Reversible RNA acylation for control of CRISPR–Cas9 gene editing

Abstract

We report the development of post-transcriptional chemical methods that enable control over CRISPR-Cas9 gene editing activity both in <i>in vitro</i> assays and in living cells. We show that an azide-substituted acyl imidazole reagent (NAI-N₃) efficiently acylates CRISPR single guide RNAs (sgRNAs) in 20 minutes in buffer. Poly-acylated ("cloaked") sgRNA was completely inactive in DNA cleavage with Cas9 <i>in vitro</i>, and activity was quantitatively restored after phosphine treatment. Delivery of cloaked sgRNA and Cas9 mRNA into HeLa cells was enabled by the use of charge-altering releasable transporters (CARTs), which outperformed commercial transfection reagents in transfecting sgRNA co-complexed with Cas9 encoding functional mRNA. Genomic DNA cleavage in the cells by CRISPR-Cas9 was efficiently restored after treatment with phosphine to remove the blocking acyl groups. Our results highlight the utility of reversible RNA acylation as a novel method for temporal control of genome-editing function.