Frequently asked questions

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Is the PAM sequence part of the CRISPR-Cas9 crRNA construct?

No. The PAM sequence is located on the non-complementary strand. That is, it is on the strand of DNA that contains the same DNA sequence as the target crRNA [1]. The PAM sequence should not be included in the design of the crRNA. The most commonly used Cas9 nuclease, derived from S. pyogenes, recognizes a PAM sequence of NGG that is found directly downstream of the target sequence in the genomic DNA, on the non-target strand.


  1. Anders C, Niewoehner O, et al. (2014) Structural basis of PAM-dependent target DNA recognition by the Cas9 endonuclease. Nature. 513(7519):569–573.