protospacer-adjacent motif (PAM)
/ PAM, rhymes with 'jam' /
The PAM is a small but crucial detail of how CRISPR-Cas9 works, and it answers a clever puzzle: how does a bacterium's CRISPR system avoid attacking its own stored viral memories? After all, the guide RNA sequence is itself written into the bacterium's genome, so why doesn't Cas9 cut there? The PAM is the answer — and for us it becomes a constraint on where we can edit.
PAM stands for protospacer-adjacent motif. It is a very short DNA signal — for the common Cas9 from Streptococcus pyogenes it is just 5'-NGG-3', meaning any base followed by two Gs — that must sit immediately next to the target sequence in the DNA being attacked. Cas9 will not even try to unwind and check a site unless it first recognises a PAM right beside it. Crucially, the bacterium's own stored memory in the CRISPR array lacks this neighbouring PAM, so Cas9 leaves the bacterium's own DNA alone and only cuts the invading DNA, which does carry a PAM. The PAM is recognised by the Cas9 protein directly contacting the DNA, not by the guide RNA.
For genome editing this means you cannot cut absolutely anywhere — your chosen target must have an appropriate PAM right next to it. For the standard Cas9, suitable NGG sites are common enough that this is usually a minor inconvenience, but it does rule out some spots. This is one reason researchers hunt for and engineer Cas proteins with different PAM requirements (some need different short motifs, broadening the reachable sites), expanding where CRISPR can be aimed. The PAM is also part of why the system is specific: a 20-letter match without an adjacent PAM is simply ignored.
For the common Cas9, a target works only if the DNA reads ...[20-letter match]NGG... — the NGG (any base, then G, then G) just downstream is the PAM that licenses the cut.
No PAM, no cut — even a perfect 20-letter match is ignored.
The PAM is in the target DNA, not in the guide RNA, and it is read by the Cas9 protein. Forgetting that the PAM must be present next to your site is a frequent reason a chosen target cannot actually be cut.