we determine that the conductance sensitivity primarily arises from the effects that the mutations have on the conformational structure of the molecules, rather than from the direct chemical substitutions. We believe that this approach can be further developed to make an electrically based sensor for diagnostic purposes.

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

Fig. 1: Break junction experiments on RNA:DNA hybrids.
Fig. 2: Stability and structure of the RNA:DNA hybrids.
Fig. 3: Electronic structure and transport calculations.
Fig. 4: Sensitivity of the SMBJ approach.

Similar content being viewed by others

Data availability

The data that support the findings of this study are available from the corresponding authors upon reasonable request.

References

  1. Batt, C. A. Food pathogen detection. Science 316, 1579–1580 (2007).

    Article  CAS  Google Scholar 

  2. Lazcka, O., Del Campo, F. J. & Muñoz, F. X. Pathogen detection: a perspective of traditional methods and biosensors. Biosens. Bioelectron. 22, 1205–1217 (2007).

    Article  CAS  Google Scholar 

  3. Skottrup, P. D., Nicolaisen, M. & Justesen, A. F. Towards on-site pathogen detection using antibody-based sensors. Biosens. Bioelectron. 24, 339–348 (2008).

    Article  CAS  Google Scholar 

  4. Kirkpatrick, B. C., Stenger, D. C., Morris, T. J. & Purcell, A. H. Cloning and detection of DNA from a nonculturable plant pathogenic mycoplasma-like organism. Science 238, 197–200 (1987).

    Article  CAS  Google Scholar 

  5. Bartlett, J. M. S. & Stirling, D. in PCR Protocols 2nd edn (eds Bartlett, J. M. S. & Stirling, D) 3–6 (Humana,Totowa, 2003).

  6. Xu, B. & Tao, N. J. Measurement of single-molecule resistance by repeated formation of molecular junctions. Science 301, 1221–1223 (2003).

    Article  CAS  Google Scholar 

  7. Venkataraman, L., Klare, J. E., Nuckolls, C., Hybertsen, M. S. & Steigerwald, M. L. Dependence of single-molecule junction conductance on molecular conformation. Nature 442, 904–907 (2006).

    Article  CAS  Google Scholar 

  8. Xiang, L. et al. Intermediate tunnelling-hopping regime in DNA charge transport. Nat. Chem. 7, 221–226 (2015).

    Article  CAS  Google Scholar 

  9. Li, Y. et al. Comparing charge transport in oligonucleotides: RNA:DNA hybrids and DNA duplexes. J. Phys. Chem. Lett. 7, 1888–1894 (2016).

    Article  CAS  Google Scholar 

  10. Gorodetsky, A. A., Buzzeo, M. C. & Barton, J. K. DNA-mediated electrochemistry. Bioconjug. Chem. 19, 2285–2296 (2008).

    Article  CAS  Google Scholar 

  11. Kelley, S. O. & Barton, J. K. Electron transfer between bases in double helical DNA. Science 283, 375–381 (1999).

    Article  CAS  Google Scholar 

  12. Lewis, F. D. & Wasielewski, M. R. Dynamics and efficiency of photoinduced charge transport in DNA: toward the elusive molecular wire. Pure Appl. Chem. 85, 1379–1387 (2013).

    Article  CAS  Google Scholar 

  13. Sorgenfrei, S. et al. Label-free single-molecule detection of DNA-hybridization kinetics with a carbon nanotube field-effect transistor. Nat. Nanotech. 6, 126–132 (2011).

    Article  CAS  Google Scholar 

  14. Michaels, P. et al. A robust DNA interface on a silicon electrode. Chem. Commun. 50, 7878–7880 (2014).

    Article  CAS  Google Scholar 

  15. Slinker, J. D., Muren, N. B., Renfrew, S. E. & Barton, J. K. DNA charge transport over 34 nm. Nat. Chem. 3, 228–233 (2011).

    Article  CAS  Google Scholar 

  16. Dulić, D. et al. Direct conductance measurements of short single DNA molecules in dry conditions. Nanotechnology. 20, 115502 (2009).

    Article  Google Scholar 

  17. Zalinge, Hvan et al. Variable-temperature measurements of the single-molecule conductance of double-stranded DNA. Angew. Chemie 118, 5625–5628 (2006).

