BioChip Journal

, Volume 12, Issue 4, pp 340–347 | Cite as

An Ultrasensitive FRET-based DNA Sensor via the Accumulated QD System Derivatized in the Nano-beads

  • Lan-Hee Yang
  • Dong June Ahn
  • Eunhae KooEmail author
Original Article


Förster resonance energy transfer (FRET) is extremely sensitive to the separation distance between the donor and the acceptor which is ideal for probing such biological phenomena. Also, FRET-based probes have been developing for detecting an unamplified, low-abundance of target DNA. Here we describe the development of FRET based DNA sensor based on an accumulated QD system for detecting KRAS G12D mutation which is the most common mutation in cancer. The accumulated QD system consists of the polystyrene beads which surface is modified with carboxyl modified QDs. The QDs are sandwich-hybridized with DNA of a capture probe, a reporter probe with Texas-red, and a target DNA by EDC-NHS coupling. Because the carboxyl modified QDs are located closely to each other in the accumulated QDs, these neighboring QDs are enough to transfer the energy to the acceptor dyes. Therefore the FRET factor in the bead system is enhancing by the additional increase of 29.2% as compared to that in a single QD system. These results suggest that the accumulated nanobead probe with conjugated QDs can be used as ultrasensitive DNA nanosensors detecting the mutation in the various cancers.


