ABSTRACT
PCR-based DNA fingerprinting methods allow for the generation of large numbers of polymorphic markers while using very small amounts of starting DNA with no need of prior knowledge of the target sequence. These methods are well suited for high-throughput applications used in genomic studies addressing the comparison of two or more samples. Various approaches take advantage of the ubiquitous presence of repetitive elements throughout the genome to produce arbitrary fingerprints. Alu-PCR employs Alu-specific primers [1] and the simple sequence-repeat anchored PCR (SS-PCR) amplification uses primers containing microsatellites and two or three additional nucleotides at the 3 end [2]. Methods based in the use of arbitrary primers, such as arbitrarily primed-PCR (AP-PCR) [3] and random amplified polymorphic DNA (RAPD) [4], are probably the most widely used in studies that range from phylogenetics in prokaryotes and eukaryotes to the genetic analysis
of many human diseases. Finally, an alternative method known as amplified fragment length polymorphism (AFLP) produces complex DNA fingerprintings by amplification of restriction fragments ligated to adaptors [5]. In this case, the PCR primers are specific to the adaptor, but include an arbitrary short sequence at the 3 end allowing the selection of a subset of all the fragments.
