DNA Multilocus Fingerprinting Using Simple Repeat Motif Oligonucleotides

Abstract

Abstract The “invention” of multilocus minisatellite DNA fingerprinting in 1985 has provided conservation geneticists with a powerful new tool (Jeffreys, 1985b). Owing to the high average mutation rate of the genomic regions analysed in DNA fingerprinting, the multilocus band patterns or fingerprints normally reveal ample genetic variation (Jeffreys et al., 1988). Thus, multilocus fingerprinting can provide information on the genetic structure of individuals (heterozygosity) or populations (allelic diversity) where less sensitive methods such as enzyme electrophoresis might fail. Like minisatellite fingerprinting, simple sequence oligonucleotide fingerprinting detects multiple loci simultaneously in the eukaryotic genome. The technique is named after the specific hybridization probe employed: a synthetic single-stranded oligonucleotide, about 20 nucleotides in length. The sequence of this probe consists of a single, very short motif, for instance “CA” or “GTC,” which is repeated several times. Such a probe can hybridize with simple repetitive DNA loci in the eukaryotic genome. Since many repetitive DNA loci in the genome consist of the same repeat motif, simple sequence oligonucleotide fingerprinting produces a multilocus fingerprint pattern (for reviews on oligonucleotide fingerprinting see: Epplen, 1988; Epplen et al., 1991, 1993). The degree of genetic variation revealed in oligonucleotide fingerprints seems to be similar to that in minisatellite fingerprints. A study analysing several loci in the human genome that hybridize with the (CAC)5 oligonucleotide probe confirmed a very high average rate of germline mutations. The mutation rate of the resolvable DNA fragments containing such loci was estimated to be approximately 0.001 per locus per gamete (Niirnberg et al., 1989). The same study showed that the fingerprint patterns were somatically stable, thus providing support for the reliability of the method.