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Single-quantum-dot-based DNA nanosensor


Rapid and highly sensitive detection of DNA is critical in diagnosing genetic diseases. Conventional approaches often rely on cumbersome, semi-quantitative amplification of target DNA to improve detection sensitivity. In addition, most DNA detection systems (microarrays, for example), regardless of their need for target amplification, require separation of unhybridized DNA strands from hybridized stands immobilized on a solid substrate, and are thereby complicated by solution–surface binding kinetics1,2. Here, we report an ultrasensitive nanosensor based on fluorescence resonance energy transfer (FRET) capable of detecting low concentrations of DNA in a separation-free format. This system uses quantum dots (QDs)3,4,5 linked to DNA probes to capture DNA targets. The target strand binds to a dye-labelled reporter strand thus forming a FRET donor–acceptor ensemble. The QD also functions as a concentrator that amplifies the target signal by confining several targets in a nanoscale domain. Unbound nanosensors produce near-zero background fluorescence, but on binding to even a small amount of target DNA (50 copies or less) they generate a very distinct FRET signal. A nanosensor-based oligonucleotide ligation assay has been demonstrated to successfully detect a point mutation6 typical of some ovarian tumours in clinical samples.

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Figure 1: Schematic of single-QD-based DNA nanosensors.
Figure 2: Detection of single-dot FRET signals.
Figure 3: Characterization of FRET.
Figure 4: Evaluation of nanosensor performance.


  1. Southern, E., Mir, K. & Shchepinov, M. Molecular interactions on microarrays. Nature Genet. 21, 5–9 (1999).

    Article  Google Scholar 

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

    Article  Google Scholar 

  3. Chan, W. C. W. & Nie, S. M. Quantum dot bioconjugates for ultrasensitive nonisotopic detection. Science 281, 2016–2018 (1998).

    Article  Google Scholar 

  4. Bruchez, M., Moronne, M., Gin, P., Weiss, S. & Alivisatos, A. P. Semiconductor nanocrystals as fluorescent biological labels. Science 281, 2013–2016 (1998).

    Article  Google Scholar 

  5. Medintz, I. L., Uyeda, H. T., Goldman, E. R. & Mattoussi, H. Quantum dot bioconjugates for imaging, labelling and sensing. Nature Mater. 4, 435–446 (2005).

    Article  Google Scholar 

  6. Ho, C. L., Karman, R. J., Dehari, R., Wang, T. L. & Shih, I. M. Mutations of BRAF and KRAS precede the development of ovarian serous borderline tumors. Cancer Res. 64, 6915–6918 (2004).

    Article  Google Scholar 

  7. Cardullo, R. A., Agrawal, S., Flores, C., Zamecnik, P. C. & Wolf, D. E. Detection of nucleic-acid hybridization by nonradiative fluorescence resonance energy-transfer. Proc. Natl Acad. Sci. USA 85, 8790–8794 (1988).

    Article  Google Scholar 

  8. Holland, P. M., Abramson, R. D., Watson, R. & Gelfand, D. H. Detection of specific polymerase chain-reaction product by utilizing the 5′→3′ exonuclease activity of thermus-aquaticus dna-polymerase. Proc. Natl Acad. Sci. USA 88, 7276–7280 (1991).

    Article  Google Scholar 

  9. Tyagi, S. & Kramer, F. R. Molecular beacons: Probes that fluoresce upon hybridization. Nature Biotechnol. 14, 303–308 (1996).

    Article  Google Scholar 

  10. Dubertret, B., Calame, M. & Libchaber, A. J. Single-mismatch detection using gold-quenched fluorescent oligonucleotides. Nature Biotechnol. 19, 365–370 (2001).

    Article  Google Scholar 

  11. Knemeyer, J. P., Marmé, N. & Sauer, M. Probes for detection of specific DNA sequences at the single-molecule level. Anal. Chem. 72, 3717–3724 (2000).

    Article  Google Scholar 

  12. Barnes, M. D., Ng, K. C., Whitten, W. B. & Ramsey, J. M. Detection of single rhodamine-6g molecules in levitated microdroplets. Anal. Chem. 65, 2360–2365 (1993).

    Article  Google Scholar 

  13. Shera, E. B., Seitzinger, N. K., Davis, L. M., Keller, R. A. & Soper, S. A. Detection of single fluorescent molecules. Chem. Phys. Lett. 174, 553–557 (1990).

    Article  Google Scholar 

  14. Nie, S. M., Chiu, D. T. & Zare, R. N. Probing individual molecules with confocal fluorescence microscopy. Science 266, 1018–1021 (1994).

