Home » Protospacer Adjacent Motif (PAM)

Protospacer Adjacent Motif (PAM)

2008
  • Luciano Marraffini
  • Erik Sontheimer
Molecular biologist analyzing DNA sequence with focus on Protospacer Adjacent Motif in a laboratory.

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.

UNESCO Nomenclature: 2417
– Molecular biology

Type

Biochemical Mechanism

Disruption

Substantial

Usage

Widespread Use

Precursors

  • characterization of the crispr-cas9 system’s components
  • understanding of protein-dna binding interactions and specificity
  • the hypothesis of crispr as a dna-targeting immune system
  • in vitro assays to test cas protein activity on different dna substrates

Applications

  • a critical rule for designing guide RNAs in CRISPR-Cas9 gene editing
  • enabling the prediction of potential off-target sites in a genome
  • engineering cas proteins with altered pam specificities to expand the range of editable genomic sites
  • a basis for developing high-fidelity cas9 variants that reduce off-target effects

Patents:

NA

Potential Innovations Ideas

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Related to: PAM, protospacer adjacent motif, cas9, self-recognition, DNA targeting, gene editing, s. pyogenes, off-target, biochemistry, NGG.

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