DNA Interrogation by the CRISPR RNA-Guided Endonuclease Cas9

Abstract

The CRISPR-associated enzyme Cas9 is an RNA-guided endonuclease that uses RNA:DNA base-pairing to target and cleave foreign DNA as part of an adaptive immune system in bacteria. Cas9 and CRISPR-derived guide RNAs (Cas9:RNA) have also been adapted for genome engineering applications in animals and plants, where nuclease-active and inactive versions are capable of targeting specific chromosomal sites for genome editing and gene regulation, respectively. Here we use single-molecule and bulk biochemical experiments to determine how Cas9:RNA interrogates DNA to find specific cleavage sites. We show that both binding and cleavage of DNA by Cas9:RNA require recognition of a short trinucleotide protospacer adjacent motif (PAM). Non-target DNA binding affinity scales with PAM density, and sequences fully complementary to the guide RNA but lacking a nearby PAM are ignored by Cas9:RNA. DNA strand separation and RNA:DNA heteroduplex formation initiate at the PAM and proceed directionally towards the distal end of the target sequence. Furthermore, PAM interactions trigger Cas9 catalytic activity. These results reveal how Cas9 employs PAM recognition to quickly identify potential target sites while scanning large DNA molecules, and to regulate double-stranded DNA scission.