a palindrome is a word that is the same forward as it is backward such as the word racecar, the name Otto, or the saying attributed to Napoleon “Able was I ere I saw Elba”. Certain sequences of DNA are the same whether they are read 5′ (five-prime) to 3′(three prime) or 3′ to 5′. These sequences are called palindromic.

Because a DNA sequence is double stranded, we read the base pairs not just the bases on one strand to determine a palindrome. The restriction enzyme EcoR1 recognizes the following palindromic sequence:

 5'- G  A  A  T  T  C -3'
 3'- C  T  T  A  A  G -5'

the top strand reads 5′-GAATTC-3′, while the bottom strand reads 3′-CTTAAG-5′. If you flip the DNA strand over, the sequences are exactly the same ( 5’GAATTC-3′ and 3′-CTTAAG-5′).

Palindromic sequences play an important role in molecular biology. Many restriction endonucleases recognize specific palindromic sequences and cut them. Palindromic sequences may also be methylation sites.

Some palindromic sites and the restriction enzymes that they recognize follow.

5'GAATTC
3'CTTAAG

5'---G     AATTC---3'
3'---CTTAA     G---5'

5'GGATCC
3'CCTAGG

5'---G     GATCC---3'
3'---CCTAG     G---5'

5'TCGA
3'AGCT

5'---T   CGA---3'
3'---AGC   T---5'

5'AGCT
3'TCGA

5'---AG  CT---3'
3'---TC  GA---5'

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