An inverted repeat (or IR) is a single stranded sequence of nucleotides followed downstream by its reverse complement. The intervening sequence of nucleotides between the initial sequence and the reverse complement can be any length including zero. For example, is an inverted repeat sequence. When the intervening length is zero, the composite sequence is a palindromic sequence.
Both inverted repeats and direct repeats constitute types of nucleotide sequences that occur repetitively. <!--The human genome has many nucleotide sequences that occur repeatedly and as such, can be grouped in two simple classes: repetitive and unique sequences. The short tandem repeat sequences may exist as just a few copies in a small region to thousands of copies dispersed all over the genome of most eukaryotes. Repeat sequences with about 10–100 base pairs are known as minisatellites, while shorter repeat sequences having mostly 2–4 base pairs are known as microsatellites. The most common repeats include the dinucleotide repeats, which have the bases AC on one DNA strand, and GT on the complementary strand. Though the most familiar loci of the repetitive sequences are the centromere and the telomere, but also to mutation and disease.
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The nucleotide sequence written in bold characters signifies the repeated sequence. Linguistically, a typical direct repeat is comparable to saying "bye-bye". There is similarity between direct and inverted repeat, or else a palindrome, with the exception of the second half of the inverted repeat positioned in the complementary strand as follows:
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The last repeats suggest that palindromes can be related linguistically to a string of characters that reads the same in both directions, such as "level". In all, repeated sequence without the reverse complement and without inversion, is a direct repeat. Subsequent shuttling of the same sequences over numerous generations ensures their multiplicity throughout the genome.
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Most common biological functions using Inverted Repeats
:This section is "under construction" and will be completed by mid-December.
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Regions where presence is obligatory
Terminal inverted repeats have been observed in the DNA of various eukaryotic transposons, even though their source remains unknown. Inverted repeats are principally found at the origins of replication of cell organism and organelles that range from phage plasmids, mitochondria, and eukaryotic viruses to mammalian cells. The replication origins of the phage G4 and other related phages comprise a segment of nearly 139 nucleotide bases that include three inverted repeats that are essential for replication priming. Other reports suggest that irrespective of the comparative shortage of repeat elements in prokaryotic genomes, they nevertheless contain hundreds or even thousands of large repeats. Current genomic analysis seem to suggest the existence of a large excess of perfect inverted repeats in many prokaryotic genomes as compared to eukaryotic genomes.
thumb|500 px| Pseudoknot with four sets of inverted repeats. Inverted repeats 1 and 2 create the stem for stem-loop A and are part of the loop for stem-loop B. Similarly, inverted repeats 3 and 4 form the stem for stem-loop B and are part of the loop for stem-loop A.
For quantification and comparison of inverted repeats between several species, namely on archaea, see
Inverted repeats in pseudoknots
Pseudoknots are common structural motifs found in RNA. They are formed by two nested stem-loops such that the stem of one structure is formed from the loop of the other. There are multiple folding topologies among pseudoknots and great variation in loop lengths, making them a structurally diverse group.
Inverted repeats are a key component of pseudoknots as can be seen in the illustration of a naturally occurring pseudoknot found in the human telomerase RNA component. Four different sets of inverted repeats are involved in this structure. Sets 1 and 2 are the stem of stem-loop A and are part of the loop for stem-loop B. Similarly, sets 3 and 4 are the stem for stem-loop B and are part of the loop for stem-loop A.
Pseudoknots play a number of different roles in biology. The telomerase pseudoknot in the illustration is critical to that enzyme's activity. The stem-loop on the 3' end is a transcriptional terminator because the sequence immediately following it is a string of uracils (U). If this stem-loop forms (due to the presence of FMN) as the growing RNA strand emerges from the RNA polymerase complex, it will create enough structural tension to cause the RNA strand to dissociate and thus terminate transcription. The dissociation occurs easily because the base-pairing between the U's in the RNA and the A's in the template strand are the weakest of all base-pairings. Long inverted repeats are deemed to greatly influence the stability of the genome of various organisms. This is exemplified in E. coli, where genomic sequences with long inverted repeats are seldom replicated, but rather deleted with rapidity.
thumb|600 px|left|Inverted repeat changing to/from an extruded cruciform. A: Inverted Repeat Sequences; B: Loop; C: Stem with base pairing of the inverted repeat sequences
The illustration shows an inverted repeat undergoing cruciform extrusion. DNA in the region of the inverted repeat unwinds and then recombines, forming a four-way junction with two stem-loop structures. The cruciform structure occurs because the inverted repeat sequences self-pair to each other on their own strand.
Extruded cruciforms can lead to frameshift mutations when a DNA sequence has inverted repeats in the form of a palindrome combined with regions of direct repeats on either side. During transcription, slippage and partial dissociation of the polymerase from the template strand can lead to both deletion and insertion mutations. This database is provided by The Advanced Biomedical Computing Center (ABCC) at then Frederick National Laboratory for Cancer Research (FNLCR). It covers the A-DNA and Z-DNA conformations otherwise known as "non-B DNAs" because they are not the more common B-DNA form of a right-handed Watson-Crick double-helix. These "non-B DNAs" include left-handed Z-DNA, cruciform, triplex, tetraplex and hairpin structures.
- P-MITE: a Plant MITE database — this database for Miniature Inverted-repeat Transposable Elements (MITEs) contains sequences from plant genomes. Sequences may be searched or downloaded from the database.
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- Genome Atlas Database — contains hundreds of examples
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- EMBOSS is the "European Molecular Biology Open Software Suite" which runs on UNIX and UNIX-like operating systems. Documentation and program source files are available on the EMBOSS website. Applications specifically related to inverted repeats are listed below:
- EMBOSS einverted: Finds inverted repeats in nucleotide sequences. Threshold values can be set to limit the scope of the search.