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Engineered CRISPR-Cas9 nuclease with expanded targeting space

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Science  21 Sep 2018:
Vol. 361, Issue 6408, pp. 1259-1262
DOI: 10.1126/science.aas9129

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Expanding the targeting space of Cas9

CRISPR-Cas9 associates with a guide RNA to target and cleave a specific DNA site next to a protospacer adjacent motif (PAM). Streptococcus pyogenes Cas9 (SpCas9), the one most often used for genome editing, only recognizes the NGG sequence (where N is any nucleobase) as the PAM, which restricts regions in the genome that can be targeted. To address this limitation, Nishimasu et al. created a SpCas9 variant that recognizes NG rather than NGG. The SpCas9-NG variant increased the targeting range, had a specificity similar to that of the wild-type enzyme, and could be used with a base editor. Thus, SpCas9-NG is a powerful addition to the CRISPR-Cas9 genome engineering toolbox and will be useful in a broad range of applications, from basic research to clinical therapeutics.

Science, this issue p. 1259

Abstract

The RNA-guided endonuclease Cas9 cleaves its target DNA and is a powerful genome-editing tool. However, the widely used Streptococcus pyogenes Cas9 enzyme (SpCas9) requires an NGG protospacer adjacent motif (PAM) for target recognition, thereby restricting the targetable genomic loci. Here, we report a rationally engineered SpCas9 variant (SpCas9-NG) that can recognize relaxed NG PAMs. The crystal structure revealed that the loss of the base-specific interaction with the third nucleobase is compensated by newly introduced non–base-specific interactions, thereby enabling the NG PAM recognition. We showed that SpCas9-NG induces indels at endogenous target sites bearing NG PAMs in human cells. Furthermore, we found that the fusion of SpCas9-NG and the activation-induced cytidine deaminase (AID) mediates the C-to-T conversion at target sites with NG PAMs in human cells.

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