RNA structure directs the targeting specificity of Cas13d.

Abstract

Type VI CRISPR enzymes exclusively bind and cleave target RNAs, and are widely used for gene regulation, RNA tracking, and diagnostics. However, a systematic understanding of their RNA binding specificity is lacking. Here, we describe RNA-CHAMP, a massively parallel platform that repurposes used next-generation DNA sequencing chips to measures the binding affinity for >10,000 RNA targets containing structural perturbations, mismatches, insertions, and deletions relative to the guide RNA. We profile the RNA binding specificity of Cas13d, a compact and widely used RNA nuclease. Contrary to other type VI CRISPR enzymes, Cas13d does not have a protospacer flanking sequence (PFS) preference. Cas13d tolerates mismatches, insertions, and deletions, but is exquisitely sensitive to secondary structure within the target RNA. Basepairing in the distal region of the target RNA strongly decreases Cas13d binding, whereas structuring the first six nucleotides inhibits nuclease activity without impacting binding. A biophysical model built from these data reveals that target recognition begins at the distal end of unstructured target RNAs and proceeds to the proximal end with limited RNA melting. Using this model, we design a series of partially mismatched guide RNAs that modulate nuclease activity to detect single nucleotide polymorphisms (SNPs) in circulating SARS-CoV-2 variants. This work describes the key determinants of RNA targeting by a type VI CRISPR enzyme to improve RNA targeting and CRISPR diagnostics. More broadly, RNA-CHAMP provides a quantitative platform for systematically measuring protein-RNA interactions.