crRNA

crRNA, or CRISPR RNA, is an RNA molecule produced from a CRISPR (clustered regularly interspaced short palindromic repeat) locus in bacteria and archaea. Each crRNA contains a spacer sequence derived from a previously encountered invader and a segment derived from the CRISPR repeats. The spacers act as molecular memories of past infections, and the crRNA serves as a guide that directs Cas effector proteins to matching genetic material.

Biogenesis and structure: CRISPR loci are transcribed into a precursor RNA that is processed into mature crRNA by Cas nucleases or associated processing factors. A typical mature crRNA includes a spacer of about 20 to 40 nucleotides, which provides sequence complementarity to the invader, flanked by repeat-derived regions that help recruit and position the Cas proteins. The exact composition and size of crRNA vary among CRISPR-Cas types.

Function and targeting mechanism: crRNA guides the Cas effector complex to complementary sequences in invading DNA or RNA. In many systems, recognition requires a short protospacer adjacent motif (PAM) near the target, enabling specific cleavage of foreign genetic material while avoiding the host genome. Some systems primarily target DNA, others target RNA, and some use crRNA as part of a larger multi-subunit effector complex such as Cascade or Csm/Cmr; in type II systems, crRNA forms a duplex with tracrRNA to guide Cas9.

Industrial and research relevance: crRNA is a central component of CRISPR-based immune defenses in microbes and serves as the guiding element in CRISPR genome editing and diagnostic tools. In engineered applications, crRNA is often combined with tracrRNA to form a single-guide RNA (sgRNA) for simplified targeting by Cas nucleases.