Guide RNA Binding

Figure: Activation of Cas9 protein by guide RNA binding. Binding of the guide RNA induces a conformational change in the Cas9 protein. The conformational change causes activation of the Cas9 nuclease activity (Jinek et al. 2014). (original figure) (crystal image rendered from PDB: 4UN3 Anders et al. 2014)

The Cas9 nuclease encloses the guide RNA and binds the structure with specific interactions in a number of domains.  Specifically, the REC1 and REC2 domains bind the complementary region of the guide RNA, and eventually the guide RNA target DNA heteroduplex upon DNA binding.  Mutations to the REC2 domain causes a small decrease in Cas9 activity, while mutations in the REC1 domain eliminate activity completely. The Rec1 domain is likely essential for Cas9 activity because it binds the repeat/anti-repeat duplex. The Protospacer Adjacent Motif (PAM) Interacting (PI) domain and RuvC nuclease domain bind the stem loops on the guide RNA.  Overall, the exact process of guide RNA binding by the nuclease is unknown.  However, a dramatic conformational change upon binding has been shown to produce an activated Cas9 nuclease capable of binding and cleaving specific sequences of double-stranded DNA (Nishimasu et al. 2014).