DNA twist drives CRISPR-Cas9 off-targeting, topology-guided activation
Negatively supercoiled DNA minicircles reveal that DNA topology promotes Cas9 binding and faster cleavage, with cryo-EM showing a 15 Å swing of the HNH domain toward the target strand and greater PAM-distal R-loop flexibility. The off-target structures OT1 and OT2 adapt via non-canonical base-pairing across the protospacer, enabling mismatches to be accommodated even in seed and distal regions; truncated guides retain activity under topology-induced stress. Collectively, the findings explain topology-driven off-target activity and offer design principles for high-fidelity Cas9 variants that consider DNA topology.