Target RNA (Cas13d-complementary) (Cas13d target RNA)

The single-stranded RNA (ssRNA) complementary to the Cas13d crRNA spacer is the primary molecular target for the Cas13d CRISPR-Cas system. Cas13d is a programmable RNA-guided ribonuclease that utilizes a CRISPR RNA (crRNA) to identify and bind specific RNA sequences through Watson-Crick base pairing (Konermann et al., 2018, Cell). This target RNA, often referred to as the protospacer, can be a viral genome, a messenger RNA (mRNA) encoding a disease-related protein, or a non-coding RNA (Abudayyeh et al., 2017, Nature). Upon successful hybridization between the crRNA spacer and the target ssRNA, the Cas13d protein undergoes a conformational shift that activates its dual HEPN catalytic domains. This activation results in the site-specific degradation of the target molecule, effectively silencing the gene or neutralizing the pathogen (Yan et al., 2018, Molecular Cell). This mechanism is leveraged in therapeutic strategies to silence oncogenes, eliminate viral pathogens like SARS-CoV-2, or correct splicing defects by targeting pre-mRNA (Abbott et al., 2020, Cell). A critical aspect of this target interaction is the potential for collateral cleavage, where the activated Cas13d may degrade non-target RNA molecules in its vicinity. This collateral activity is a significant consideration for safety and specificity in therapeutic applications (Lotfi et al., 2021, Journal of Biological Engineering). Cas13d is particularly favored for clinical development due to its small size, which facilitates efficient packaging into viral delivery vectors like AAV.

Other names

ProtospacerTarget transcriptComplementary ssRNACas13d substrate RNA

RNA-guided endoribonuclease-mediated cleavage of target RNA