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

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.