Oligonucleotide Fingerprinting Using Simple Repeat Motifs: A Convenient, Ubiquitously Applicable Method to Detect Hypervariability for Multiple Purposes

Abstract

A panel of simple repetitive oligonucleotide probes has been designed and tested for multilocus DNA fingerprinting in some 200 fungal, plant and animal species as well as man. To date at least one of the probes has been found to be informative in each species. The human genome, however, has been the major target of many fingerprintins studies. Using the probe (CAC) 5 or (GTG) 5 , individualization of all humans is possible except for monozygotic twins. Paternity analyses are now perfonned on a routine basis by the use of multilocus fingerprints, inctuding also cases of deficiency, i.e. where one of the parents is not available for analysis. In forensie science stain analysis is feasible in all tissue remains containing nuc)eated cells. Depending on the degree of DNA degradation a variety of oligonucleotides are informative, and they have been proven useful in actual case work. Advantages in comparison to other methods including enzymatic DNA amplification techniques (PCR) are evident. Fingerprint patterns of tumors may be changed due to the gain or loss of chromosomes and/or intrachromosomal deletion and amplification events. Locus-specific probes were isolated from the human (CAC) 5 /(GTG) 5 fingerprint with a varying degree of informativeness (monomorphic versus truly hypervariable markers). The feasibility of three different approaches. for the isolation of hypervariable mono-locus probes was evaluated. Finally, one particular mixed simple (gt)n(ga)m repeat locus in the second intron of the HLA-DRB genes has been scrutinized to allow comparison of the extent of exon-encoded (protein-) polymorphisms versus intronie bypervariability of simple repeats: adjacent to a single gene sequence (e.g. HLAMDRBl•0401) many different length alleles were found. Group-specific structures of basic repeats were identified within the evolutionarily related DRB alleles. As a further application it is suggested here that due to the ubiquitous interspersion of their targets, short probes for simple repeat sequences are especially useful tools for ordering genomic cosmid, yeast artificial chromosome and phage banks.

(CT)n and (GT)n microsatellites: a new class of genetic markers for Salmo trutta L. (brown trout)

“…The restriction fragment length polymorphism obtained with probes homologous to these mini and microsatellite sequences reflects allelic variation at many loci (Jeifreys et a!., 1985;Epplen et a!., 1991;Taggart & Ferguson, 1991). These highly polymorphic 'fingerprints' are convenient in situations requiring paternity testing and in forensic medicine, but are inadequate for many population genetics purposes because of the inability to assign the observed bands to specific loci.…”

On the stability of dispensable constituents of the eukaryotic genome: stability of coding sequences versus truly hypervariable sequences in a clonal vertebrate, the amazon molly, Poecilia formosa.

“…In the gynogenetic fish these loci, which vary by differing restriction fragment lengths even between the siblings of one brood, lend support to the notion that these otherwise clonal organisms are not genetically identical sensu stricto. The nature and meaning of truly hypervariable loci are discussed in the context of obligatory rearrangements, as examplified by a paradigmatic locus in the chicken that defies the Mendelian rules (32).…”

Genomic simple repetitive DNAs are targets for differential binding of nuclear proteins

“…One of the repeats which we studied for binding nuclear proteins was (GAA)n. The motif (GAA)~ was first cloned in the context of a most intriguing single-copy locus in the chicken that defies Mendelian inheritance laws [31]. Non-Mende- Table 1 Results of competition experiments between various genome-derived target sequences containing simple repeat blocks as primary components a Labelled targets (GT)22(GAh~ (GAA)24…”