DNA amplification fingerprinting

DNA amplification fingerprinting (DAF) is a highly sensitive DNA profiling technique that generates complex, reproducible genomic fingerprints without prior knowledge of sequence information. Developed in the very early 1990s by Gustavo Caetano-Anollés and colleagues at the University of Tennessee, DAF offered a high-resolution alternative to nucleic acid scanning methods such as random amplified polymorphic DNA (RAPD), arbitrarily primed PCR (AP-PCR), and amplified fragment length polymorphism (AFLP) for genetic typing, strain discrimination, genome mapping, and population analysis.

DAF employs single, very short arbitrary oligonucleotide primers, typically 5-8 nucleotides (nt) in length, and a polymerase chain reaction (PCR) to amplify multiple anonymous regions dispersed throughout the genome. Because the primers are extremely short, they anneal at numerous partially complementary sites. When two sites occur in opposite orientation and within amplifiable distance (generally < 3–5 kb), the intervening segment is amplified. Resolution of the resulting products by high-resolution denaturing or native polyacrylamide gel electrophoresis (PAGE), followed by silver staining, produces dozens to hundreds of bands that together form a characteristic genomic "fingerprint," with individual bands often serving as genetic markers.

DAF is distinguished from related arbitrarily amplified DNA techniques by its high primer-to-template ratios, procedural simplicity, strong reproducibility, and high multiplex capacity. In addition to whole genomes, fingerprints can be generated from subgenomic fragments such as PCR amplified products, cloned DNA, and complementary DNA (cDNA) populations.