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.

  • Research Paper
  • Published:

DNA Amplification Fingerprinting Using Very Short Arbitrary Oligonucleotide Primers

Abstract

The surprising finding that amplification of genomic DNA can be directed by only one oligonucleotide primer of arbitrary sequence to produce a characteristic spectrum of short DNA products of varying complexity, was applied as a strategy to detect genetic differences between organisms. This approach, DNA amplification fingerprinting (DAF), does not depend on cloning or DNA sequence information and can generate fingerprints from DNA of viral, bacterial, fungal, plant and animal origins. Primers as short as 5 nucleotides in length can produce complex banding patterns that are resolved by polyacrylamide gel electrophoresis and silver staining. Amplification fragment length polymorphisms (AFLPs) were detected between different human individuals as well as between soybean cultivars. It is anticipated that DAF will have wide application for DNA analysis.

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

Access options

Buy this article

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

Similar content being viewed by others

References

  1. Jeffreys, A.J., Wilson, V. and Thein, S.L. 1985. Hypervariable ‘minisatcllite’ regions in human DNA. Nature 314: 67–73.

    Article  CAS  PubMed  Google Scholar 

  2. Nakamura, Y., Leppert, M., O'Connell, P., Wolff, R., Holm, T., Culver, M., Martin, C., Fujimoto, E., Hoff, M., Kumlin, E. and White, R. 1987. Variable number of tandem repeat (VNTR) markers for human gene mapping. Science 235: 1616–1622.

    Article  CAS  PubMed  Google Scholar 

  3. Wong, Z., Wilson, V., Patel, I., Povey, S. and Jeffreys, A.J. 1987. Characterization of a panel of highly variable minisatellites cloned from human DNA. Annu. Hum. Genet. 51: 269–288.

    Article  CAS  Google Scholar 

  4. Watkins, P.C. 1988. Restriction fragment length polymorphism (RFLP): applications in human chromosome mapping and genetic disease research. Biotechniques 6: 310–320.

    CAS  PubMed  Google Scholar 

  5. Donis-Keller, H., Green, P., Helms, C., Cartinhour, S. et al. 1987. A genetic linkage map of the human genome. Cell 51: 319–337.

    Article  CAS  PubMed  Google Scholar 

  6. Landegren, U., Kaiser, R., Caskey, C.T. and Hood, L. 1988. DNA diagnostics-molecular techniques and automation. Science 242: 229–237.

    Article  CAS  PubMed  Google Scholar 

  7. Jeffreys, A.J., Wilson, V. and Thein, S.L. 1985. Individual-specific ‘fingerprints’ of human DNA. Nature 316: 76–79.

    Article  CAS  PubMed  Google Scholar 

  8. Vassart, G., Georges, M., Monsieur, R., Broca, H., Lequarre, A.S. and Cristophe, D. 1987. A sequence in M13 phage detects hypervariable minisatellites in human and animal DNA. Science 235: 683–684.

    Article  CAS  PubMed  Google Scholar 

  9. Armour, J.A.L., Wong, Z., Wilson, V., Royle, N.J. and Jeffreys, A.J. 1989. Sequences flanking the repeat arrays of human minisatellites: association with tandem and dispersed repeat elements. Nucleic Acids Res. 17: 4925–4935.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Wong, Z., Wilson, V., Jeffreys, A.J. and Thien, S.L. 1986. Cloning a selected fragment from a human DNA fingerprint: isolation of an extremely polymorphic minisatellite. Nucleic Acids Res. 14: 4607–4616.

    Article  Google Scholar 

  11. Jeffreys, A.J., Wilson, V., Neumann, R. and Keyte, J. 1988. Amplification of human minisatellites by the polymerase chain reaction: towards DNA fingerprinting of single cells. Nucleic Acids Res. 16: 10953–10971.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Boerwinkle, E., Xiong, W., Fourest, E. and Chan, L. 1989. Rapid typing of tandemly repeated hypervariable loci by the polymerase chain reaction: application to the apolipoprotein B 3′ hypervariable region. Proc. Natl. Acad. Sci. USA 86: 212–216.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Horn, G.T., Richards, B. and Klinger, K.W. 1989. Amplification of a highly polymorphic VNTR segment by the polymerase chain reaction. Nucleic Acids Res. 17: 2140.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Tautz, D. 1989. Hypervariability of simple sequences as a general source for polymorphic DNA markers. Nucleic Acids Res. 17: 6463–6472.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Jeffreys, A.J., Neumann, R. and Wilson, V. 1990. Repeat unit sequence variation in minisatellites: a novel source of DNA polymorphism for studying variation and mutation by single molecule analysis. Cell 60: 473–485.

