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Interference-based detection of nucleic acid targets on optically coated silicon

Nature Biotechnology volume 19, pages 62–65 (2001)Cite this article

Abstract

Sequence-specific detection of polynucleotides typically requires modified reporter probes that are labeled with radioactive, fluorescent, or luminescent moieties. Although these detection methods are capable of high sensitivity, they require instrumentation for signal detection. In certain settings, such as clinical point of care, instrumentation might be impractical or unavailable. Here we describe a detection approach in which formation of a nucleic acid hybrid is enzymatically transduced into a molecular thin film that can be visually detected in white light. The system exploits a flat, optically coated silicon-based surface to which capture oligonucleotides are covalently attached. The optimized system is capable of detection of nucleic acid targets present at sub-attomole levels. To supplement visual detection, signals can be quantitated by a charge-coupled device. The design and composition of the optical surface, optimization of immobilization chemistry for attachment of capture probes, and characterization of the efficiency of the hybridization process are presented. We describe the application of this system to detection of a clinically relevant target, the mecA gene present in methicillin-resistant Staphylococcus aureus.

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Figure 1: Schematic representation of the coated-silicon hybridization-based biosensor.
Figure 2: Chromaticity coordinates for interference colors on the TSPS/PPL surface as a function of thin-film formation.
Figure 3: Sensitivity of TSPS/PPL surface for detection of model DNA target.
Figure 4: Detection of mecA gene sequences in S. aureus genomic DNA.

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References

  1. Kricka, L.J. Nucleic acid detection technologies–labels, strategies, and formats . Clin. Chem. 45, 453–458 (1999).

    CAS  PubMed  Google Scholar 

  2. Whitcombe, D., Newton, C.R. & Little, S. Advances in approaches to DNA-based diagnostics. Curr. Opin. Biotechnol. 9, 602–608 (1998).

    Article  CAS  Google Scholar 

  3. Sandstrom, T., Stenberg, M. & Nygren, H. Visual detection of organic monomolecular films by interference colors. Appl. Optics 24, 472– 479 (1985).

    Article  CAS  Google Scholar 

  4. Ostroff, R., Hopkins, D., Haeberli, A.B., Baouchi, W. & Polisky, B. Thin film biosensor for rapid visual detection of nucleic acid targets. Clin. Chem. 45, 1659–1664 (1999).

    CAS  PubMed  Google Scholar 

  5. Urdea, M.S. et al. A comparison of non-radioisotopic hybridization assay methods using fluorescent, chemiluminescent and enzyme labeled synthetic oligodeoxyribonucleotide probes. Nucleic Acids Res. 16, 4937– 4957 (1998).

    Article  Google Scholar 

  6. The Committee on Colorimetry of the Optical Society of America. The science of color. (Edwards Brothers, Inc., Ann Arbor, MI; 1953).

  7. Born, M. & Wolf, E. Principles of optics, Edn. 6. (Pergamon Press, Oxford, UK; 1980).

    Google Scholar 

  8. Running, J.A. & Urdea, M.S. A procedure for productive coupling of synthetic oligonucleotides to polystyrene microtiter wells for hybridization capture. BioTechniques 8, 276–277 (1990).

    CAS  PubMed  Google Scholar 

  9. Brown, D.F.J. & Reynolds, P.E. Intrinsic resistance to β-lactam antibiotics in Staphylococcus aureus. FEBS Lett. 122, 275–278 (1980).

    Article  CAS  Google Scholar 

  10. Hartman, B.J. & Tomasz, A. Low-affinity penicillin-binding protein associated with β-lactam resistance in Staphylococcus aureus . J. Bacteriol. 158, 513– 516 (1984).

    CAS  PubMed  PubMed Central  Google Scholar 

  11. Covalciuc, K.A., Webb, K.H. & Carlson, C.A. Comparison of four clinical specimen types for detection of Influenza A and B viruses by optical immunoassay (FLU OIA Test) and cell culture methods. J. Clin. Microbiol. 37, 3971–3974 (1999).

    CAS  PubMed  PubMed Central  Google Scholar 

  12. Gerber, M.A. et al. Optical immunoassay test for group A β-hemolytic streptococcal pharyngitis. JAMA 277, 899– 903 (1997).

    Article  CAS  Google Scholar 

  13. Bobrow, M.N., Shaughnessy, K.J. & Litt, G.J. Catalyzed reporter deposition. II. Application to membrane immunoassays. J. Immunol. Methods 137, 103–112 (1991).

    Article  CAS  Google Scholar 

  14. Lin, V.S.-Y., Motesharei, K., Dancil, K.-P.S., Sailor, M.J. & Ghadiri, M.R. A porous silicon-based optical interferometric biosenor. Science 278, 840–843 (1997).

    Article  CAS  Google Scholar 

  15. Elghanian, R., Storhoff, J.J., Mucic, R.C., Letsinger, R.L. & Mirkin, C.A. Selective colorimetric detection of polynucleotides based on the distance-dependent optical properties of gold nanoparticles. Science 277, 1078 –1080 (1997).

    Article  CAS  Google Scholar 

  16. Rule, G.S., Montagna, R.A. & Durst, R.A. Rapid method for visual identification of specific DNA sequences based on DNA-tagged liposomes. Clin. Chem. 42, 1206–1209 (1996).

    CAS  PubMed  Google Scholar 

  17. Pospiech, A. & Neumann, B. A versatile quick-prep of genomic DNA from gram-positive bacteria. Trends Genet. 11, 217–218 (1995).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank Dr. Rachel Ostroff and Dr. Diana Maul for advice and critical evaluation of the manuscript. We also thank Wahab Baouchi for preparation of the optical surfaces, Chris High for preparation of the figures, and Brenda Bolton for assistance in preparation of the manuscript.

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  1. BioStar, Inc., 6655 Lookout Road, Boulder, 80301, CO

    Robert Jenison, Shao Yang, Ayla Haeberli & Barry Polisky

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  1. Robert Jenison
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Correspondence to Barry Polisky.

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Jenison, R., Yang, S., Haeberli, A. et al. Interference-based detection of nucleic acid targets on optically coated silicon. Nat Biotechnol 19, 62–65 (2001). https://doi.org/10.1038/83530

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