Molecular biology · BEGINNER LESSON
PAM
A protospacer adjacent motif, or PAM, is a short DNA sequence next to a CRISPR target that a Cas protein must detect before it can bind and cut. It acts as a gatekeeper for target recognition in CRISPR-Cas systems.
What PAM is and what is measured
In CRISPR-Cas systems, a PAM is a short DNA sequence flanking the intended target site. What matters is whether a particular DNA sequence is recognized by a given Cas protein, because this recognition helps determine if the protein will continue toward binding and cleavage. Different Cas proteins recognize different PAM sequences, and these can differ in length, orientation, and exact letters. [source 0, 2]
[1] CRISPR technologies and the search for the PAM-free nuclease - Nature Communications [3] Efficient cleavage resolves PAM preferences of CRISPR-Cas in ...
How PAM works in target recognition
Cas nucleases use two checkpoints. First, they scan nearby DNA for a PAM. Only after passing this step do they test whether the guide RNA (gRNA), meaning the RNA guide, can base-pair with the target DNA. Base pairing means matching chemical partners between the two strands. If a target matches the guide but lacks the right PAM, it is ignored. This makes the PAM a gatekeeper rather than the full target by itself. [source 0]
[1] CRISPR technologies and the search for the PAM-free nuclease - Nature Communications
Why PAM matters in natural CRISPR defense
In bacteria and other prokaryotes, CRISPR arrays contain spacer sequences copied from past invaders. The PAM is absent from the CRISPR array repeat region, so the Cas protein can distinguish foreign DNA from the organism’s own stored CRISPR DNA. This self/nonself discrimination helps prevent the immune system from attacking its own CRISPR locus. [source 0, 2]
[1] CRISPR technologies and the search for the PAM-free nuclease - Nature Communications [3] Efficient cleavage resolves PAM preferences of CRISPR-Cas in ...
Limits and variation
PAM requirement limits which DNA sites can be targeted, even when the guide RNA matches perfectly. Because different Cas proteins recognize different PAMs, one protein may work at a site that another cannot. Research therefore looks for proteins or variants with relaxed PAM requirements, and experiments in human cells have been used to identify functional PAMs for specific Cas systems. [source 0, 2]
[1] CRISPR technologies and the search for the PAM-free nuclease - Nature Communications [3] Efficient cleavage resolves PAM preferences of CRISPR-Cas in ...
SEE THE IDEA
How a Cas protein uses a PAM
The Cas protein looks for a short nearby motif first.
The guide RNA tests whether the target DNA matches by base pairing.
If both checks succeed, the target can be cut; if not, it is ignored.
The PAM is the first checkpoint that enables later guide-target pairing and, only then, cleavage.
A PAM does not replace sequence matching; it is an upstream filter that controls whether the Cas protein keeps testing a site. [source 0]
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Sources and further reading
This general lesson was generated from public source material. It explains a concept; it does not interpret a private paper or provide medical advice.