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I am trying to find out the requirements for a segment of DNA to be the recognition site of a restriction enzyme.

Acording to the article on Restriction Enzymes in Wikipedia, "many of them" (referring to recognition sites) are ‘palindromic’ (in the sense that the sequence of nucleotides on one strand should read the same as the that on the other strand, from the opposite direction).

Is this true for all recognition sites?

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  • $\begingroup$ Please read our homework policy which requires that you demonstrate that you have done some research to answer the question yourself before posting here. Did you read the Wikipedia article on this topic? $\endgroup$ – David May 21 at 15:32
  • $\begingroup$ Yes i did, and it tells that "many of them" (referring to recognition sites) are palindromic and that left me in confusion. Does that mean there are recognition sites that aren't palindromic? Unless i didn't see some certain part in that article. $\endgroup$ – user51714 May 21 at 15:39
  • $\begingroup$ Instead of writing "I suppose" you should have stated that you had read the Wikipedia article, giving a link, and quoted the phrase, as in your comment. You can find the answer by reading further in the article, but so as not to discourage you, I will rephrase your question, and briefly answer it. $\endgroup$ – David May 21 at 22:32
  • $\begingroup$ thanks and i apologize for the late reply.i get it now $\endgroup$ – user51714 May 25 at 8:48
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The article cited in the question goes on to discuss the different classes of restriction enzyme, for which the recognition ‘style’ differs. Not all recognize palindromic sequences.

Type II restriction enzymes

These have been divided into a number of subclasses (reviewed by Pingoud and Jeltsch). Those regarded as orthodox — which are the ones generally used in DNA cloning — appear always to require palindromic sequences in their recognition sites, although those in some other classes do not (see list here).

This statement is subject to the proviso that you regard as palindromic 5-base recognition sites, such as AlwXI, GCAGC, and others with a ‘non-conforming’ central region, such as ApaBI, GCAN5TGC. The reasons for including the latter (which provides an alternative way of defining the requirements of the recognition sequence) can be seen by examining the symmetrical manner enzymes of this class bind the site, which can tolerate a non-symmetrical central region. This is described in more detail in an answer I gave to another SE question on restriction enzymes.

Type I restriction enzymes:

…cut at a site that differs, and is a random distance (at least 1000 bp) away, from their recognition site. Cleavage at these random sites follows a process of DNA translocation, which shows that these enzymes are also molecular motors. The recognition site is asymmetrical and is composed of two specific portions—one containing 3–4 nucleotides, and another containing 4–5 nucleotides—separated by a non-specific spacer of about 6–8 nucleotides.

Type III restriction enzymes:

…recognize two separate non-palindromic sequences that are inversely oriented. They cut DNA about 20–30 base pairs after the recognition site.

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