DAF-amplified fragments can be used as markers for DNA from pulse field gels

PCR-type amplification of genomic sequences using short, single and arbitrarily chosen primers (by DNA amplification fingerprinting [DAF]) was developed in our laboratory. Here we show that it is possible to produce specific fingerprints for subgenomic DNA fragments embedded in agarose, including fractions from conventional and pulse field gels. Fractions of restricted genomic DNA differing in mobility by only 2-3 mm gave one to three different products with different single primers. Yeast chromosome specific markers were easily produced and cloned. We also used DAF to generate specific amplification products of DNA cloned into a yeast artificial chromosome. These products were readily cloned into a plasmid vector.