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.

  • Review Article
  • Published:

A Prospectus for Multispectral-Multiplex DNA Sequencing

Bio/Technology volume 7, pages 576–580 (1989)Cite this article

Abstract

First-generation automated DNA sequencers are based on operations, manipulations, and methodologies not unlike those performed by their human predecessors. While these instruments may reduce labor, they do not increase sequencing rates by exponential factors. Here we review several new methodologies that could enhance sequencing rates by orders-of-magnitude. From the perspective of combining separate techniques into future second generation sequencers, we review: (1) multispectral sequencing, (2) fluorophore photochemistry, (3) multiplex sequencing, (4) direct blotting electrophoresis, and (5) electronic imaging techniques. Hardware and an operational protocol (including a novel kit of primers and probes) are proposed for a multispectral-multiplex sequencer, capable of processing one million DNA bases per sequencing gel blot.

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

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Similar content being viewed by others

References

  1. Mapping and Sequencing the Human Genome 1988. National Academy Press.

  2. Martin, W.J. and Davies, R.W. 1986. Automated DNA sequencing: Progress and Prospects. Bio/Technology 4:890–895.

    CAS  Google Scholar 

  3. Wada, A. 1987. Automated high-speed DNA sequencing. Nature 325:771–772.

    Article  CAS  Google Scholar 

  4. Landegren, U., Kaiser, R., Caskey, C.T. and Hood, L. 1988. DNA diagnostics—Molecular techniques and automation. Science 242:229–237.

    Article  CAS  Google Scholar 

  5. Maxam, A.M. and Gilbert, W. 1977. A new method for sequencing DNA. Proc. Nat. Acad. Sci. USA 74:560–564.

    Article  CAS  Google Scholar 

  6. Sanger, F., Nicklen, S. and Coulson, A.R. 1977. DNA sequencing with chain-terminating inhibitors. Proc. Nat. Acad. Sci. USA 74:5463–5467.

    Article  CAS  Google Scholar 

  7. Smith, L.M., Fung, S., Hunkapiller, M.W., Hunkapiller, T.J. and Hood, L.E. 1985. The synthesis of oligonucleotides containing an aliphatic amino group at the 5′ terminus: synthesis of fluorescent DNA primers for use in DNA sequence analysis. Nuc. Acids Research 13:2399–2412.

    Article  CAS  Google Scholar 

  8. Smith, L.M., Sanders, J.Z., Kaiser, R.J., Hughes, P., Dodd, C., Connell, C.R., Heiner, C., Kent, S.B.H. and Hood, L.E. 1986. Fluorescence detection in automated DNA sequence analysis. Nature 321:674–679.

    Article  CAS  Google Scholar 

  9. Prober, J.M., Trainor, G.L., Dam, R.J., Hobbs, F.W., Robertson, C.W., Zagursky, R.J., Cocuzza, A.J., Jensen, M.A. and Baumeister, K. 1987. A system for rapid DNA sequencing with fluorescent chain-terminating dideoxynucleotides. Science 238:336–341.

    Article  CAS  Google Scholar 

  10. Ansorge, W., Sproat, B.S., Stegemann, J. and Schwage, C.J. 1986. A non-radioactive automated method for DNA sequence determination. Biochem. Biophy. Methods 13:315–323.

    Article  CAS  Google Scholar 

  11. Ansorge, W., Sproat, B., Stegemann, J., Schwager, C. and Zenke, M. 1987. Automated DNA sequencing; ultrasensitive detection of fluorescent bands during electrophoresis. Nuc. Acids Research 15:4593–4602.

    Article  CAS  Google Scholar 

  12. Brumbaugh, J.A., Middendorf, L.R., Grone, D.L. and Ruth, J.L. 1988. Continuous, on-line DNA sequencing using oligodeoxynucleotide primers with multiple fluorophores. Proc. Nat. Acad. Sci. USA 85:5610–5614.

    Article  CAS  Google Scholar 

  13. Kambara, H., Nishikawa, T., Katayama, Y. and Yamaguchi, T. 1988. Optimization of parameters in a DNA sequenator using fluorescence detection. Bio/Technology 6:816–821.

    CAS  Google Scholar 

  14. Mathies, R.A. and Stryer, L. Single molecule fluorescence detection: a feasibility study using phycoerythrin, p. 129–140. In: Applications of Fluorescence in the Biomedical Sciences. Alan R. Liss, Inc., NY.