    Article  Google Scholar 

  18. Guo, X., Gorodetsky, A. A., Hone, J., Barton, J. K. & Nuckolls, C. Conductivity of a single DNA duplex bridging a carbon nanotube gap. Nat. Nanotech. 3, 163–167 (2008).

    Article  CAS  Google Scholar 

  19. Hihath, J., Xu, B., Zhang, P. & Tao, N. Study of single-nucleotide polymorphisms by means of electrical conductance measurements. Proc. Natl Acad. Sci. USA 102, 16979–16983 (2005).

    Article  CAS  Google Scholar 

  20. Tenaillon, O., Skurnik, D., Picard, B. & Denamur, E. The population genetics of commensal Escherichia coli. Nat. Rev. Microbiol. 8, 207–217 (2010).

    Article  CAS  Google Scholar 

  21. O’Brien, A. D. et al. Shiga-like toxin-converting phages from Escherichia coli strains that cause hemorrhagic colitis or infantile diarrhea. Science 226, 694–696 (1984).

    Article  Google Scholar 

  22. Johannes, L. & Römer, W. Shiga toxins from cell biology to biomedical applications. Nat. Rev. Microbiol. 8, 105–116 (2010).

    Article  CAS  Google Scholar 

  23. Rieger, R., Michaelis, A. & Green, M. M. Glossary of Genetics: Classical and Molecular (Springer, Berlin, 2012).

  24. Nirenberg, M. & Leder, P. RNA codewords and protein synthesis. Science 145, 1399–1407 (1964).

    Article  CAS  Google Scholar 

  25. 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 

  26. Maie, K., Miyagi, K., Takada, T., Nakamura, M. & Yamana, K. RNA-mediated electron transfer: double exponential distance dependence. J. Am. Chem. Soc. 131, 13188–13189 (2009).

    Article  CAS  Google Scholar 

  27. O’Neill, M. A. & Barton, J. K. 2-Aminopurine: a probe of structural dynamics and charge transfer in DNA and DNA:RNA hybrids. J. Am. Chem. Soc. 124, 13053–13066 (2002).

    Article  Google Scholar 

  28. Perna, N. T. et al. Genome sequence of enterohaemorrhagic Escherichia coli O157:H7. Nature 409, 529–533 (2001).

    Article  CAS  Google Scholar 

  29. Altschul, S. F. et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389–3402 (1997).

    Article  CAS  Google Scholar 

  30. Prager, R., Fruth, A., Busch, U. & Tietze, E. Comparative analysis of virulence genes, genetic diversity, and phylogeny of Shiga toxin 2g and heat-stable enterotoxin STIa encoding Escherichia coli isolates from humans, animals, and environmental sources. Int. J. Med. Microbiol. 301, 181–191 (2011).

    Article  CAS  Google Scholar 

  31. Touchon, M. et al. Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths. PLoS Genet. 5, e1000344 (2009)..

  32. Toranzo, A. E., Magarinos, B. & Romalde, J. L. A review of the main bacterial fish diseases in mariculture systems. Aquaculture 246, 37–61 (2005).

    Article  Google Scholar 

  33. Seidel, C. A. M., Schulz, A. & Sauer, M. H. M. Nucleobase-specific quenching of fluorescent dyes. 1. Nucleobase one-electron redox potentials and their correlation with static and dynamic quenching efficiencies. J. Phys. Chem. 100, 5541–5553 (1996).

    Article  CAS  Google Scholar 

  34. Yakovchuk, P., Protozanova, E. & Frank-Kamenetskii, M. D. Base-stacking and base-pairing contributions into thermal stability of the DNA double helix. Nucleic Acids Res. 34, 564–574 (2006).

    Article  CAS  Google Scholar 

  35. Kypr, J., Kejnovská, I., Renčiuk, D. & Vorlíčková, M. Circular dichroism and conformational polymorphism of DNA. Nucleic Acids Res. 37, 1713–1725 (2009).

    Article  CAS  Google Scholar 

  36. Lesnik, E. A. & Freier, S. M. Relative thermodynamic stability of DNA, RNA, and DNA:RNA hybrid duplexes: relationship with base composition and structure. Biochemistry 34, 10807–10815 (1995).

    Article  CAS  Google Scholar 

  37. Vogtherr, M., Schübel, H. & Limmer, S. Structural and dynamic helix geometry alterations induced by mismatch base pairs in double-helical RNA. FEBS Lett. 429, 21–26 (1998).

