Microsatellite

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This article is about the DNA sequence. See miniaturized satellites for small orbiting spacecraft.

A microsatellite is a short block of DNA sequence (a Tandemly Repetitive DNA sequence), often less than 150 base pairs long, that is repeated many times within the genome of an organism. Many repeats tend to be concentrated at the same locus.

In a microsatellite, the repeated sequence is very simple, consisting of two, three or four nucleotides (di-, tri-, and tetranucleotide repeats respectively), and can be repeated 10 to 100 times. Classically, the first microsatellites identified were dinucleotide repeats often called "Ka-Ka" repeats or "CACACACACA....". These are highly frequent in human and other genomes, and present every few thousand basepairs. Variability or dynamism of a dinucleotide repeat is typically a function of size: repeats larger than 10-15 repeats and without interruptions, tend to be polymorphic. Larger repeats are often more polymorphic.

The following example illustrates a typical microsatellite sequence derived from orchid. The repeat units are trinucleotide motifs (GAT)11 and (CAT)9 GGTAGGTATGATGATGATGATGATGATGATGATGATGATGGTTCTCGTGGCCTATTTGTTGTTGCAGGAGGGTATGCGACAGGACCCATGG TGGGTTCATTTGGTGGAAAATATGGGGAAGAGGATATGGATGCATAAGCTTTGTCAGCTTTGTCAGCCATTTTCCTTAGTACAGGATATTCAAAATA TTAAGCTGAGTTTCTATACTTGGGTAGGCTATCTCAGGCTTTGGTGTTTCGGGTGGATTTTCAGGGTTGGGAAGGATTTCTTGGATAAGTGGAGTTT GGGTGGATGGCTCTAGTTTGAGTGGTGCTATTTCCGATTTTGTTGGGAATTTTTAAGGGGTTCATCATCAGTAGGAGACGAACTTATGCACCCGCTC AGGATTGAGATAAATTTGTCAGAATTGATTTCAAAATCATCATCATCATCATCATCATCATCATACCAGCC

The number of repeats at a particular locus is hypervariable (highly polymorphic) between individuals of the same species. It is for this reason that microsatellite sequences can be used for genetic fingerprinting and paternity testing. Most loci of the genome, even non-coding parts, would be too similar to allow individuals to be reliably distinguished. They are often less useful in evolutionary studies since they are unstable and prone to mutating to different sizes.

The hypervariability arises because the repeated simple sequences cause a high frequency of loss or insertion of additional repeats by confusing the DNA replication machinery. Self-complementary sequences may aid this process.

In tumor cells, where controls on replication may be damaged, microsatellites may be gained or lost at an especially high frequency during each round of mitosis. Hence a tumour cell line might show a different genetic fingerprint from that of the host tissue.

Microsatellite loci can be isolated from genomic DNA using the 5' anchored PCR process developed by [3].

Primers are short sequences of DNA designed to amplify the microsatellite loci. They can be designed using the Primer3 sofrware available on-line at: http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www.cgi [4]

References

1. P. J. Gardener, R. C.Fisher, T. E. Richardson. Single locus microsatellites isolated using 5’ anchored PCR. Nucleic Acids Research. 1996. 24: 4369-4371.

2. S. V. Kumar, S. G. Tan, S. C. Quah and K. Yusoff. Isolation and characterization of seven tetranucleotide loci in mungbean, Vigna radiata. Molecular Ecology Notes. 2002. 2: 293-295.

3. S. Brachet, M. F. Jubier, M. Tichard, B. Jung-Muller, N. Frascaria-Lacoste. Rapid isolation of microsatellite loci using 5’ anchored PCR in the common ash Fraxinus excelsior. Molecular Ecology. 1999. 8: 160 – 163.

4.Steve Rozen and Helen J. Skaletsky (2000) Primer3 on the WWW for general users and for biologist programmers. In: Krawetz S, Misener S (eds) Bioinformatics Methods and Protocols: Methods in Molecular Biology. Humana Press, Totowa, NJ, pp 365-386

See also

minisatellite, mobile element, transposon, short interspersed repetitive element, long interspersed repetitive element, junk DNA, variable number tandem repeats, short tandem repeats, Trinucleotide repeat disordersde:Mikrosatellit fr:Microsatellite id:Mikrosatelit nl:Microsatelliet ja:マイクロサテライト