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AAT Bioquest

What is the protospacer adjacent motif (PAM) in CRISPR-Cas9?

Posted June 22, 2020


Answer

The protospacer adjacent motif (PAM) is a short DNA sequence (usually 2-6 base pairs in length) that is about 3-4 nucleotides downstream from the DNA sequence targeted by Cas9. Cas9 cannot bind to or cleave the target DNA sequence if it is not followed by the PAM sequence. Hence, the presence and locations of the PAM sequences determine the genomic locations that can be targeted for editing by CRISPR.

The canonical PAM sequence associated with the Cas9 nuclease of Sreptococcus pyogenes, which is most commonly used in CRISPR, is 5’-NGG-3’, where “N” is any nucleobase followed by two guanines. Cas9 proteins from other organisms are associated with other different PAMs.

Additional resources

Helixyte™ Green *10,000X Aqueous PCR Solution*

6-ROX glycine *25 uM fluorescence reference solution for PCR reactions*

Doudna, J. A., & Charpentier, E. (2014). The new frontier of genome engineering with CRISPR-Cas9. Science, 346(6213), 1258096.

Ran, F. A., Hsu, P. D., Wright, J., Agarwala, V., Scott, D. A., & Zhang, F. (2013). Genome engineering using the CRISPR-Cas9 system. Nature protocols, 8(11), 2281.