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.

DNA nanomechanics allows direct digital detection of complementary DNA and microRNA targets

Abstract

Techniques to detect and quantify DNA and RNA molecules in biological samples have had a central role in genomics research1,2,3. Over the past decade, several techniques have been developed to improve detection performance and reduce the cost of genetic analysis4,5,6,7,8,9,10. In particular, significant advances in label-free methods have been reported11,12,13,14,15,16,17. Yet detection of DNA molecules at concentrations below the femtomolar level requires amplified detection schemes1,8. Here we report a unique nanomechanical response of hybridized DNA and RNA molecules that serves as an intrinsic molecular label. Nanomechanical measurements on a microarray surface have sufficient background signal rejection to allow direct detection and counting of hybridized molecules. The digital response of the sensor provides a large dynamic range that is critical for gene expression profiling. We have measured differential expressions of microRNAs in tumour samples; such measurements have been shown to help discriminate between the tissue origins of metastatic tumours18. Two hundred picograms of total RNA is found to be sufficient for this analysis. In addition, the limit of detection in pure samples is found to be one attomolar. These results suggest that nanomechanical read-out of microarrays promises attomolar-level sensitivity and large dynamic range for the analysis of gene expression, while eliminating biochemical manipulations, amplification and labelling.

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

Relevant articles

Open Access articles citing this article.

Access options

Buy article

Get time limited or full article access on ReadCube.

$32.00

All prices are NET prices.

Figure 1: Nanomechanical detection of DNA hybridization.
Figure 2: Direct detection and quantification of miRNA expression in cancer tissues.
Figure 3: High-throughput, robust nanomechanical read-out for multiplexed detection.

References

  1. Higuchi, R., Dollinger, G., Walsh, P. S. & Griffith, R. Simultaneous amplification and detection of specific DNA sequences. Nature Biotechnol. 10, 413–417 (1992)

    CAS  Article  Google Scholar 

  2. Schena, M., Shalon, D., Davis, R. W. & Brown, P. O. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270, 467–470 (1995)

    ADS  CAS  Article  Google Scholar 

  3. Lockhart, D. J. & Winzeler, E. A. Genomics, gene expression and DNA arrays. Nature 405, 827–836 (2000)

    CAS  Article  Google Scholar 

  4. Taton, T. A., Mirkin, C. A. & Letsinger, R. L. Scanometric DNA array detection with nanoparticle probes. Science 289, 1757–1760 (2000)

    ADS  CAS  Article  Google Scholar 

  5. Fritz, J., Cooper, E. B., Gaudet, S., Sorger, P. K. & Manalis, S. R. Electronic detection of DNA by its intrinsic molecular charge. Proc. Natl Acad. Sci. USA 99, 14142–14146 (2002)

    ADS  CAS  Article  Google Scholar 

  6. Cao, Y. C., Jin, R. & Mirkin, C. A. Nanoparticles with Raman spectroscopic fingerprints for DNA and RNA detection. Science 297, 1536–1540 (2002)

    ADS  CAS  Article  Google Scholar 

  7. Park, S. J., Taton, T. A. & Mirkin, C. A. Array-based electrical detection of DNA with nanoparticle probes. Science 295, 1503–1506 (2002)

    ADS  CAS  Article  Google Scholar 

  8. Nam, J. M., Stoeva, S. I. & Mirkin, C. A. Bio-bar-code-based DNA detection with PCR-like sensitivity. J. Am. Chem. Soc. 126, 5932–5933 (2004)

    CAS  Article  Google Scholar 

  9. Fang, S., Lee, H. J., Wark, A. W. & Corn, R. M. Attomole microarray detection of microRNAs by nanoparticle-amplified SPR imaging measurements of surface polyadenylation reactions. J. Am. Chem. Soc. 128, 14044–14046 (2006)

    CAS  Article  Google Scholar 

  10. Geiss, G. K. et al. Direct multiplexed measurement of gene expression with color-coded probe pairs. Nature Biotechnol. 26, 317–325 (2008)

    CAS  Article  Google Scholar 

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

    ADS  CAS  Article  Google Scholar 

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

    ADS  CAS  Article  Google Scholar 

  13. Ilic, B. et al. Enumeration of DNA molecules bound to a nanomechanical oscillator. Nano Lett. 5, 925–929 (2005)

    ADS  CAS  Article  Google Scholar 

  14. Zhang, J. et al. Rapid and label-free nanomechanical detection of biomarker transcripts in human RNA. Nature Nanotechnol. 1, 214–220 (2006)

    ADS  CAS  Article  Google Scholar 

  15. Mertens, J. et al. Label-free detection of DNA hybridization based on hydration-induced tension in nucleic acid films. Nature Nanotechnol. 3, 301–307 (2008)

