Hypervariable repeats

Fig. 2. Fingerprint analysis. Three separate human genomic DNA samples were digested with Hinfl and transfered to Hybond-N (2 pg loadings). Hybridized at 10 n mL with a 28-base oligonucleotide probe, specific for the insulin hypervariable repeat region, labeled at the 3 end with fluorescein-dUTP. Hybridized for 2 h at 42 C stringent wash IX SSC, 0.1% SDS at 42 C 30-min exposure on Hyperfilm-MP.

Microsatellites are hypervariable co-dominant loci composed of arrays of 2-9 bp repeating motifs. Differences in the number of repeat motifs in an array define microsatellite polymorphisms. Method development requires the identification of microsatellite loci, and for each locus, the design of PCR primers to anneal to conserved regions flanking the microsatellite. Analysis involves PCR amplification with fluorescently labeled primers followed by electrophoresis to distinguish microsatellite alleles of different array size. 

Litt M, Luty J A (1989). A hypervariable microsatellite revealed by in vitro amplification of a dinucleotide repeat within the cardiac muscle actin gene. Am. J. Hum. Genet. 44(3) 397-401. 

Short DNA repeats often appear as multiple copies in higher genomes, positioned in a head-to-tail orientation, and are known as tandem repeats. The number of copies of these repeats varies between individuals and between chromosomes within an individual s genome. This hypervariability, known as polymorphism, can be exploited in paternity testing and forensics. 

Gilmore, S., Peakall, R., and Robertson, J., Short tandem repeat (STR) DNAmarkers are hypervariable and informative in Cannabis sativa Implications for forensic investigations. Forensic Sci Int, 131,65,... 

The way in which individuals differ at hypervariable loci is elucidated by restriction analysis of chromosomal DNA. This is made possible by the fact that restriction sites for many restriction endonucleases (see) do not occur in minisatellite DNA. This means that when the chromosomal DNA is digested with such an endonuclease all the species of minisatellite DNA remain intact, cleavages having occurred on either side of them. Thus individuals with different numbers of tandemly repeated monomers at specific hypervariable loci will produce restriction fi-a ents of different length from those loci these can be separated by gel electrophoresis and detected with an appropriate probe after Southern blotting (see). 

The diagnostic capabilities of DNA fingerprinting, first demonstrated in 1985 [A. J. Jeffreys etal. Nature (1985) 314, 67-73], are demonstrated in Fig.l which depicts a specific hypervariable locus, bounded by a pair of restriction sites (indicated by the shaded boxes), in a homologous pair of chromosomes in four human individuals A and B are the father and mother, respectively, of C and D, who are not identical twins. A and B are both heterozygous at the locus, A having four tandem repeats of the monomer (indicated by the arrow) in one homolog (labeled al) and seven in the other (labeled a2) while B has two (bl) and five (b2). The children, C (with 4 2 repeats) and D... 

More recently a different DNA fingerprinting procedure has been described [A. J. Jeffreys etal. Nature 354 (1991) 204-209] based on sequence variation in hypervariable loci rather than the number of tandem repeats that are present. It has been applied successfully to hypervariable locus D1S8 and overcomes many of the limitations of conventional DNA fingerprinting. 

Investigations of the structure of monoclonal proteins have revealed the repeated occurrence of polypeptide chains with identical structure. For example, several monoclonal X chains, derived from individual BALB/c mice bearing plasma cell tumors, have been shown to possess identical amino acid sequences. These identical X chains occurred in combination with H chains of different classes or as free Bence Jones proteins (77-79). In addition to eight identical X chains, four others were found which differed in sequence in the V region by 1-3 amino acid residues (1-4 nucleotide interchanges in the DNA). All interchanges occurred in the hypervariable regions of the chain (near positions 30,50 or 95) (78, 79). 

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