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Screening unlabeled DNA targets with randomly ordered fiber-optic gene arrays

Nature Biotechnology volume 18, pages 91–94 (2000)Cite this article

Abstract

We have developed a randomly ordered fiber-optic gene array for rapid, parallel detection of unlabeled DNA targets with surface immobilized molecular beacons (MB) that undergo a conformational change accompanied by a fluorescence change in the presence of a complementary DNA target. Microarrays are prepared by randomly distributing MB-functionalized 3-μm diameter microspheres in an array of wells etched in a 500-μm diameter optical imaging fiber. Using several MBs, each designed to recognize a different target, we demonstrate the selective detection of genomic cystic fibrosis related targets. Positional registration and fluorescence response monitoring of the microspheres was performed using an optical encoding scheme and an imaging fluorescence microscope system.

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Figure 1: (A) Schematic of a fiber-optic DNA microarray. In this illustration microspheres functionalized with DNA sensing chemistry are randomly distributed on an optical imaging fiber surface.
Figure 2: Fluorescence hybridization patterns upon exposure of the array to the synthetic targets.
Figure 3: Fluorescence hybridization patterns upon exposure of the array with the PCR amplified samples.

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References

  1. Nature Genetics supplement. 21:3– 50 (1999).

  2. Ramsay, G. DNA chips: state-of-the-art. Nat. Biotechnol. 16: 40–44 (1998).

    Article  CAS  Google Scholar 

  3. Whitecombe, D., Newton, C.R. & Little, S. Advantages in approaches to DNA-based diagnostics. Curr. Opin. Biotechnol. 9:602–608 (1998).

    Article  Google Scholar 

  4. Burns, M.A. et al. An integrated nanoliter DNA analysis device. Science 282:484–487 (1998).

    Article  CAS  Google Scholar 

  5. Case-Green, S. C., Mir, K. U., Pritchard, C. E. & Southern, E. M. Analyzing genetic information with DNA arrays. Curr. Opin. Chem. Biol. 2:404–410 ( 1998).

    Article  CAS  Google Scholar 

  6. Chee, M. et al. Accessing genetic information with high-density DNA arrays. Science 274: 610–614 ( 1996).

    Article  CAS  Google Scholar 

  7. 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).

    Article  CAS  Google Scholar 

  8. McGall, G., Labadie, J., Brock, P., Wallraff, G., Nguyen, T. & Hinsberg, W. Light-directed synthesis of high-density oligonucleotide arrays using semiconductor photoresists . Proc. Natl. Acad. Sci. USA 93:13555– 13560 (1996).

    Article  CAS  Google Scholar 

  9. Michael K. L., Taylor, L. C., Schultz, S. L. & Walt, D. R. Randomly-ordered high-density optical sensor arrays. Anal. Chem. 70:1242–1248 ( 1998).

    Article  CAS  Google Scholar 

  10. Tyagi S., Kramer F. R. Molecular beacons: probes that fluoresce upon hybridization. Nat. Biotechnol. 14: 303–308 (1996).

    Article  CAS  Google Scholar 

  11. Kostrikis, L. G., Tyagi, S., Mhlanga, M. M., Ho, D. D. & Kramer, F. R. Spectral genotyping of human alleles . Science 279:1228–1229 (1998).

    Article  CAS  Google Scholar 

  12. Tyagi, S., Bratu, D. P. & Kramer, F. R. Multicolor molecular beacons for allele discrimination . Nat. Biotechnol. 16:49– 53 (1998).

    Article  CAS  Google Scholar 

  13. Ortiz, E., Estrada, G. & Lizardi, P. M. PNA molecular beacons for rapid detection of PCR amplicons. Mol. Cell. Probes 12:219– 226 (1998).

    Article  CAS  Google Scholar 

  14. Fang, X., Liu, X., Schuster, S. & Tan, W. Designing a novel molecular beacon for surface-immobilized DNA hybridization studies. J. Am. Chem. Soc. 127:2921–2922 (1999).

    Article  Google Scholar 

  15. Piatek, A. S. et al. Molecular beacon sequence analysis for detecting drug resistance in Mycobacterium tuberculosis. Nat. Biotechnol. 16: 359–363 (1998).