    Article  CAS  Google Scholar 

  38. Cooper, J. & Cass, T. Biosensors 2nd edn (Oxford Univ. Press, New York, 2004).

  39. Kennard, O. Structural studies of DNA fragments: the G·T wobble base pair in A, B and Z DNA; the G·A base pair in B-DNA. J. Biomol. Struct. Dyn. 3, 205–226 (1985).

    Article  CAS  Google Scholar 

  40. Berlin, Y. A. et al. Charge hopping in DNA. J. Am. Chem. Soc. 104, 260–268 (2001).

    Article  Google Scholar 

  41. Giese, B., Amaudrut, J., Köhler, A., Spormann, M. & Wessely, S. Direct observation of hole transfer through DNA by hopping between adenine bases and by tunnelling. Nature 412, 318–320 (2001).

    Article  CAS  Google Scholar 

  42. Artés, J. M., Li, Y., Qi, J., Anantram, M. P. & Hihath, J. Conformational gating of DNA conductance. Nat. Commun. 6, 8870 (2015).

    Article  Google Scholar 

  43. Huang, Z., Xu, B., Chen, Y., Di Ventra, M. & Tao, N. Measurement of current-induced local heating in a single molecule junction. Nano Lett. 6, 1240–1244 (2006).

    Article  CAS  Google Scholar 

  44. Case, D. A. et al. Computer Code AMBER 2016 (University of California, 2016); http://ambermd.org/.

  45. Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W. & Klein, M. L. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79, 926–935 (1983).

    Article  CAS  Google Scholar 

  46. Perez, A. et al. Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers. Biophys. J. 92, 3817–3829 (2007).

    Article  CAS  Google Scholar 

  47. Zgarbova, M. et al. Refinement of the Cornell et al. nucleic acids force field based on reference quantum chemical calculations of glycosidic torsion profiles. J. Chem. Theory. Comput. 7, 2886–2902 (2011).

    Article  CAS  Google Scholar 

  48. Ivani, I. et al. Parmbsc1: a refined force field for DNA simulations. Nat. Methods 13, 55–58 (2016).

    Article  CAS  Google Scholar 

  49. Ryckaert, J. P., Ciccotti, G. & Beÿrendsen, H.J.C. Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J. Comput. Phys. 23, 327–341 (1977).

    Article  CAS  Google Scholar 

  50. Darden, T., York, D. & Pedersen, L. Particle mesh Ewald: an N-log(N) method for Ewald sums in large systems. J. Chem. Phys. 98, 10089 (1998).

    Article  Google Scholar 

  51. Stephens, P. J., Devlin, F. J., Chabalowski, C. F. & Frisch, M. J. Ab initio calculation of vibrational absorption and circular dichroism spectra using density functional force fields. J. Phys. Chem. 98, 11623–11627 (1994).

    Article  CAS  Google Scholar 

  52. Petersson, G. A. & Al-Laham, M. A. A. complete basis set model chemistry. II Open-shell systems and the total energies of the first-row atoms.J. Chem. Phys. 94, 6081–6090 (1991).

    Article  CAS  Google Scholar 

  53. Hehre, W. J., Ditchfield, R. & Pople, J. A. Self-consistent molecular orbital methods. XII. Further extensions of Gaussian-type basis sets for use in molecular orbital studies of organic molecules.J. Chem. Phys. 56, 2257 (1972).

    Article  CAS  Google Scholar 

  54. Cau‰t, E., Valiev, M. & Weare, J. H. Vertical ionization potentials of nucleobases in a fully solvated DNA environment. J. Phys. Chem. B 114, 5886–5894 (2010).

    Article  Google Scholar 

  55. Close, D. M. & Ohman, K. T. Ionization energies of the nucleotides. J. Phys. Chem. A 112, 11207–11212 (2008).

    Article  CAS  Google Scholar 

  56. Russo, N., Toscano, M. & Grand, A. Theoretical determination of electron affinity and ionization potential of DNA and RNA bases. J. Comput. Chem. 21, 1243–1250 (2000).

    Article  CAS  Google Scholar 

  57. CauëtE., Dehareng, D. & Liévin, J. Ab initio study of the ionization of the DNA bases: ionization potentials and excited states of the cations. J. Phys. Chem. A 110, 9200–9211 (2006).

