protospacer adjacent motif

The PAM is a tiny “password” the DNA must show before Cas9 will cut. Even if the guide RNA matches perfectly, Cas9 ignores the site unless a short specific sequence sits right beside it. Think of it as a doorman who checks for a badge before letting the scissors in.

PAM stands for Protospacer Adjacent Motif: a short DNA sequence (for the common Streptococcus pyogenes Cas9, the three letters NGG, where N is any base) immediately next to the target. Cas9 first recognizes the PAM, then unwinds the neighboring DNA to test whether the guide RNA pairs with it. No PAM, no cut.

The PAM evolved as a clever self-versus-nonself check: bacteria store viral spacers without the adjacent PAM, so Cas9 attacks viral DNA but spares the bacterium's own stored copy. For editing, the PAM requirement limits which sites can be targeted, though engineered Cas variants with relaxed or altered PAM rules now widen the reachable genome.