1. An engineered S. pyogenes Cas9 protein comprising an HNH domain, a RuvC domain, and at least one modified amino acid residue in a groove between the HNH and RuvC domains, wherein the modified amino acid residue is an Alanine, and the unmodified amino acid residue is a K, R, or Q at a corresponding position of wild-type S. pyogenes Cas9 which has been substituted with said Alanine.