Inverted repeat

An inverted repeat (or IR) is a single stranded sequence of nucleotides followed downstream by its reverse complement.^[1] The intervening sequence of nucleotides between the initial sequence and the reverse complement can be any length including zero. For example, 5'---TTACGnnnnnnCGTAA---3' is an inverted repeat sequence. When the intervening length is zero, the composite sequence is a palindromic sequence.^[2]

Both inverted repeats and direct repeats constitute types of nucleotide sequences that occur repetitively. These repeated DNA sequences often range from a pair of nucleotides to a whole gene, while the proximity of the repeat sequences varies between widely dispersed and simple tandem arrays.^[3] 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.^[4] 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.^[5] The most common repeats include the dinucleotide repeats, which have the bases AC on one DNA strand, and GT on the complementary strand.^[3] Some elements of the genome with unique sequences function as exons, introns and regulatory DNA.^[6] Though the most familiar loci of the repetitive sequences are the centromere and the telomere,^[6] a large portion of the repeated sequences in the genome are found among the noncoding DNA.^[5]

Inverted repeats have a number of important biological functions. They define the boundaries in transposons and indicate regions capable of self-complementary base pairing (regions within a single sequence which can base pair with each other). These properties play an important role in genome instability^[7] and contribute not only to cellular evolution and genetic diversity^[8] but also to mutation and disease.^[9] In order to study these effects in detail, a number of programs and databases have been developed to assist in discovery and annotation of inverted repeats in various genomes.