The Protospacer Adjacent Motif (PAM) is a short, specific DNA sequence, typically 2-6 base pairs long, that is required for a Cas nuclease to bind and cleave a target DNA sequence. It is located immediately downstream of the target site (protospacer) in the invading DNA. The PAM is not present in the host’s own CRISPR locus, which serves as a critical self-versus-non-self recognition mechanism, preventing autoimmune destruction.
The discovery of the Protospacer Adjacent Motif (PAM) was a pivotal moment in understanding how the CRISPR-Cas system functions with such precision. Researchers observed that for the system to successfully target and cleave foreign DNA, a specific short sequence had to be present next to the target sequence (the protospacer). For the widely used Cas9 from *Streptococcus pyogenes*, this sequence is 5′-NGG-3′, where ‘N’ can be any nucleotide. The Cas9 protein, loaded with its guide RNA, first scans the DNA for this PAM sequence. Only upon binding to a PAM does the protein attempt to unwind the adjacent DNA and test for a match with its guide RNA sequence. If a match is found, the nuclease domains of Cas9 are activated to create a double-strand break.
This PAM-dependent targeting mechanism is the key to how the system avoids attacking the bacterium’s own genome. The CRISPR array, from which the guide RNAs are derived, contains the same spacer sequences as the targets. However, the repeat sequences within the CRISPR array do not contain the PAM sequence. Consequently, the Cas9-gRNA complex cannot bind stably to the CRISPR locus itself, preventing an autoimmune catastrophe. This elegant solution for self/non-self discrimination is a hallmark of the system’s efficiency. For gene editing applications, the PAM requirement is a double-edged sword: it ensures specificity but also constrains the set of possible target sites in a genome. This has driven significant research into discovering or engineering Cas variants with different, more flexible, or even non-existent PAM requirements to make any part of the genome accessible to editing.
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