Three types of CRISPR mechanisms have been identified, of which type II is the most studied. In this case, invading DNA from viruses or plasmids is cut into small fragments and incorporated into a CRISPR locus amidst a series of short repeats (around 20 bps). The loci are transcribed, and transcripts are then processed to generate small RNAs (crRNA CRISPR RNA), which are used to guide effector endonucleases that target invading DNA based on sequence complementarity
One Cas protein, Cas9 (also known as Csn1), has been shown, through knockdown and rescue experiments to be a key player in certain CRISPR mechanisms (specifically type II CRISPR systems). The type II CRISPR mechanism is unique compared to other CRISPR systems, as only one Cas protein (Cas9) is required for gene silencing . In type II systems, Cas9 participates in the processing of crRNAs, and is responsible for the destruction of the target DNA . Cas9s function in both of these steps relies on the presence of two nuclease domains, a RuvC-like nuclease domain located at the amino terminus and a HNH-like nuclease domain that resides in the mid-region of the protein .
To achieve site-specific DNA recognition and cleavage, Cas9 must be complexed with both a crRNA and a separate trans-activating crRNA (tracrRNA or trRNA), that is partially complementary to the crRNA . The tracrRNA is required for crRNA maturation from a primary transcript encoding multiple pre-crRNAs. This occurs in the presence of RNase III and Cas9 .
During the destruction of target DNA, the HNH and RuvC-like nuclease domains cut both DNA strands, generating double-stranded breaks (DSBs) at sites defined by a 20-nucleotide target sequence within an associated crRNA transcript . The HNH domain cleaves the complementary strand, while the RuvC domain cleaves the noncomplementary strand.
The double-stranded endonuclease activity of Cas9 also requires that a short conserved sequence, (25 nts) known as protospacer-associated motif (PAM), follows immediately 3´- of the crRNA complementary sequence. In fact, even fully complementary sequences are ignored by Cas9-RNA in the absence of a PAM sequence