Single-stranded RNA (ssRNA) complementary to the RfxCas13d guide RNA (RfxCas13d target RNA)

Single-stranded RNA complementary to the RfxCas13d guide RNA is the specific nucleic acid substrate targeted by the Type VI-D CRISPR-Cas system from Ruminococcus flavefaciens (Konermann et al., 2018, Cell). This target RNA is identified by the RfxCas13d effector protein through complementary base-pairing with a programmable guide RNA (gRNA), which directs the enzyme to the site of interest. Upon binding, the RfxCas13d protein activates its HEPN domains to perform site-specific endoribonuclease cleavage of the target transcript (Abudayyeh et al., 2017, Science). This molecular interaction is the basis for therapeutic strategies like PAC-MAN (Prophylactic Antiviral CRISPR in huMAN cells), which aims to degrade viral genomes such as SARS-CoV-2 and Influenza A (Abbott et al., 2020, Cell). Beyond antivirals, this target is utilized for programmable gene knockdown to treat conditions involving toxic RNA gain-of-function or overexpressed oncogenes. A primary therapeutic challenge is the potential for collateral cleavage, where the activated Cas13d may degrade non-target RNA molecules in the vicinity, although this effect is often attenuated in eukaryotic environments (Wessels et al., 2020, Nature Biotechnology). Effective delivery of the RfxCas13d system to specific tissues remains a significant hurdle for clinical translation. The specificity of the RfxCas13d-crRNA complex is critical for ensuring that only the intended single-stranded RNA sequence is processed, minimizing unintended transcriptomic disruptions.

Other names

Target RNARfxCas13d substrateComplementary ssRNAProtospacer RNAcrRNA-complementary RNA

RNA-guided endoribonuclease cleavage of complementary single-stranded RNA