串聯重複
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串聯重複(英語:Tandem repeats)是指DNA中的一個或多個核苷酸前後相連接的重複[1]。
一個例子:
- ATTCGATTCGATTCG
其中的ATTCG在這裡重複了三次。
幾種蛋白質結構域也是由串聯重複的胺基酸序列產生,如犰狳重複。但很少有串聯重複出現在體內的蛋白質中,多數為人工設計的蛋白[2]。
術語
當重複核苷酸數在10到60之間時,被稱為小衛星,低於10則被稱為短串聯重複或微衛星。
當重複核苷酸只有兩個的時候,稱為「雙核苷酸重複」(如:ACACACAC…)。遺傳性非息肉病性結直腸癌的微衛星不穩定性常為這種類型[3]。
當重複核苷酸有三個時,稱為「三核苷酸重複」(如:CAGCAGCAGCAG…)在這一區域的異常常導致三核苷酸重複疾病。
當重複單元的拷貝數在人群中存在不同時。被稱為可變數目串聯重複序列(VNTR)[4]。
應用
串聯重複可以作為確定個體的遺傳特徵的一種描述模式,在確定親子關係中非常有用。短串聯重複序列可用於一些系譜DNA檢驗。
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.
Polymorphic tandem repeats (alias VNTRs) are also present in microorganisms and can be used to trace the origin of an outbreak. The corresponding assay in which a collection of VNTRs is typed to characterize a strain is most often called MLVA (Multiple Loci VNTR Analysis).
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.[5]
參考文獻
- ^ 醫學主題詞表(MeSH):Tandem+Repeat
- ^ Jorda J, Xue B, Uversky VN, Kajava AV. Protein tandem repeats - the more perfect, the less structured. The FEBS Journal. June 2010, 277 (12): 2673–82. PMC 2928880 . PMID 20553501. doi:10.1111/j.1742-464X.2010.07684.x.
- ^ Oki E, Oda S, Maehara Y, Sugimachi K. Mutated gene-specific phenotypes of dinucleotide repeat instability in human colorectal carcinoma cell lines deficient in DNA mismatch repair. Oncogene. March 1999, 18 (12): 2143–7. PMID 10321739. doi:10.1038/sj.onc.1202583.
- ^ 醫學主題詞表(MeSH):Variable+Number+of+Tandem+Repeats
- ^ Pennisi E. Genetics. A ruff theory of evolution: gene stutters drive dog shape. Science. December 2004, 306 (5705): 2172. PMID 15618495. doi:10.1126/science.306.5705.2172.
外部連結
- 例子:
- 資料庫:
- 搜索工具:
- Tandem Repeats Finder(頁面存檔備份,存於網際網路檔案館)
- Mreps(頁面存檔備份,存於網際網路檔案館)
- STAR(頁面存檔備份,存於網際網路檔案館)
- 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(頁面存檔備份,存於網際網路檔案館)
- UGENE - an ultra fast and memory efficient open-source tandem repeats finder implementation.