direct repeat
Direct repeats are a type of genetic sequence that consists of two or more repeats of a specific sequence.{{cite book |title=Computing for Comparative Microbial Genomics: Bioinformatics for Microbiologists |chapter=Word Frequencies and Repeats §Word Frequencies, Repeats, and Repeat-related Structures in Bacterial Genomes |chapter-url=https://link.springer.com/chapter/10.1007/978-1-84800-255-5_8 |doi=10.1007/978-1-84800-255-5_8 |series=Computational Biology |volume=8 |pages=133–144 |first1=David W. |last1=Ussery |first2=Trudy |last2=Wassenaar |first3=Stefano |last3=Borini |publisher=Springer |edition=1 |date=2009 |isbn=978-1-84800-254-8}} In other words, the direct repeats are nucleotide sequences present in multiple copies in the genome. Generally, a direct repeat occurs when a sequence is repeated with the same pattern downstream. There is {{Clarify | text = no inversion | date = November 2021 | reason = What is an inversion on a single-strand sequence? This may need to be dropped.}} and no reverse complement associated with a direct repeat. It may or may not have intervening nucleotides. The nucleotide sequence written in bold characters signifies the repeated sequence.
:::{{color|blue |5´ TTACGnnnnnnTTACG 3´}}
:::{{color|green|3´ AATGCnnnnnnAATGC 5´}}
Linguistically, a typical direct repeat is comparable to saying "bye-bye".
Types
There are several types of repeated sequences:
- Interspersed (or dispersed) DNA repeats (interspersed repetitive sequences) are copies of transposable elements interspersed throughout the genome.
- Flanking (or terminal) repeats (terminal repeat sequences) are sequences that are repeated on both ends of a sequence, for example, the long terminal repeats (LTRs) on retroviruses. Direct terminal repeats are in the same direction and inverted terminal repeats are opposite to each other in direction.
- Tandem repeats (tandem repeat sequences) are repeated copies which lie adjacent to each other. These can also be direct or inverted repeats.{{Citation needed | date = November 2021 | reason = This is in conflict with the Tandem repeat article itself which seems to be defined as only a direct repeat with no intervening nucleotide.}} The ribosomal RNA and transfer RNA genes belong to the class of middle repetitive DNA.
=Microsatellite DNA=
A tract of repetitive DNA in which a motif of a few base pairs is tandemly repeated numerous times (e.g. 5 to 50 times) is referred to as microsatellite DNA. Thus direct repeat tandem sequences are a form of microsattelite DNA. The process of DNA mismatch repair plays a prominent role in the formation of direct trinucleotide repeat expansions.{{cite journal|pmid=33925919 |date=2021 |last1=Richard |first1=G. F. |title=The Startling Role of Mismatch Repair in Trinucleotide Repeat Expansions |journal=Cells |volume=10 |issue=5 |page=1019 |doi=10.3390/cells10051019 |pmc=8145212 |doi-access=free }} Such repeat expansions underlie several neurological and developmental disorders in humans.
Homologous recombination
In directly repeated sequences of the tobacco plant genome, DNA double-strand breaks can be efficiently repaired by homologous recombination between the repeated sequences.{{cite journal |vauthors=Siebert R, Puchta H |title=Efficient repair of genomic double-strand breaks by homologous recombination between directly repeated sequences in the plant genome |journal=Plant Cell |volume=14 |issue=5 |pages=1121–31 |date=May 2002 |pmid=12034901 |pmc=150611 |doi=10.1105/tpc.001727 }}