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This question already has an answer here:

Any restriction site given in any fragment of DNA or vector molecule is a palindrome. eg restriction site for the endonuclease EcoRI is

5'...GAATTC...3'
3'...CTTAAG...5'

Clearly, this is a palindromic sequence. Why is that?

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marked as duplicate by De Novo supports GoFundMonica, theforestecologist, David, Community Mar 4 at 15:45

This question has been asked before and already has an answer. If those answers do not fully address your question, please ask a new question.

  • $\begingroup$ I was going to answer this question, covering what I regard as a key point that other answers ignored. However as this is a duplicate I have answered it on the original. You may be interested to look at it there. $\endgroup$ – David Mar 4 at 18:01
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Not all restriction sites are palindromes : https://en.wikipedia.org/wiki/List_of_restriction_enzyme_cutting_sites:_E%E2%80%93F#Whole_list_navigation

EcoRI: GAATTC (note that this is not 'palindromic' in the usual sense (e.g.'anna', GAATTC read backwards actually gives CTTAAG), but only if given the G-C A-T binding)

The double strand of DNA is composed of one strand in direction 5'-3' and another into the other direction (3'-5'). Restriction enzymes tend to be homodimers, thus would bind to both sides of the double strand, expecting the same recognition sequence. But as one strand runs into the other direction, the strands need to be palindromic to form a double strand.

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  • $\begingroup$ EcoRI has a palindromic recognition site in the sense of the term used in molecular biology. Perhaps I'm not understanding your point. $\endgroup$ – canadianer Feb 28 at 18:56
  • $\begingroup$ @canadianer my point is that someone asking this question possibly is not well versed in molecular biology, and might thus be only privy to the non-m.-b. sense of the word: 'Palindrome' = 'A Word that looks the same, if the order of characters is reversed' $\endgroup$ – bukwyrm Mar 1 at 6:47
  • $\begingroup$ You really need an example of the structure of a complex to justify and explain your answer better. What is the point of. binding to both strands? $\endgroup$ – David Mar 1 at 8:36
  • $\begingroup$ bukwyrm gives a good answer for "Why" palindrome: to cut both strands. To expand the evidence, apart from clear demonstration of the current utility of restriction enzymes (they cleave recognized nucleotide sequences), the best proof indicating their evolutionary persistence is the relative lack of palindromic sequences in genomes of a wide variety of organisms.1 The idea is that the presence of endonucleases with palindromic recognition has caused organisms with such patterns to lose out to those that lack the patterns over time. $\endgroup$ – Plantaloons Mar 2 at 19:10
  • $\begingroup$ Thank you so much! I had found out lately too! $\endgroup$ – Puja Roychowdhury Mar 4 at 15:46
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So that these enzymes can recognize the sequence on the both strands. It's the mechanism bacteria have evovled to degrade the only double stranded RNA and not single stranded.

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  • $\begingroup$ Welcome to Biology.SE, Sujeet. Your answer could use a little more detail, and ideally a reference to an authoritative source. $\endgroup$ – De Novo supports GoFundMonica Mar 2 at 16:35

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