Protospacer recognition motifs: mixed identities and functional diversity

RNA Biol. 2013 May;10(5):891-9. doi: 10.4161/rna.23764. Epub 2013 Feb 12.


Protospacer adjacent motifs (PAMs) were originally characterized for CRISPR-Cas systems that were classified on the basis of their CRISPR repeat sequences. A few short 2-5 bp sequences were identified adjacent to one end of the protospacers. Experimental and bioinformatical results linked the motif to the excision of protospacers and their insertion into CRISPR loci. Subsequently, evidence accumulated from different virus- and plasmid-targeting assays, suggesting that these motifs were also recognized during DNA interference, at least for the recently classified type I and type II CRISPR-based systems. The two processes, spacer acquisition and protospacer interference, employ different molecular mechanisms, and there is increasing evidence to suggest that the sequence motifs that are recognized, while overlapping, are unlikely to be identical. In this article, we consider the properties of PAM sequences and summarize the evidence for their dual functional roles. It is proposed to use the terms protospacer associated motif (PAM) for the conserved DNA sequence and to employ spacer acqusition motif (SAM) and target interference motif (TIM), respectively, for acquisition and interference recognition sites.

Keywords: CRISPR; PAM; SAM; TIM; adaptive immunity; protospacer.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Archaea / genetics*
  • Archaea / metabolism
  • Bacteria / genetics*
  • Bacteria / metabolism
  • Base Sequence
  • CRISPR-Cas Systems / genetics*
  • Clustered Regularly Interspaced Short Palindromic Repeats*
  • DNA, Intergenic
  • DNA, Viral / genetics
  • Escherichia coli / genetics
  • Escherichia coli / metabolism
  • Molecular Sequence Data
  • Nucleotide Motifs*
  • Plasmids
  • Sulfolobales / genetics
  • Sulfolobales / metabolism


  • DNA, Intergenic
  • DNA, Viral