    Article  CAS  Google Scholar 

  16. Pantano, P. & Walt, D. R. Ordered nanowells arrays. Chem. Mater. 8:2832–2835 (1996).

    Article  CAS  Google Scholar 

  17. Walt, D. R. Fiber optic imaging sensors. Acc. Chem. Res. 31: 267–278 (1998).

    Article  CAS  Google Scholar 

  18. Ferguson, J. A., Boles, T. C., Adams, C. P. & Walt, D. R. A fiber-optic DNA biosensor microarray for the analysis of gene expression . Nat. Biotechnol. 14:1681– 1684 (1996).

    Article  CAS  Google Scholar 

  19. Egner, B. J. et al. Tagging in combinatorial chemistry: the use of coloured and fluorescent beads. Chem. Commun. Vol. 8, 735– 736 (1997).

    Article  Google Scholar 

  20. Fulton, R. J., McDade, R. L., Smith, P. L., Kienker, L. J. & Kettman, J. R. Advanced multiplexed analysis with the flowmetrix™ system. Clin. Chem. 43: 1749–1756 (1997).

    CAS  PubMed  Google Scholar 

  21. Cronin, M. T., Fucini, R. V., Kim, S. M., Masino, R. S., Wespi, R. M. and Miyada, C. G. Cystic fibrosis mutation detection by hybridization to light-generated DNA probe arrays. Hum. Mutat. 7: 244–255 (1996).

    Article  CAS  Google Scholar 

  22. Zielenski, J. et al. Identification of mutations in exons 1 through 8 of the cystic fibrosis transmembrane conductance regular (CFTR) gene. Genomics 10:29–235 (1991).

    Article  Google Scholar 

  23. Bronk, K. S., Michael, K. L., Pantano, P. & Walt, D. R. Combined imaging and chemical sensing using a single optical fiber. Anal. Chem. 67:2750–2757 (1995).

    Article  CAS  Google Scholar 

  24. Slaterbeck, A. F., Ridgway, T. H., Seliskar, C. J. & Heineman, W. R. Spectroelectrochemical sensing based on multimode selectivity simultaneously achievable in a single device. 3. Effect on signal averaging on limit of detection, Anal. Chem. 71:1196–1203 (1999).

    Article  CAS  Google Scholar 

  25. Maldonado-Rodriguez, R., Espinosa-Lara, M., Calixto-Suárez, Beattie, W. G., Beattie, K. L. Hybridization of glass-tethered oligonucleotide probes to target strands preannealed with labeled auxiliary oligonucleotides. Mol. Biotechnol. 11:1– 12 (1999).

    Article  CAS  Google Scholar 

  26. Zielenski, J. et al. Genomic DNA sequence of the cystic fibrosis transmembrane conductance regulator (CFTR) gene. Genomics 10:214– 228 (1991).

    Article  CAS  Google Scholar 

  27. Longo, M. C., Berninger, M. S., Hartley, J. L. Use of uracil DNA glycosylase to control carry-over contamination in polymerase chain reactions. Gene 93 :125–128 (1990).

    Article  CAS  Google Scholar 

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Acknowledgements

This research was supported by the National Institutes of Health (Grant GM–48142). F.S. acknowledges the Technology Foundation (S.T.W.), Technical Science Branch of the Netherlands Organization for Scientific Research (NWO) for a postdoctoral fellowship. Genomic DNA samples with characterized CFTR mutations (Wt507 and F508) were obtained as a gift from Dr. Lap-Chee Tsui and Dr. Julian Zielenski at the University of Toronto. We gratefully acknowledge the support of Dr. Yeon Kim (Tufts University) for his assistance with the asymmetric PCR.

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  1. Department of Chemistry, The Max Tishler Laboratory for Organic Chemistry, Tufts University, Medford, MA

    Frank J. Steemers, Jane A. Ferguson & David R. Walt

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  1. Frank J. Steemers
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  2. Jane A. Ferguson
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  3. David R. Walt
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Correspondence to David R. Walt.

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Steemers, F., Ferguson, J. & Walt, D. Screening unlabeled DNA targets with randomly ordered fiber-optic gene arrays. Nat Biotechnol 18, 91–94 (2000). https://doi.org/10.1038/72006

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