Dna amplification fingerprinting using arbitrary mini-hairpin oligonucleotide primers

Gustavo Caetano-Anollés, Peter M. Gresshoff

Research output: Contribution to journalArticlepeer-review


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.

Original languageEnglish (US)
Pages (from-to)619-623
Number of pages5
Issue number6
StatePublished - Jun 1994
Externally publishedYes

ASJC Scopus subject areas

  • Biotechnology


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