    Article  CAS  PubMed  Google Scholar 

  16. Williams, J.G.K., Kubelik, A.R., Livak, K.J., Rafalski, J.A. and Tingey, S.V. 1990. DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res. 18: 6531–6535.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Welsh, J. and McClelland, M. 1990. Fingerprinting genomes using PCR with arbitrary primers. Nucl. Acids Res. 18: 7213–7218.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Mullis, K.B. and Faloona, F.A. 1987. Specific synthesis of DNA in vitro via a polymerase catalysed reaction. Meth. Enzymol. 255: 335–350.

    Article  Google Scholar 

  19. Saiki, R.K., Gelfand, D.H., Stoffel, S., Scharf, S.J., Higuchi, R., Horn, G.T. and Erlich, H.A. 1988. Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239: 487–491.

    Article  CAS  PubMed  Google Scholar 

  20. Ochman, H., Gerber, A.S. and Hartl, D.L. 1988. Genetic applications of an inverse polymerase chain reaction. Genetics 120: 621–623.

    CAS  PubMed  PubMed Central  Google Scholar 

  21. Doyle, J.J. and Beachy, R.N. 1985. Ribosomal gene variation in soybean (Glycine) and its relatives. Theor. Appl. Genet. 70: 369–376.

    Article  CAS  PubMed  Google Scholar 

  22. Doyle, J.J. 1988. 5S ribosomal gene variation in the soybean and its progenitor. Theor. Appl. Genet. 75: 621–624.

    Article  CAS  Google Scholar 

  23. Apuya, N., Frazier, B., Keim, P., Roth, E.J. and Lark, K.J. 1988. Restriction length polymorphisms as genetic markers in soybean, Glycine max (L.) Merr. Theor. Appl. Genet. 75: 889–901.

    Article  CAS  Google Scholar 

  24. Keim, P., Shoemaker, R.C. and Palmer, R.G. 1989. Restriction fragment length polymorphism diversity in soybean. Theor. Appl. Genet. 77: 786–792.

    Article  CAS  PubMed  Google Scholar 

  25. Botstein, D., White, R.L., Skolnick, M. and Davis, R.W. 1980. Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am. J. Hum. Genet. 32: 314–331.

    CAS  PubMed  PubMed Central  Google Scholar 

  26. Chesney, R.H., Scott, J.R. and Vapnek, D. 1979. Integration of the plasmid prophages P1 and P7 into the chromosome of Escherichia coli. J. Mol. Biol. 130: 161–173.

    Article  CAS  PubMed  Google Scholar 

  27. Dellaporta, S.L., Wood, J. and Hicks, J.B. 1983. A plant DNA minipreparation: Version II. Plant Mol. Biol. Reporter 1: 19–21.

    Article  CAS  Google Scholar 

  28. Sarkar, G. and Sommer, S.S. 1990. Avoidance of false positives. Nature 343: 27.

    Article  CAS  PubMed  Google Scholar 

  29. Goldman, D. and Merril, C.R. 1982. Silver staining of DNA in polyacrylamide gels: linearity and effect of fragment size. Electrophoresis 3: 24–26.

    Article  CAS  Google Scholar 

  30. Blum, H., Beier, H. and Gross, H.J. 1987. Improved silver staining of plant proteins, RNA and DNA in polyacrylamide gels. Electrophoresis 8: 93–99.

    Article  CAS  Google Scholar 

  31. Bassam, B.J., Caetano-Anollés, G. and Gresshoff, P.M. 1991. Fast and sensitive silver staining of DNA in polyacrylamide gels. Anal. Biochem. In press.

    Google Scholar 

  32. Franssen, H.J., Nap, J.P., Gloudemans, T., Stiekema, W., van Dam, H., Govers, F., Louwerse, J., van Kammen, A. and Bisseling, T. 1987. Characterization of cDNA for nodulin-75 of soybean: a gene product involved in early stages of root nodule development. Proc. Natl. Acad. Sci. USA 84: 4495–4499.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Dickstein, R., Bisseling, T., Reinhold, V.N. and Ausubel, F.M. 1988. Expression of nodule-specific genes in alfalfa root nodules blocked at an early stage of development. Genes Dev. 2: 677–687.

    Article  CAS  PubMed  Google Scholar 

  34. Scheres, B., Van De Wiel, C., Zalensky, A., Horvath, B., Spaink, H., Van Eck, H., Zwartkruis, F., Wolters, A.M., Gloudemans, T., Van Kammen, A. and Bisseling, T. 1990. The ENOD12 gene product is involved in the infection process during the pest-Rhizobium interaction. Cell 60: 281–294.

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Rights and permissions

Reprints and permissions

About this article

Cite this article

Caetano-Anollés, G., Brant J., B. & Peter M., G. DNA Amplification Fingerprinting Using Very Short Arbitrary Oligonucleotide Primers. Nat Biotechnol 9, 553–557 (1991). https://doi.org/10.1038/nbt0691-553

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nbt0691-553

This article is cited by

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