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:

Rapid and label-free nanomechanical detection of biomarker transcripts in human RNA

Nature Nanotechnology volume 1, pages 214–220 (2006)Cite this article

Abstract

The availability of entire genome sequences has triggered the development of microarrays for clinical diagnostics that measure the expression levels of specific genes. Methods that involve labelling can achieve picomolar detection sensitivity, but they are costly, labour-intensive and time-consuming. Moreover, target amplification or biochemical labelling can influence the original signal. We have improved the biosensitivity of label-free cantilever-array sensors by orders of magnitude to detect mRNA biomarker candidates in total cellular RNA. Differential gene expression of the gene 1-8U, a potential marker for cancer progression or viral infections, has been observed in a complex background. The measurements provide results within minutes at the picomolar level without target amplification, and are sensitive to base mismatches. This qualifies the technology as a rapid method to validate biomarkers that reveal disease risk, disease progression or therapy response. We foreseee cantilever arrays being used as a tool to evaluate treatment response efficacy for personalized medical diagnostics.

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: Setup showing sensor and reference cantilevers and the biofunctionalized cantilever array.
Figure 2: Calibration of the mechanical response and the biosensitivity of the cantilever array sensors.
Figure 3: Cantilever response as function of BioB2C concentration.
Figure 4: Differential nanomechanical response of cantilevers during specific hybridization.
Figure 5: Differential gene fishing in a complex genomic background.
Figure 6: Nanomechanical measurement of the upregulation of a gene.

Similar content being viewed by others

References

  1. Lander, E. S. et al. Initial sequencing and analysis of the human genome. Nature 409, 860–921 (2001).

    Article  CAS  Google Scholar 

  2. Venter, J. C. et al. The sequence of the human genome. Science 291, 1304–1351 (2001)

    Article  CAS  Google Scholar 

  3. Gershon, D. DNA microarrays: More than gene expression. Nature 437, 1195–1198 (2005).

    Article  CAS  Google Scholar 

  4. Saiki, R. K. et al. Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239, 487–491 (1988).

    Article  CAS  Google Scholar 

  5. ‘t Hoen, P. A. C., de Kort, F., van Ommen, G. J. B. & den Dunnen, J. T. Fluorescent labelling of cRNA for microarray applications. Nucleic Acids Res. 31, e20 (2003).

    Article  Google Scholar 

  6. van Bakel, H. & Holstege, F. C. P. In control: systematic assessment of microarray performance. EMBO Rep. 5, 964–969 (2004).

    Article  CAS  Google Scholar 

  7. Larkin, J. E., Frank, B. C., Gavras, H., Sultana, R. & Quackenbush, J. Independence and reproducibility across microarray platforms. Nat. Methods 2, 337–343 (2005).

    Article  CAS  Google Scholar 

  8. McKendry, R. et al. Multiple label-free biodetection and quantitative DNA-binding assays on a nanomechanical cantilever array. Proc. Natl Acad. Sci. USA 99, 9783–9788 (2002).

    Article  CAS  Google Scholar 

  9. Lang, H. P., Hegner, M., Meyer, E. & Gerber, C. Nanomechanics from atomic resolution to molecular recognition based on atomic force microscopy technology. Nanotechnology 13, R29–R36 (2002).

    Article  CAS  Google Scholar 

  10. Yue, M. et al. A 2-D microcantilever array for multiplexed biomolecular analysis. J. MEMS 13, 290–229 (2004)

    Article  CAS  Google Scholar 

  11. Wang, D. G. et al. Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. Science 280, 1077–1082 (1998).

    Article  CAS  Google Scholar 

  12. Fritz, J. et al. Translating biomolecular recognition into nanomechanics. Science 288, 316–318 (2000).

    Article  CAS  Google Scholar 

  13. Savran, C. A., Knudsen, S. M., Ellington, A. D. & Manalis, S. R. Micromechanical detection of proteins using aptamer-based receptor molecules. Anal. Chem. 76, 3194–3198 (2004).

    Article  CAS  Google Scholar 

  14. Zhang, Y. F. et al. Micromechanical measurement of membrane receptor binding for label-free drug discovery. Biosens. Bioelectr. 19, 1473–1478 (2004).

    Article  CAS  Google Scholar 

  15. Arntz, Y. et al. Label-free protein assay based on a nanomechanical cantilever array. Nanotechnology 14, 86–90 (2003).

    Article  CAS  Google Scholar 

  16. Backmann, N. et al. A label-free immunosensor array using single-chain antibody fragments. Proc. Natl Acad. Sci. USA 102, 14587–14592 (2005).

    Article  CAS  Google Scholar 

  17. Huber, F., Hegner, M., Gerber, C., Güntherodt, H. J. & Lang, H. P. Label free analysis of transcription factors using microcantilever arrays. Biosens. Bioelectr. 21, 1599–1605 (2006).

    Article  CAS  Google Scholar 

  18. Shekhawat, G., Tark, S.-H. & Dravid, V.P. MOSFET-embedded microcantilevers for measuring deflection in biomolecular sensors. Science 311, 1592–1595 (2006).

    Article  CAS  Google Scholar 

  19. Hood, L., Heath, J. R., Phelps, M. E. & Lin, B. Systems biology and new technologies enable predictive and preventative medicine. Science 306, 640–643 (2004).

    Article  CAS  Google Scholar 

  20. Ferrari, M. Cancer nanotechnology: Opportunities and challenges. Nat. Rev. Cancer 5, 161–171 (2005).

    Article  CAS  Google Scholar 

  21. Stoney, G. G. The tension of metallic films deposited by electrolysis. Proc. Roy. Soc. London Ser. A 82, 172–175 (1909).

