Local sliding PAMs alter CRISPR/Cas9 gRNA activity

A major challenge of CRISPR/Cas9-mediated genome engineering is that not all guide RNAs cleave DNA efficiently. Here, we show that local gRNA-DNA interactions resulting from Cas9 sliding on overlapping protospacer adjacent motifs profoundly impact gRNA activities. Using an energy model, we identify a sweet-spot range of binding energies for optimal efficiency which largely explains why favourable gRNAs can display changes in efficiency depending on the Cas9 binding context. Our results provide novel insights into the mechanisms of Cas9-PAM compatibility and cleavage activation and underline the importance of accounting for local sliding in gRNA design.