Genomic DNA target sequence (Protospacer) (Protospacer)

Genomic DNA loci complementary to the guide RNA (gRNA) spacer sequence, scientifically known as protospacers, are the specific sequences within a genome targeted by CRISPR-Cas systems for molecular intervention (Jinek et al., 2012, Science). These loci are identified by the Cas nuclease through Watson-Crick base pairing with the gRNA's spacer region, provided a suitable Protospacer Adjacent Motif (PAM) is present nearby (Cong et al., 2013, Science). In therapeutic applications, these DNA sequences are chosen because their modification—via gene disruption, correction, or regulation—can treat or cure diseases at the genetic level. For example, targeting the BCL11A erythroid enhancer allows for the induction of fetal hemoglobin to treat sickle cell disease (Frangoul et al., 2021, NEJM). The interaction between the drug (the CRISPR complex) and the target DNA locus results in site-specific changes that are permanent and heritable within the cell lineage. Ensuring high specificity for the intended locus is a primary challenge in drug development to avoid off-target effects at other genomic sites (Gillmore et al., 2021, NEJM). Advanced modalities like base editing and prime editing also target these loci to perform precise nucleotide substitutions without requiring double-strand breaks (Anzalone et al., 2019, Nature). Monitoring efficacy typically involves measuring the frequency of insertions and deletions (indels) or specific sequence changes at the target site.

Other names

ProtospacerCRISPR target siteTarget DNA locusgRNA-binding sitePAM-adjacent target

RNA-guided site-specific DNA cleavage or modification followed by cellular DNA repair (NHEJ/HDR) or direct nucleotide conversion (base/prime editing).