Palindromic sequence

Not to be confused with inverted repeat.
Palindrome of DNA structure
A: Palindrome, B: Loop, C: Stem

A palindromic sequence is a nucleic acid sequence in a double-stranded DNA or RNA molecule whereby reading in a certain direction (e.g. 5' to 3') on one strand is identical to the sequence in the same direction (e.g. 5' to 3') on the complementary strand. This definition of palindrome thus depends on complementary strands being palindromic of each other.

The meaning of palindrome in the context of genetics is slightly different from the definition used for words and sentences. Since a double helix is formed by two paired antiparallel strands of nucleotides that run in opposite directions, and the nucleotides always pair in the same way (adenine (A) with thymine (T) in DNA or uracil (U) in RNA; cytosine (C) with guanine (G)), a (single-stranded) nucleotide sequence is said to be a palindrome if it is equal to its reverse complement. For example, the DNA sequence ACCTAGGT is palindromic with its nucleotide-by-nucleotide complement TGGATCCA because reversing the order of the nucleotides in the complement gives the original sequence.

A palindromic nucleotide sequence is capable of forming a hairpin. The stem portion of the hairpin is a pseudo-double stranded portion since the entire hairpin is a part of same (single) strand of nucleic acid. Palindromic motifs are found in most genomes or sets of genetic instructions. They have been specially researched in bacterial chromosomes and in the so-called Bacterial Interspersed Mosaic Elements (BIMEs) scattered over them. In 2008, a genome sequencing project discovered that large portions of the human X and Y chromosomes are arranged as palindromes.[1] A palindromic structure allows the Y chromosome to repair itself by bending over at the middle if one side is damaged.

Palindromes also appear to be found frequently in the peptide sequences that make up proteins,[2][3] but their role in protein function is not clearly known. It has been suggested that the existence of palindromes in peptides might be related to the prevalence of low-complexity regions in proteins, as palindromes are frequently associated with low-complexity sequences. Their prevalence may also be related to the propensity of such sequences to form alpha helices[4] or protein/protein complexes.[5]

  1. ^ Larionov S, Loskutov A, Ryadchenko E (February 2008). "Chromosome evolution with naked eye: palindromic context of the life origin". Chaos. 18 (1): 013105. Bibcode:2008Chaos..18a3105L. doi:10.1063/1.2826631. PMID 18377056.
  2. ^ Ohno S (1990). "Intrinsic evolution of proteins. The role of peptidic palindromes". Riv. Biol. 83 (2–3): 287–91, 405–10. PMID 2128128.
  3. ^ Giel-Pietraszuk M, Hoffmann M, Dolecka S, Rychlewski J, Barciszewski J (February 2003). "Palindromes in proteins". J. Protein Chem. 22 (2): 109–13. doi:10.1023/A:1023454111924. PMID 12760415. S2CID 28294669. Archived from the original (PDF) on 2019-12-14. Retrieved 2011-02-25.
  4. ^ Sheari A, Kargar M, Katanforoush A, et al. (2008). "A tale of two symmetrical tails: structural and functional characteristics of palindromes in proteins". BMC Bioinformatics. 9: 274. doi:10.1186/1471-2105-9-274. PMC 2474621. PMID 18547401.
  5. ^ Pinotsis N, Wilmanns M (October 2008). "Protein assemblies with palindromic structure motifs". Cell. Mol. Life Sci. 65 (19): 2953–6. doi:10.1007/s00018-008-8265-1. PMC 11131741. PMID 18791850. S2CID 29569626.