RNA structure modulates Cas13 activity and enables mismatch detection.

Secondary structure in target RNAs inhibits Cas13 activity, but strand displacement can enhance mismatch discrimination up to 50-fold in cellular environments.

• Why it matters: Understanding how RNA structure affects Cas13 targeting is crucial for improving RNA-based diagnostics and therapeutics, especially for detecting low-frequency mutations in complex samples.
• What they did: The study systematically examined the effects of RNA secondary structure on Cas13 activity, using a strand displacement framework to generate an 'occluded' Cas13 variant that improves mismatch detection and mutation identification.
• The result: This approach enabled detection of mutations in SARS-CoV-2, influenza A, and KRAS with low allele frequencies (<1%), expanding the potential for structure-informed RNA diagnostics.