Inverted Repeat

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An inverted repeat is a nucleotide sequence in a double-stranded nucleic acid that is repeated on the other strand in reverse order. Because of the base pairing , an inverted repeat occurs down the strand on the same strand in a reverse complementary manner. If the inverted repeats are located at both 5 ' or both 3' ends of a double-stranded nucleic acid, they are referred to as inverted terminal repeats .

properties

Inverted repeats are used by some viruses, such as retroviruses or the adeno-associated virus, to insert the viral genome into the host's genome . They also occur in insertion sequences , transposons and miniature inverted-repeat transposable elements . Furthermore, inverted repeats occur - but without nucleotides in between - in the palindromic recognition sequences of restriction endonucleases of type II. In some cases, inverted repeats occur as tandem repeats in multiple repetitions in a nucleotide sequence.

Mechanism of recombination with inverted repeats

Inverted repeats are often a place for recombination , partly through the formation of secondary structures such as hairpin structures or cross-shaped structures. They are also involved in gene amplification and thereby increase the evolutionary adaptability . At the same time, however, they are also a source of mutations that can result in genetic defects .

Databases for inverted repeats are, for example, non-B DB, Inverted Repeats Database, P-MITE, EMBOSS and Palindrome Analyzer,

example

5'- TTACG nnnnnn CGTAA -3 '
3'- AATGC nnnnnn GCATT -5 '

Individual evidence

  1. ^ DM McCarty: Self-complementary AAV vectors; advances and applications. In: Molecular therapy: the journal of the American Society of Gene Therapy. Volume 16, number 10, October 2008, pp. 1648–1656, doi : 10.1038 / mt.2008.171 , PMID 18682697 .
  2. ↑ I. Ammar, Z. Izsvák, Z. Ivics: The Sleeping Beauty transposon toolbox. In: Methods in molecular biology. Volume 859, 2012, pp. 229-240, doi : 10.1007 / 978-1-61779-603-6_13 , PMID 22367875 .
  3. ^ I. Fattash, R. Rooke, A. Wong, C. Hui, T. Luu, P. Bhardwaj, G. Yang: Miniature inverted-repeat transposable elements: discovery, distribution, and activity. In: Genome. Volume 56, Number 9, September 2013, pp. 475-486, doi : 10.1139 / gen-2012-0174 , PMID 24168668 .
  4. ↑ AG Tsai, MR Lieber: Mechanisms of chromosomal rearrangement in the human genome. In: BMC genomics. Volume 11 Suppl 1, February 2010, S. S1, doi : 10.1186 / 1471-2164-11-S1-S1 , PMID 20158866 , PMC 2822523 (free full text).
  5. ↑ I. Voineagu, V. Narayanan, KS Lobachev, SM Mirkin: Replication stalling at unstable inverted repeats: interplay between DNA hairpins and fork stabilizing protein. In: Proceedings of the National Academy of Sciences . Volume 105, number 29, July 2008, pp. 9936-9941, doi : 10.1073 / pnas.0804510105 , PMID 18632578 , PMC 2481305 (free full text).
  6. ↑ CT Lin, WH Lin, YL Lyu, J. Whang-Peng: Inverted repeats as genetic elements for promoting DNA inverted duplication: implications in gene amplification. In: Nucleic acids research. Volume 29, Number 17, September 2001, pp. 3529-3538, PMID 11522822 , PMC 55881 (free full text).
  7. ↑ JJ Bissler: DNA inverted repeats and human disease. In: Frontiers in bioscience: a journal and virtual library. Volume 3, March 1998, pp. D408-d418, PMID 9516381 .
  8. ↑ non-B DB ( Memento of the original from November 13, 2013 in the Internet Archive ) Info: The archive link was inserted automatically and has not yet been checked. Please check the original and archive link according to the instructions and then remove this notice. @1@ 2Template: Webachiv / IABot / nonb.abcc.ncifcrf.gov
  9. ↑ RZ Cer, DE Donohue, US Mudunuri, NA Temiz, MA Loss, NJ Starner, GN Halusa, N. Volfovsky, M. Yi, BT Luke, A. Bacolla, JR Collins, RM Stephens: Non-B DB v2.0 : a database of predicted non-B DNA-forming motifs and its associated tools. In: Nucleic acids research. Volume 41, Database issue January 2013, pp. D94 – D100, doi : 10.1093 / nar / gks955 , PMID 23125372 , PMC 3531222 (free full text).
  10. ↑ Inverted Repeats Database
  11. ^ Y. Gelfand, A. Rodriguez, G. Benson: TRDB - the Tandem Repeats Database. In: Nucleic acids research. Volume 35, Database issue January 2007, pp. D80 – D87, doi : 10.1093 / nar / gkl1013 , PMID 17175540 , PMC 1781109 (free full text).
  12. ^ P-MITE: a Plant MITE database
  13. ↑ J. Chen, Q. Hu, Y. Zhang, C. Lu, H. Kuang: P-MITE: a database for plant miniature inverted-repeat transposable elements. In: Nucleic acids research. Volume 42, Database issue January 2014, pp. D1176 – D1181, doi : 10.1093 / nar / gkt1000 , PMID 24174541 , PMC 3964958 (free full text).
  14. ^ P. Rice, I. Longden, A. Bleasby: EMBOSS: the European Molecular Biology Open Software Suite. In: Trends in genetics: TIG. Volume 16, Number 6, June 2000, pp. 276-277, PMID 10827456 .
  15. ↑ Palindrome analyzer
  16. ↑ V. Brázda, J. Kolomazník, J. Lýsek, L. Hároníková, J. Coufal, J. Št'astný: Palindrome analyzer - A new web-based server for predicting and evaluating inverted repeats in nucleotide sequences. In: Biochemical and biophysical research communications. Volume 478, number 4, 09 2016, pp. 1739-1745, doi : 10.1016 / j.bbrc.2016.09.015 , PMID 27603574 .