The CRISPR-Cas system is an interference system employed by bacteria, allowing the prevention of bacteriophage infection and subsequent death.
This is caused by the transcription of a spacer mRNAs from the CRISPR loci, allowing the targeting of the cas endonucleases to the phage DNA, breaking it down preventing phage DNA from being replicated.
Cas1, cas2, and csn2 bind to the incoming phage DNA, cleaving it and inducing the insertion into the repeat spacer array, by identifying PAM sites in the phage DNA. The tracrRNA binds cas9 and the relevant section of pre-crRNA, targeting RNAse III to cleave the necessary repeat sequence. The complex of the tracrRNA and crRNA base-pairs with homologous sections of the phage DNA, binding near the PAM site. This activates the Cas9 nuclease, producing ds breaks and preventing the phage DNA from being replicated - ceasing the infection event.
This system is exploited in CRISPR-Cas9 gene editing, where specific guide RNAs are designed to allow highly specific ds breaks to be formed, allowing the accurate replacement or removal of genes of interest.