    CAS  Article  Google Scholar 

  16. Clack, N. G., Salaita, K. & Groves, J. T. Electrostatic readout of DNA microarrays with charged microspheres. Nature Biotechnol. 26, 825–830 (2008)

    CAS  Article  Google Scholar 

  17. Burg, T. P. et al. Weighing of biomolecules, single cells and single nanoparticles in fluid. Nature 446, 1066–1069 (2007)

    ADS  CAS  Article  Google Scholar 

  18. Rosenfeld, N. et al. MicroRNAs accurately identify cancer tissue origin. Nature Biotechnol. 26, 462–469 (2008)

    CAS  Article  Google Scholar 

  19. Cheng, M. M. C. et al. Nanotechnologies for biomolecular detection and medical diagnostics. Curr. Opin. Chem. Biol. 10, 11–19 (2006)

    CAS  Article  Google Scholar 

  20. Sinensky, A. K. & Belcher, A. M. Label-free and high-resolution protein/DNA nanoarray analysis using Kelvin probe force microscopy. Nature Nanotechnol. 2, 653–659 (2007)

    ADS  CAS  Article  Google Scholar 

  21. Ke, Y., Lindsay, S., Chang, Y., Liu, Y. & Yan, H. Self-assembled water-soluble nucleic acid probe tiles for label-free RNA hybridization assays. Science 319, 180–183 (2008)

    ADS  CAS  Article  Google Scholar 

  22. Sahin, O., Su, C., Magonov, S., Quate, C. F. & Solgaard, O. An atomic force microscope tip designed to measure time-varying nanomechanical forces. Nature Nanotechnol. 2, 507–514 (2007)

    Article  Google Scholar 

  23. Sahin, O. & Erina, N. High-resolution and large dynamic range nanomechanical mapping in tapping-mode atomic force microscopy. Nanotechnology 19, 445717 (2008)

    ADS  Article  Google Scholar 

  24. Zhou, D. J., Sinniah, K., Abell, C. & Rayment, T. Label-free detection of DNA hybridization at the nanoscale: a highly sensitive and selective approach using atomic-force microscopy. Angew. Chem. Int. Ed. 42, 4934–4937 (2003)

    CAS  Article  Google Scholar 

  25. Mirmomtaz, E. et al. Nano Lett. 8, 4134–4139 (2008)

    Google Scholar 

  26. He, L. & Hannon, G. J. MicroRNAs: small RNAs with a big role in gene regulation. Nature Rev. Genet. 5, 522–531 (2004)

    CAS  Article  Google Scholar 

  27. Chen, C. et al. Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Res. 33, e179 (2005)

    Article  Google Scholar 

  28. Demers, L. M. et al. Direct patterning of modified oligonucleotides on metals and insulators by dip-pen nanolithography. Science 296, 1836–1838 (2002)

    ADS  CAS  Article  Google Scholar 

  29. Yu, A. A. et al. Supramolecular nanostamping: using DNA as movable type. Nano Lett. 5, 1061–1064 (2005)

    ADS  CAS  Article  Google Scholar 

  30. Herne, T. M. & Tarlov, M. J. Characterization of DNA probes immobilized on gold surfaces. J. Am. Chem. Soc. 119, 8916–8920 (1997)

    CAS  Article  Google Scholar 

  31. Sahin, O. Harnessing bifurcations in tapping-mode atomic force microscopy to calibrate time-varying tip-sample force measurements. Rev. Sci. Instrum. 78, 103707 (2007)

    ADS  Article  Google Scholar 

Download references

Acknowledgements

This research is supported by the Rowland Junior Fellows Program. H.H.J.P. was supported in part by US National Institutes of Health grant HG000205. We thank R. W. Davis for discussions.

Author Contributions S.H. performed the experiments, prepared gold substrates and developed experimental protocols; H.H.J.P. and O.S. contributed to the experiments. S.H. and H.H.J.P. designed and performed the surface chemistry, O.S. designed the cantilevers and wrote the stiffness calculation program, and H.H.J.P. and O.S. designed the biological assay. O.S. directed the research and wrote the paper; all authors discussed the results and commented on the manuscript.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Ozgur Sahin.

Ethics declarations

Competing interests

A patent application has been filed by Stanford University.

Supplementary information

Supplementary Information

This file contains Supplementary Data, Supplementary Notes and Supplementary Figures 1-4 and 6-8 with Legends. (PDF 1407 kb)

Supplementary Figure

This file contains Supplementary Figure 5 in its original high pixel density version. (JPG 4340 kb)

PowerPoint slides

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Husale, S., Persson, H. & Sahin, O. DNA nanomechanics allows direct digital detection of complementary DNA and microRNA targets. Nature 462, 1075–1078 (2009). https://doi.org/10.1038/nature08626

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature08626

Further reading

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

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