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DNA Amplification Fingerprinting Using Arbitrary Mini-hairpin Oligonucleotide Primers

Abstract

The enzymatic amplification of DNA directed by very short oligonucleotides of arbitrary sequence produces complex DNA profiles useful for genome analysis and identity testing. Mini-hairpins harboring a “core” arbitrary sequence at the 3′ terminus primed the amplification of a wide range of templates ranging from plasmid DNA to plant and animal genomes. Primer core regions of only 3 nucleotides produced complex fingerprints, but the hairpin sequence also influenced the amplification reaction. Oligonucleotide substitution with degenerate bases tailored the complexity of fingerprint patterns. Simulation studies of the amplification of plasmids pUC18 and pBR322 using primers with short arbitrary cores allowed assignment of amplification products to expected regions and revealed physical interaction between annealing sites during amplification of first-round products. Mini-hairpin primers can increase detection of polymorphic DNA, and be used to study subgenomic fragments like yeast artificial chromosomes (YACs), cloned DNA and PCR products.

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References

  1. Caetano-Anollés, G. 1993. Amplifying DNA with arbitrary oligonucleotide primers. PCR Methods Applic. 3: 85–94.

    Article  Google Scholar 

  2. 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. Nucl. Acids Res. 18: 6531–6535.

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  4. Caetano-Anollés, G., Bassam, B.J. and Gresshoff, P.M. 1991. DNA amplification fingerprinting using short arbitrary oligonucleotide primers. Bio/Technology 9: 553–557.

    Google Scholar 

  5. Caetano-Anollés, G., Bassam, B.J. and Gresshoff, P.M. 1993. Enhanced detection of polymorphic DNA by multiple arbitrary amplicon profiling of endonuclease digested DNA: Identification of markers linked to the supernodulation locus in soybean. Mol. Gen. Genet. 241: 57–64.

    Article  Google Scholar 

  6. Caetano-Anollés, G., Bassam, B.J. and Gresshoff, P.M. 1992. Primer-template interactions during DNA amplification fingerprinting with single arbitrary oligonucleotides. Mol. Gen. Genet. 235: 157–165.

    Article  Google Scholar 

  7. Hirao, I., Nishimura, Y., Naraoka Y., Watanabe, K., Arata, Y. and Miura, K. 1989. Extraordinary stable structure of short single-stranded DNA fragments containing a specific base sequence: d(GCGAAAGC). Nucl. Acids Res. 17: 2223–2231.

    Article  CAS  Google Scholar 

  8. Hirao, I., Nishimura Y., Tagawa, Y., Watanabe, K. and Miura, K. 1992. Extraordinarily stable mini-hairpins: electrophoretical and thermal properties of the various sequence variants of d(GCGAAAGC) and their effect on DNA sequencing. Nucl. Acids Res. 20: 3891–3896.

    Article  CAS  Google Scholar 

  9. Bassam, B.J., Caetano-Anollés, G. and Gresshoff, P.M. 1992. DNA amplification fingerprinting of bacteria. Appl. Microbiol. Biotechnol. 38: 70–76.

    Article  CAS  Google Scholar 

  10. Caetano-Anollés, G. 1994. MAAP: a versatile and universal tool for genome analysis. Plant Mol. Biol. In press.

  11. Xodo, L.E., Manzini, G., Quadrifoglio, F., van der Marel, G. and van Boom, J. 1991. DNA hairpin loops in solution. A correlation between primary structure, thermostabiiity and reactivity with single-strand-specific nuclease from mung bean. Nucl. Acids Res. 19: 1505–1511.

    Article  CAS  Google Scholar 

  12. Weaver, K.R. 1993. DNA amplification fingerprinting of centipedegrass. M.Sc. Thesis. University of Tennessee. Knoxville.

    Google Scholar 

  13. Riley, J., Butler, R., Ogilvie, D., Finniear, R., Jenner, D., Powell, S., Anand, R., Smith, J.C., and Markham, A.F. 1990. A novel, rapid method for the isolation of terminal sequences from yeast artificial chromosome (YAC) clones. Nucl. Acids Res. 18: 2887–2890.

    Article  CAS  Google Scholar 

  14. Nelson, D.L., Ledbetter, S.A., Corbo, L., Victoria, M.F., Ramirez-Solis, R., Webster, T.D., Ledbetter, D.H. and Caskey, C.T. 1989. Alu polymerase chain reaction: a method for rapid isolation of human-specific sequences from complex DNA sources. Proc. Natl. Acad. Sci. USA 86: 6686–6690.

    Article  CAS  Google Scholar 

  15. Landau-Ellis, D., Angermüller, S., Shoemaker, R. and Gresshoff, P.M. 1991. The genetic locus controlling supernodulation in soybean (Glycine max L. ) co-segregates tightly with a cloned molecular marker. Mol. Gen. Genet. 228: 221–226.

    Article  CAS  Google Scholar 

  16. Caetano-Anollés, G. and Bassam, B.J. 1993. DNA amplification fingerprinting using arbitrary oligonucleotide primers. Appl. Biochem. Biotechnol. 42: 189–200.

    Article  Google Scholar 

  17. Bassam, B.J., Caetano-Anollés, G. and Gresshoff, P.M. 1991. Fast and sensitive silver staining of DNA in polyacrylamide gels. Anal. Biochem. 196: 80–83.

    Article  CAS  Google Scholar 

  18. Bassam, B.J. and Caetano-Anollés, G. 1993. Silver staining of DNA in polyacrylamide gels. Appl. Biochem. Biotechnol. 42: 181–188.

    Article  CAS  Google Scholar 

  19. Antao, V.P., Lai, S.Y. and Tinoco, I. Jr., 1991. A thermodynamic study of unusually stable RNA and DNA hairpins. Nucl. Acids Res. 19: 5901–5905.

    Article  CAS  Google Scholar 

  20. Antao, V.P. and Tinoco, I. Jr., 1991. Thermodynamic parameters for loop formation in RNA and DNA hairpin tetraloops. Nucl. Acids Res. 20: 819–824.

    Article  Google Scholar 

  21. Tuerk, C., Gauss, P., Thermes, C., Groebe, D.R., Gayle, M., Guild, N., Stormo, G., D'Aubenton-Carafa, Y., Uhlenbeck, O.C., Tinoco, I. Jr., Brody, E.N. and Gold, L. 1988. CUUCGG hairpins: extraordinarily stable RNA secondary structures associated with various biochemical processes. Proc. Natl. Acad. Sci. USA 85: 1364–1368.

    Article  CAS  Google Scholar 

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Caetano-Anollés, G., Gresshoff, P. DNA Amplification Fingerprinting Using Arbitrary Mini-hairpin Oligonucleotide Primers. Nat Biotechnol 12, 619–623 (1994). https://doi.org/10.1038/nbt0694-619

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