FRET QD DNA sensor Bead 


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. 1.
    Downward, J. Targeting RAS signalling pathways in cancer therapy. Nat. Rev. Cancer 3, 11–22 (2003).CrossRefGoogle Scholar
  2. 2.
    Karnoub, A.E. & Weinberg, R.A. Ras oncogenes: split personalities. Nat. Rev. Mol. Cell Biol. 9, 517–531 (2008).CrossRefGoogle Scholar
  3. 3.
    Vasan, N., Boyer, J.L. & Herbst, R.S. A RAS Renaissance: Emerging Targeted Therapies for KRAS-Mutated Non-Small Cell Lung Cancer. Clin. Cancer Res. 20, 3921–3930 (2014).CrossRefGoogle Scholar
  4. 4.
    Riely, G.J., Marks, J. & Pao, W. KRAS mutations in non-small cell lung cancer. Proc. Am. Thorac. Soc. 6, 201–205 (2009).CrossRefGoogle Scholar
  5. 5.
    Patolsky, F. et al. Lighting-Up the Dynamics of Telomerization and DNA Replication by CdSe-ZnS Quantum Dots. J. Am. Chem. Soc. 125, 13918–13919 (2003).CrossRefGoogle Scholar
  6. 6.
    Medintzi, I.L. et al. Self-assembled nanoscale biosensors based on quantum dot FRET donors. Nat. Mater. 2, 630–638 (2003).CrossRefGoogle Scholar
  7. 7.
    Medintz, I.L. et al. A fluorescence resonance energy transfer-derived structure of a quantum dot-protein bioconjugate nanoassembly. Proc. Natl. Acad. Sci. U.S.A. 101, 9612–9617 (2004).CrossRefGoogle Scholar
  8. 8.
    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).CrossRefGoogle Scholar
  9. 9.
    Zhang, C.Y., Yeh, H.C., Kuroki, M.T. & Wang, T.H. Single-quantum-dot-based DNA nanosensor. Nat. Mater. 4, 826–831 (2005).CrossRefGoogle Scholar
  10. 10.
    Bakalova, R., Zhelev, Z., Ohba, H. & Baba, Y., Quantum Dot-Conjugated Hybridization Probes for Preliminary Screening of siRNA Sequences. J. Am. Chem. Soc. 127, 11328–11335 (2005).CrossRefGoogle Scholar
  11. 11.
    Zhou, D. et al. Fluorescence resonance energy transfer between a quantum dot donor and a dye acceptor attached to DNA. Chem. Commun. 4807–4809 (2005).Google Scholar
  12. 12.
    Zhang, C. & Johnson, L.W. Quantum Dot-Based Fluorescence Resonance Energy Transfer with Improved FRET Efficiency in Capillary Flows. Anal. Chem. 78, 5532–5537 (2006).CrossRefGoogle Scholar
  13. 13.
    Wargnier, R. et al. Energy transfer in aqueous solutions of oppositely charged CdSe/ZnS core/shell quantum dots and in quantum dot-nanogold assemblies. Nano Lett. 4, 451–457 (2004).CrossRefGoogle Scholar
  14. 14.
    Mamedova, N.N., Kotov, N.A., Rogach, A.L. & Studer, J. Albumin-CdTe nanoparticle bioconjugates: preparation, structure, and interunit energy transfer with antenna effect. Nano Lett. 1, 281–286 (2001).CrossRefGoogle Scholar
  15. 15.
    Medintz, I.L., Trammell, S.A., Mattoussi, H. & Mauro, J.M. Reversible modulation of quantum dot photoluminescence using a protein-bound photochromic fluorescence resonance energy transfer acceptor. J. Am. Chem. Soc. 126, 30–31 (2004).CrossRefGoogle Scholar
  16. 16.
    Pons, T., Medintz, I.L., Wang, X., English, D.S. & Mattoussi, H. Solution-phase single quantum dot fluorescence resonance energy transfer. J. Am. Chem. Soc. 128, 15324–15331 (2006).CrossRefGoogle Scholar
  17. 17.
    Knemeyer, J.P., Marm’e, N. & Sauer, M. Probes for detection of specific DNA sequences at the single-molecule level. Anal. Chem. 72, 3717–3724 (2000).CrossRefGoogle Scholar
  18. 18.
    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).CrossRefGoogle Scholar
  19. 19.
    Shera, E.B. et al. Detection of single fluorescent molecules. Chem. Phys. Lett. 174, 553–557 (1990).CrossRefGoogle Scholar
  20. 20.
    Nie, S.M., Chiu, D.T. & Zare, R.N. Probing individual molecules with confocal fluorescence microscopy. Science 266, 1018–1021 (1994).CrossRefGoogle Scholar
  21. 21.
    Eigen, M. & Rigler, R. Sorting single molecules-application to diagnostics and evolutionary biotechnology. Proc. Natl Acad. Sci. U.S.A 91, 5740–5747 (1994).CrossRefGoogle Scholar
  22. 22.
    Castro, A. & Williams, J.G.K. Single-molecule detection of specific nucleic acid sequences in unamplified genomic DNA. Anal. Chem. 69, 3915–3920 (1997).CrossRefGoogle Scholar
  23. 23.
    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).CrossRefGoogle Scholar
  24. 24.
    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).CrossRefGoogle Scholar
  25. 25.
    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).CrossRefGoogle Scholar
  26. 26.
    Dabbousi, B.O. et al. (CdSe)ZnS core-shell quantum dots: synthesis and optical and structural characterization of a size series of highly luminescent materials. J. Phys. Chem. B 101, 9463–9475 (1997).CrossRefGoogle Scholar
  27. 27.
    Leatherdale, C.A., Woo, W.K., Mikulec, F.V. & Bawendi, M.G. On the absorption cross section of CdSe nanocrystal quantum dots. J. Phys. Chem. B 106, 7619–7622 (2002).CrossRefGoogle Scholar
  28. 28.
    Ute, R-G. et al. Quantum dots versus organic dyes as fluorescent labels. Nat. Methods 5, 763–775 (2008).CrossRefGoogle Scholar
  29. 29.
    Zhang, C.-Y., Yeh, H.-C., Kuroki, M.T. & Wang, T.-H. Single-quantum-dot-based DNA nanosensor. Nat. Mater. 4, 826–831 (2005).CrossRefGoogle Scholar
  30. 30.
    Zhang, C. & Johnson, L.W. Microfluidic control of fluorescence resonance energy transfer: Breaking the FRET limit, Angew. Chem. Int. Ed. 46, 3482–3485 (2007).CrossRefGoogle Scholar
  31. 31.
    Yang, L.-H., Ahn, D.J. & Koo, E. Ultrasensitive FRETbased DNA sensor using PNA/DNA hybridization, Mater. Sci. Eng., C 69, 625–630 (2016).CrossRefGoogle Scholar
  32. 32.
    Bae, W.K. & Lee, S. Single-Step Synthesis of Quantum Dots with Chemical Composition, Gradients. Chem. Mater. 20, 531–539 (2008).CrossRefGoogle Scholar
  33. 33.
    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).CrossRefGoogle Scholar

Copyright information

© The Korean BioChip Society and Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Electronic Materials Convergence DivisionKorea Institute of Ceramic Engineering and Technology (KICET)Jinju-si, Gyeongsangnam-doRepublic of Korea
  2. 2.Department of Biomicrosystem TechnologyKorea UniversitySeoulRepublic of Korea
  3. 3.Department of Chemical & Biological Engineering, and KU-KIST Graduate SchoolKorea UniversitySeoulRepublic of Korea

Personalised recommendations