MAAP - A VERSATILE AND UNIVERSAL TOOL FOR GENOME ANALYSIS

Multiple arbitrary amplicon profiling (MAAP) uses one or more oligonuc leotide primers (greater than or equal to 5 nt) of arbitrary sequence to initiate DNA amplification and generate characteristic fingerprints from anonymous genomes or DNA templates. MAAP markers can be used in general fingerprinting as well as in mapping applications, either dire ctly or as sequence-characterized amplified regions (SCARs). MAAP prof iles can be tailored in the number of monomorphic and/or polymorphic p roducts. For example, multiple endonuclease digestion of template DNA or the use of mini-hairpin primers can enhance detection of polymorphi c DNA. Comparison of the expected and actual number of amplification p roducts produced with primers differing in length, sequence and GC con tent from templates of varying complexity reveal severe departures fro m theoretical formulations with interesting implications in primer-tem plate interaction. Extensive primer-template mismatching can occur whe n using templates of low complexity or long primers. Primer annealing and extension appears directed by an 8 nt 3'-terminal primer domain, r equires sites with perfect homology to the first 5-6 nt fom the 3' ter minus, and involves direct physical interaction between amplicon annea ling sites.