CRISPR – an acronym for Clustered Regularly Interspaced Short Palindromic Repeats – describes a family of DNA sequences endogenously found in bacteria and archaea. CRISPR loci consist of short, direct, and typically palindromic repeats alternating with unique spacer sequences, and are usually associated with Cas (CRISPR-associated system) genes. Two things initially struck researchers regarding this arrangement: first, the spacers potentially contained identical sequences to viral gene fragments, and second, Cas genes encoded nucleic acid-manipulating proteins such as nucleases, helicases, and polymerases. Together, this prompted the hypothesis (later confirmed) that the CRISPR/Cas system integrated short genomic segments of foreign DNA in order to utilize them via an RNA interference-esque mechanism to defend against foreign genetic material.1
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K.S. Makarova, et al., “Unification of Cas protein families and a simple scenario for the origin and evolution of CRISPR-Cas systems,” Biol Direct