    Article  Google Scholar 

  15. Eigen, M. & Rigler, R. Sorting single molecules—application to diagnostics and evolutionary biotechnology. Proc. Natl Acad. Sci. USA 91, 5740–5747 (1994).

    Article  Google Scholar 

  16. Castro, A. & Williams, J. G. K. Single-molecule detection of specific nucleic acid sequences in unamplified genomic DNA. Anal. Chem. 69, 3915–3920 (1997).

    Article  Google Scholar 

  17. Wang, T. H., Peng, Y. H., Zhang, C. Y., Wong, P. K. & Ho, C. M. Single-molecule tracing on a fluidic microchip for quantitative detection of low-abundance nucleic acids. J. Am. Chem. Soc. 127, 5354–5359 (2005).

    Article  Google Scholar 

  18. Zhang, C. Y., Chao, S. Y. & Wang, T. H. Comparative quantification of nucleic acids using single-molecule detection and molecular beacons. Analyst 130, 483–488 (2005).

    Article  Google Scholar 

  19. Wabuyele, M. B. et al. Approaching real-time molecular diagnostics: Single-pair fluorescence resonance energy transfer (spFRET) detection for the analysis of low abundant point mutations in K-ras oncogenes. J. Am. Chem. Soc. 125, 6937–6945 (2003).

    Article  Google Scholar 

  20. Medintz, I. L. et al. A fluorescence resonance energy transfer-derived structure of a quantum dot-protein bioconjugate nanoassembly. Proc. Natl Acad. Sci. USA 101, 9612–9617 (2004).

    Article  Google Scholar 

  21. Medintz, I. L. et al. Self-assembled nanoscale biosensors based on quantum dot FRET donors. Nature Mater. 2, 630–638 (2003).

    Article  Google Scholar 

  22. Willard, D. M., Carillo, L. L., Jung, J. & Van Orden, A. CdSe-ZnS quantum dots as resonance energy transfer donors in a model protein-protein binding assay. Nano Lett. 1, 469–474 (2001).

    Article  Google Scholar 

  23. Mattoussi, H. et al. Self-assembly of CdSe-ZnS quantum dot bioconjugates using an engineered recombinant protein. J. Am. Chem. Soc. 122, 12142–12150 (2000).

    Article  Google Scholar 

  24. Clapp, A. R. et al. Fluorescence resonance energy transfer between quantum dot donors and dye-labeled protein acceptors. J. Am. Chem. Soc. 126, 301–310 (2004).

    Article  Google Scholar 

  25. Lakowicz, J. R. Principles of Fluorescence Spectroscopy (Kluwer Academic/Plenum, New York, 1999).

    Book  Google Scholar 

  26. Ha, T. et al. Ligand-induced conformational changes observed in single RNA molecules. Proc. Natl Acad. Sci. USA 96, 9077–9082 (1999).

    Article  Google Scholar 

  27. Deniz, A. A. et al. Single-pair fluorescence resonance energy transfer on freely diffusing molecules: Observation of Forster distance dependence and subpopulations. Proc. Natl Acad. Sci. USA 96, 3670–3675 (1999).

    Article  Google Scholar 

  28. Bonnet, G., Krichevsky, O. & Libchaber, A. Kinetics of conformational fluctuations in DNA hairpin-loops. Proc. Natl Acad. Sci. USA 95, 8602–8606 (1998).

    Article  Google Scholar 

  29. Landegren, U., Kaiser, R., Sanders, J. & Hood, L. A ligase-mediated gene detection technique. Science 241, 1077–1080 (1988).

    Article  Google Scholar 

  30. Nickerson, D. A. et al. Automated DNA diagnostics using an elisa-based oligonucleotide ligation assay. Proc. Natl Acad. Sci. USA 87, 8923–8927 (1990).

    Article  Google Scholar 

  31. Kwok, P. Y. Single Nucleotide Polymorphisms Methods and Protocols (Human Press, Totowa, New Jersey, 2003).

    Google Scholar 

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The authors thank Y. Peng, S. Yang, S. Lin and Y. P. Ho for valuable discussions, I. M. Shih for providing us with PCR products from clinical samples for Kras point mutation detections, and L. Brand and D. Toptygin for providing support with the TCSPC fluorescence lifetime measurements. This work was supported primarily by NSF under award no. DBI-0352407 and also by the Whitaker Foundation.

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Correspondence to Tza-Huei Wang.

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Zhang, CY., Yeh, HC., Kuroki, M. et al. Single-quantum-dot-based DNA nanosensor. Nature Mater 4, 826–831 (2005).

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