    Article  CAS  Google Scholar 

  22. Hahm, J & Lieber, C. M. Direct ultrasensitive electrical detection of DNA and DNA sequence variations using nanowire nanosensors. Nano Lett. 4, 51–54 (2004).

    Article  CAS  Google Scholar 

  23. Brem, R., Oroszlan-Szovik, K., Foser, S., Bohrmann, B. & Certa, U. Inhibition of proliferation by 1-8U in interferon-α-responsive and non-responsive cell lines. Cell. Mol. Life Sci. 60, 1235–1248 (2003).

    Article  CAS  Google Scholar 

  24. Zhu, H., Butera, M., Nelson, D. R. & Liu, C. Novel type I interferon IL-28A suppresses hepatitis C viral RNA replication. Viral. J. 2, 80 (2005).

    Article  Google Scholar 

  25. Der, S. D., Zhou, A., Williams, B. R. G. & Silverman, R. H. Identification of genes differentially regulated by interferon α, ß, or γ using oligonucleotide arrays. Proc. Natl Acad. Sci. USA 95, 15623–15628 (1998).

    Article  CAS  Google Scholar 

  26. Rogge, L. et al. Transcript imaging of the development of human T helper cells using oligonucleotide arrays. Nature Genet. 25, 96–101 (2000).

    Article  CAS  Google Scholar 

  27. Certa, U., Wilhelm-Seiler, M., Foser, S., Broger, C. & Neeb, M. Expression modes of interferon-α inducible genes in sensitive and resistant human melanoma cells stimulated with regular and pegylated interferon-α. Gene 315, 79–86 (2003).

    Article  CAS  Google Scholar 

  28. Vial, T. & Descotes, J. Clinical toxicity of the interferons. Drug Saf. 10, 115–150 (1994).

    Article  CAS  Google Scholar 

  29. Kirkwood, J. M. Systemic adjuvant treatment of high-risk melanoma: the role of interferon alfa-2b and other immunotherapies. Eur. J. Cancer 34(Suppl. 2), S12–S17 (1998).

    Article  CAS  Google Scholar 

  30. Lang, H. P., Hegner, M. & Gerber, C. Cantilever array sensors. Mater. Today 8 (4), 30–36 (2005).

    Article  CAS  Google Scholar 

  31. Binnig, G., Quate, C. F. & Gerber, Ch. Atomic force microscope. Phys. Rev. Lett. 56, 930–933 (1986)

    Article  CAS  Google Scholar 

  32. Su, X. D., Wu, Y. J., Robelek, R. & Knoll, W. Surface plasmon resonance spectroscopy and quartz crystal microbalance study of streptavidin film structure effects on biotinylated DNA assembly and target DNA hybridization. Langmuir 21, 348–353 (2005).

    Article  CAS  Google Scholar 

  33. Zheng, G. F., Patolsky, F., Cui, Y., Wang, W. U. & Lieber, C. M. Multiplexed electrical detection of cancer markers with nanowire sensor arrays. Nat. Biotech. 23, 1294–1301 (2005).

    Article  CAS  Google Scholar 

  34. Despont, M., Drechsler, U., Yu, R. R., Pogge, B. H. & Vettiger, P. Wafer-scale microdevice transfer/interconnect: Its application in an AFM-based data-storage system. J. Microelectromech. Syst. 13, 895–901 (2004).

    Article  CAS  Google Scholar 

  35. Alvarez, M. et al. Nanomechanics of the formation of DNA self-assembled monolayers and hybridization on microcantilevers. Langmuir 20, 9663–9668 (2004).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

This paper was supported by the Swiss National Center of Competence in Research (NCCR) ‘Nanoscale Science’, the Swiss National Science Foundation (grant no. 3152A0-1059531 to M.H.) and by the ELTEM Regio network. The support of IBM Research GmbH as a research partner of the NCCR and the Cleven-Becker foundation is acknowledged. We thank I. Redwanz (RCMG) for cell culture and RNA isolation work.

Author information

Authors and Affiliations

  1. NCCR Nanoscale Science, Institute of Physics, University of Basel, Klingelbergstrasse 82, Basel, CH-4056, Switzerland

    J. Zhang, H. P. Lang, F. Huber, A. Bietsch, W. Grange, H.-J. Güntherodt, M. Hegner & Ch. Gerber

  2. IBM Research GmbH, Zurich Research Laboratory, Säumerstrasse 4, Rüschlikon, 8803, Switzerland

    H. P. Lang & A. Bietsch

  3. Roche Centre for Medical Genomics, F. Hoffmann–La Roche Ltd, Basel, 4070, Switzerland

    U. Certa

  4. Department of Medicine, London Centre for Nanotechnology, 5 University Street, London, WC1E 6JJ, United Kingdom

    R. Mckendry

Authors
  1. J. Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. H. P. Lang
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. F. Huber
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. A. Bietsch
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. W. Grange
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. U. Certa
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. R. Mckendry
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. H.-J. Güntherodt
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. M. Hegner
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Ch. Gerber
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

U.C., C.G. and M.H. conceived and designed the experiments, J.Z. performed the experiments, J.Z., H.P.L. and A.B. functionalized the cantilever arrays, J.Z., F.H., H.P.L and M.H. analysed the data, and W.G. programmed the hardware and software of the instrumentation. All authors discussed the results and commented on the manuscript.

Corresponding author

Correspondence to M. Hegner.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Zhang, J., Lang, H., Huber, F. et al. Rapid and label-free nanomechanical detection of biomarker transcripts in human RNA. Nature Nanotech 1, 214–220 (2006). https://doi.org/10.1038/nnano.2006.134

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nnano.2006.134

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