  15. Turro, N.J. 1978. Modern Molecular Photochemistry. Benjamin/Cummings Pub. Co.

  16. Glazer, A.N. and Stryer, K. 1984. Phycofluor probes, TIBS Oct.: 423–427.

    Google Scholar 

  17. White, J.C. and Stryer, L. 1987. Photostability studies of phycobiliprotein fluorescent labels. Anal. Biochem. 161:442–452.

    Article  CAS  Google Scholar 

  18. Church, G.M. and Gilbert, W. 1984. Genomic sequencing. Proc. Nat. Acad. Sci. USA 81:1991–1995.

    Article  CAS  Google Scholar 

  19. Church, G.M. and Kieffer-Higgins, S. 1988. Multiplex DNA sequencing. Science 240:185–188.

    Article  CAS  Google Scholar 

  20. Beck, S. and Pohl, F.M. 1984. DNA sequencing with direct blotting electrophoresis. EMBO J. 3:2905–2909.

    Article  CAS  Google Scholar 

  21. Beck, S. 1988. Protein blotting with direct blotting electrophoresis. Anal. Biochem. 170:361–366.

    Article  CAS  Google Scholar 

  22. UCLA forum in the medical sciences 9. Image Processing in Biological Science. 1968. D. M. Ramsey (Ed). Univ. of California Press.

  23. Inoue, S., 1986. Video Microscopy, Plenum Press, New York.

    Book  Google Scholar 

  24. Elder, J.K., Green, D.K. and Southern, E.M. 1986. Automatic reading of DNA sequencing gel autoradiographs using a large format digital scanner. Nuc. Acids Research 14:417–424.

    Article  CAS  Google Scholar 

  25. Gray, A.J., Beecher, D.E. and Olson, M.V. 1984. Computer-based image analysis of one-dimensional electrophoretic gels used for the separation of DNA restriction fragments. Nuc. Acids Research 12:473–491.

    Article  CAS  Google Scholar 

  26. Sutherland, J.C., Lin, B., Monteleone, D.C., Mugavero, J., Sutherland, B.M. and Trunk, J. 1987. Electronic imaging system for direct and rapid quantitation of fluorescence from electrophoretic gels: Application to ethidium bromide-stained DNA. Anal. Biochem. 163:446–457.

    Article  CAS  Google Scholar 

  27. Gonzalez, R.C. and Wintz, P. 1987. Digital Image Processing. Addison-Wesley.

    Google Scholar 

  28. Yang, M.M. and Youvan, D.C. 1988. Applications of imaging spectroscopy in molecular biology: 1. Screening photosynthetic bacteria. Bio/Technology 6:939–942.

    CAS  Google Scholar 

  29. Yang, M.M. and Youvan, D.C. 1989. In preparation.

  30. Waggoner, A.S. 1986. Fluorescent probes for analysis of cell structure, function, and health by flow and imaging cytometry, p. 3–28. In: Applications of Fluorescence in the Biomedical Sciences. Alan R. Liss, Inc.

    Google Scholar 

  31. Hemmila, I., Dakubu, S., Mukkala, V., Siitari, H. and Lovgren, T. 1984. Europium as a label in time-resolved immunofluorometric assays. Anal. Biochem. 137:335–343.

    Article  CAS  Google Scholar 

  32. Oser, A., Roth, W.K. and Valet, G. 1988. Sensitive non-radioactive dot-blot hybridization using DNA probes labelled with chelate group substituted psoralen and quantitative detection by europium ion fluorescence. Nuc. Acids Research 16:1181–1196.

    Article  CAS  Google Scholar 

Download references

Author information

Author notes

  1. Douglas C. Youvan: Corresponding author.

Authors and Affiliations

  1. Department of Chemistry, Rm 56–213, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139

    Mary M. Yang & Douglas C. Youvan

Authors
  1. Mary M. Yang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Douglas C. Youvan
    View author publications

    You can also search for this author in PubMed Google Scholar

Rights and permissions

Reprints and permissions

About this article

Cite this article

Yang, M., Youvan, D. A Prospectus for Multispectral-Multiplex DNA Sequencing. Nat Biotechnol 7, 576–580 (1989). https://doi.org/10.1038/nbt0689-576

Download citation

  • Issue Date:

  • DOI: https://doi.org/10.1038/nbt0689-576

This article is cited by

Search

Advanced 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