Tandem repeat
Tandem repeats occur in DNA when a pattern of one or more nucleotides are repeated and the repetitions are directly adjacent to each other.[1]
An example would be:
- ATTCG ATTCG ATTCG
in which the sequence ATTCG is repeated three times.
Terminology
When between 10 and 60 nucleotides are repeated, it is called a minisatellite. Those with fewer are known as microsatellites or short tandem repeats.
When exactly two nucleotides are repeated, it is called a dinucleotide repeat (for example: ACACACAC…). The microsatellite instability in hereditary nonpolyposis colon cancer most commonly affects such regions.[2]
When three nucleotides are repeated, it is called a trinucleotide repeat (for example: CAGCAGCAGCAG…), and abnormalities in such regions can give rise to trinucleotide repeat disorders.
When the number is not known, variable, or irrelevant, it is sometimes called a variable number tandem repeat (VNTR). MeSH classifies variable number tandem repeats under minisatellites.[3]
Uses
Tandem repeat describes a pattern that helps determine an individual's inherited traits.
Tandem repeats can be very useful in determining parentage. Short tandem repeats are used for certain genealogical DNA tests.
DNA is examined from microsatellites within the chromosomal DNA. Minisatellite is another way of saying special regions of the loci. Polymerase chain reaction (or PCR) is performed on the minisatellite areas. The PCR must be performed on each organism being tested. The amplified material is then run through electrophoresis. By checking the percentage of bands that match, parentage is determined.
In the field of Computer Science, tandem repeats in strings (e.g., DNA sequences) can be efficiently detected using suffix trees or suffix arrays.
Studies in 2004 linked the unusual genetic plasticity of dogs to mutations in tandem repeats.[4]
See also
- Variable number tandem repeats
- Short tandem repeats
- Satellite DNA
- Minisatellite
- Microsatellite
- Tandem Repeats Database
- Amino acid tandem repeat
References
- ↑ Tandem Repeat at the US National Library of Medicine Medical Subject Headings (MeSH)
- ↑ Oki, E.; Oda, S.; Maehara, Y.; Sugimachi, K. (1999). "Mutated gene-specific phenotypes of dinucleotide repeat instability in human colorectal carcinoma cell lines deficient in DNA mismatch repair". Oncogene 18 (12): 2143–2147. doi:10.1038/sj.onc.1202583. PMID 10321739.
- ↑ Variable Number of Tandem Repeats at the US National Library of Medicine Medical Subject Headings (MeSH)
- ↑ Pennisi, E. (Dec 2004). "Genetics. A ruff theory of evolution: gene stutters drive dog shape". Science 306 (5705): 2172–2120. doi:10.1126/science.306.5705.2172. ISSN 0036-8075. PMID 15618495.
External links
- Examples:
- VNTRs - info and animated example
- Databases:
- Search tools:
- Tandem Repeats Finder
- Mreps
- STAR
- TRED - Tandem Repeats over the Edit Distance
- TandemSWAN
- Microsatellite repeats finder
- JSTRING - Java Search for Tandem Repeats in genomes
- Phobos - a tandem repeat search tool for perfect and imperfect repeats - the maximum pattern size depends only on computational power
- UGENE - an ultra fast and memory efficient open-source tandem repeats finder implementation.
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