Palindromic sequence

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A palindrome is where a word can be read the same way in either the forward or backwards directions, for example, Hannah, racecar, and the longest palindrome in the Oxford English Dictionary, tattarrattat.

In molecular biology however, palindromic sequences are used; their basic principles vary from those of a palindromic word. In DNA or RNA, the nucleotide base sequence is the same on the two different complementary strands of the helical structure. For example, a sequence may be CAAGCTTG in the 5’ to 3’ direction on one strand, and therefore it will be GTTCGAAC in the 3’ to 5’ direction on the complementary strand. The nucleotide bases match up in their Watson-Crick pairs – A (Adenine) with T (Thymine) for DNA or U (Uracil) for RNA, and G (Guanine) with C (Cytosine).

Restriction endonucleases are a common example of how palindromic sequences are used. They recognise specific sequences (palindromic sequence) on a double-stranded DNA molecule and cleave it into fragments of different sizes[1]. A good example is EcoR1 which creates sticky ends in DNA fragments after the digest.


  1. Hartl L. D., Ruvolo M. Genetics analysis of genes and genomes. 8th Ed. Jones and Bartlett Learning. 2012.
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