    Article  Google Scholar 

  58. Slavíček, P., Winter, B., Faubel, M., Bradforth, S. E. & Jungwirth, P. Ionization energies of aqueous nucleic acids: photoelectron spectroscopy of pyrimidine nucleosides and ab initio calculations. J. Am. Chem. Soc. 131, 6460–6467 (2009).

    Article  Google Scholar 

  59. Frisch, M. J. et al. Computer code Gaussian 09, Revision D.1 (Gaussian, 2009)..

  60. Rudberg, E. Difficulties in applying pure Kohn-Sham density functional theory electronic structure methods to protein molecules. J. Phys. Condens. Matter. 24, 072202 (2012).

    Article  Google Scholar 

  61. Löwdin, P. O. On the nonorthogonality problem. Adv. Quantum Chem. 5, 185–199 (1970).

    Article  Google Scholar 

  62. D'Amato, J. L. & Pastawski, H. M. Conductance of a disordered linear chain including inelastic scattering events. Phys. Rev. B 41, 7411 (1990).

    Article  CAS  Google Scholar 

  63. Qi, J., Edirisinghe, N., Rabbani, M. G. & Anantram, M. P. Unified model for conductance through DNA with the Landauer–Büttiker formalism.Phys. Rev. B 87, 085404 (2013).

    Article  Google Scholar 

Download references

Acknowledgements

The authors thank M. Marco, W. Ju and D. Heeney for assistance with the BLASTn databases. This work is supported by the University of California, the Davis RISE program, the National Science Foundation (NSF, CBET-1605338) and the ONR (N00014-16-1-2658). M.P.A. acknowledges support from the NSF under grant nos. 102781 (CHE) and 1231927 (ECCS). E.E.O. acknowledges support from the Turkish Academy of Sciences under TUBA GEBIP grant.

Author information

Author notes

  1. Juan M. Artés

    Present address: Chemistry Department, University of Massachusetts Lowell, Lowell, MA, USA

Authors and Affiliations

  1. Electrical and Computer Engineering Department, University of California Davis, Davis, CA, USA

    Yuanhui Li, Juan M. Artés, Mashari Alangari & Joshua Hihath

  2. Biophysics and Photosynthesis, Vrije Universiteit Amsterdam, Amsterdam, Netherlands

    Juan M. Artés

  3. Bionanodesign Laboratory, Department of Biomedical Engineering, TOBB University of Economics and Technology, Ankara, Turkey

    Busra Demir, Sumeyye Gokce & Ersin Emre Oren

  4. Department of Materials Science & Nanotechnology Engineering, TOBB University of Economics and Technology, Ankara, Turkey

    Busra Demir, Sumeyye Gokce & Ersin Emre Oren

  5. Department of Electrical Engineering, University of Washington, Seattle, WA, USA

    Hashem M. Mohammad & M. P. Anantram

Authors
  1. Yuanhui Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Juan M. Artés
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Busra Demir
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Sumeyye Gokce
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Hashem M. Mohammad
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Mashari Alangari
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. M. P. Anantram
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Ersin Emre Oren
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Joshua Hihath
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

J.H., Y.L., E.E.O. and M.P.A. designed the research. Y.L., J.M.A., M.A. and J.H. performed and analysed CD and SMBJ experiments. B.D., S.G. and E.E.O. performed and analysed molecular dynamics simulations and provided a structural interpretation of the experimental data. B.D., E.E.O., H.M.M. and M.P.A. performed and analysed the DFT and transport calculations. Y.L. and J.H. wrote the paper with input from all authors. All authors contributed to revising the manuscript and agreed on its final content.

Corresponding authors

Correspondence to M. P. Anantram, Ersin Emre Oren or Joshua Hihath.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

Publisher’s note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary information

Supplementary information

Supplementary figures 1–6; supplementary table 1

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Li, Y., Artés, J.M., Demir, B. et al. Detection and identification of genetic material via single-molecule conductance. Nature Nanotech 13, 1167–1173 (2018). https://doi.org/10.1038/s41565-018-0285-x

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41565-018-0285-x

This article is cited by

Search

Advanced search

Quick links

Nature Briefing: Translational Research

Sign up for the Nature Briefing: Translational Research newsletter — top stories in biotechnology, drug discovery and pharma.

Get what matters in translational research, free to your inbox weekly. Sign up for Nature Briefing: Translational Research