CRISPR (clustered regularly interspaced short palindromic repeat) is an adaptive immune system that provides protection against mobile genetic elements (viruses, transposable elements and conjugative plasmids) (PubMed:21455174). CRISPR clusters contain spacers, sequences complementary to antecedent mobile elements, and target invading nucleic acids. CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA). In type II CRISPR systems correct processing of pre-crRNA requires a trans-encoded small RNA (tracrRNA), endogenous ribonuclease 3 (rnc) and this protein. The tracrRNA serves as a guide for ribonuclease 3-aided processing of pre-crRNA; Cas9 only stabilizes the pre-crRNA:tracrRNA interaction and has no catalytic function in RNA processing (PubMed:24270795). Subsequently Cas9/crRNA/tracrRNA endonucleolytically cleaves linear or circular dsDNA target complementary to the spacer; Cas9 is inactive in the absence of the 2 guide RNAs (gRNA). The target strand not complementary to crRNA is first cut endonucleolytically, then trimmed 3'-5' exonucleolytically. DNA-binding requires protein and both gRNAs, as does nuclease activity. Cas9 recognizes the protospacer adjacent motif (PAM) in the CRISPR repeat sequences to help distinguish self versus nonself, as targets within the bacterial CRISPR locus do not have PAMs. DNA strand separation and heteroduplex formation starts at PAM sites; PAM recognition is required for catalytic activity (PubMed:24476820). Confers immunity against a plasmid with homology to the appropriate CRISPR spacer sequences (CRISPR interference) (PubMed:21455174).