CAS9 variants and uses thereof
Some aspects of this disclosure provide compositions, methods, and kits for improving the specificity of RNA-programmable endonucleases, such as Cas9. Also provided are variants of Cas9, e.g., Cas9 dimers and fusion proteins, engineered to have improved specificity for cleaving nucleic acid targets. Also provided are compositions, methods, and kits for site-specific nucleic acid modification using Cas9 fusion proteins (e.g., nuclease-inactivated Cas9 fused to a nuclease catalytic domain or a recombinase catalytic domain). Such Cas9 variants are useful in clinical and research settings involving site-specific modification of DNA, for example, genomic modifications.
1. A fusion protein comprising two domains: (i) a nuclease-inactivated Cas9 domain; and (ii) a nuclease domain; wherein the two domains are separated by a peptide linker, wherein the peptide linker comprises a sequence selected from the group consisting of (GGS) 3 (SEQ ID NO:14), (GGS) 6 (SEQ ID NO:15), SGSETPGTSESATPES (SEQ ID NO:16), SGSETPGTSESA (SEQ ID NO:17), SGSETPGTSESATPEGGSGGS (SEQ ID NO:18), VPFLLEPDNINGKTC (SEQ ID NO:19), GSAGSAAGSGEF (SEQ ID NO:20), SIVAQLSRPDPA (SEQ ID NO:21), MKIIEQLPSA (SEQ ID NO:22), VRHKLKRVGS (SEQ ID NO:23), GHGTGSTGSGSS (SEQ ID NO:24), MSRPDPA (SEQ ID NO:25), and GGSM (SEQ ID NO:301).
2. A dimer of the fusion protein of claim 1 .
3. The fusion protein of claim 1 , wherein the nuclease-inactivated Cas9 domain comprises an amino acid sequence that is at least about 80% identical to SEQ ID NO: 2, 4, or 5.
4. The fusion protein of claim 1 , wherein the nuclease-inactivated Cas9 domain comprises an amino acid sequence that is as least about 80% identical to SEQ ID NO: 2, 4, or 5 and comprises amino acid substitutions at positions corresponding to D10 and H840 of SEQ ID NO: 5.
5. The fusion protein of claim 1 , wherein the nuclease-inactivated Cas9 domain is bound to a gRNA.
6. The fusion protein of claim 1 , wherein the fusion protein comprises the structure [the nuclease-inactivated Cas9 domain]-[the nuclease domain] or [the nuclease domain]-[the nuclease-inactivated Cas9 domain], wherein the “-” represents the peptide linker.
7. The fusion protein of claim 6 , wherein the linker is selected from the group consisting of: (GGS) 3 (SEQ ID NO:14), (GGS) 6 (SEQ ID NO:15); SGSETPGTSESATPES (SEQ ID NO:16); SGSETPGTSESA (SEQ ID NO:17); SGSETPGTSESATPEGGSGGS (SEQ ID NO:18); VPFLLEPDNINGKTC (SEQ ID NO:19); GSAGSAAGSGEF (SEQ ID NO:20); SIVAQLSRPDPA (SEQ ID NO:21); MKIIEQLPSA (SEQ ID NO:22); VRHKLKRVGS (SEQ ID NO:23); GHGTGSTGSGSS (SEQ ID NO:24); MSRPDPA (SEQ ID NO:25); and GGSM (SEQ ID NO:301).
8. The fusion protein of claim 1 , wherein the fusion protein further comprises a nuclear localization signal (NLS) domain.
9. The fusion protein of claim 1 , wherein the nuclease domain comprises a FokI DNA cleavage domain.
10. The fusion protein of claim 9 , wherein the FokI DNA cleavage domain is at least 80% identical to SEQ ID NO: 6.
11. The fusion protein of claim 1 , wherein the nuclease domain comprises a FokI DNA cleavage domain comprising amino acids 300-583, 320-583, 340-583, 360-583, or 388-583 of FokI (MFLSMVSKIRTFGWVQNPGKFENLKRVVQVFDRNSKVHNEVKNIKIPTLVKESKIQKELV AIMNQHDLIYTYKELVGTGTSIRSEAPCDAIIQATIADQGNKKGYIDNWSSDGFLRWAHAL GFIEYINKSDSFVITDVGLAYSKSADGSAIEKEILIEAISSYPPAIRILTLLEDGQHLTKFDLGK NLGFSGESGFTSLPEGILLDTLANAMPKDKGEIRNNWEGSSDKYARMIGGWLDKLGLVKQ GKKEFIIPTLGKPDNKEFISHAFKITGEGLKVLRRAKGSTKFTRVPKRVYWEMLATNLTDKE YVRTRRALILEILIKAGSLKIEQIQDNLKKLGFDEVIETIENDIKGLINTGIFIEIKGRFYQLKDH ILQFVIPNRGVTKQLVKSELEEKKSELRHKLKYVPHEYIELIEIARNSTQDRILEMKVMEFFM KVYGYRGKHLGGSRKPDGAIYTVGSPIDYGVIVDTKAYSGGYNLPIGQADEMQRYVEENQ TRNKHINPNEWWKVYPSSVTEFKFLFVSGHFKGNYKAQLTRLNHITNCNGAVLSVEELLIG GEMIKAGTLTLEEVRRKFNNGEINF, SEQ ID NO: 340).
12. The fusion protein of claim 1 , wherein the peptide linker comprises the sequence (GGS) 3 (SEQ ID NO:14).
13. The fusion protein of claim 1 , wherein the peptide linker comprises the sequence SGSETPGTSESATPES (SEQ ID NO:16).
14. The fusion protein of claim 1 , wherein the peptide linker comprises the sequence SGSETPGTSESA (SEQ ID NO:17).
15. The fusion protein of claim 1 , wherein the peptide linker comprises the sequence SGSETPGTSESATPEGGSGGS (SEQ ID NO:18).
16. The fusion protein of claim 1 , wherein the peptide linker comprises the sequence VPFLLEPDNINGKTC (SEQ ID NO:19).
17. The fusion protein of claim 1 , wherein the peptide linker comprises the sequence GSAGSAAGSGEF (SEQ ID NO:20).
18. The fusion protein of claim 1 , wherein the peptide linker comprises the sequence SIVAQLSRPDPA (SEQ ID NO:21).
19. The fusion protein of claim 1 , wherein the peptide linker comprises the sequence MKIIEQLPSA (SEQ ID NO:22).
20. The fusion protein of claim 1 , wherein the peptide linker comprises the sequence VRHKLKRVGS (SEQ ID NO:23).
21. The fusion protein of claim 1 , wherein the peptide linker comprises the sequence GHGTGSTGSGSS (SEQ ID NO:24).
22. The fusion protein of claim 1 , wherein the peptide linker comprises the sequence MSRPDPA (SEQ ID NO:25).
23. The fusion protein of claim 1 , wherein the peptide linker comprises the sequence GGSM (SEQ ID NO:301).