Cas9 fusion molecules, gene editing systems, and methods of use thereof

1. A Cas9 fusion molecule, comprising a Cas9 molecule covalently linked to a template nucleic acid by a polypeptide linker,

wherein the Cas9 molecule is a polypeptide, and wherein the Cas9 molecule is an enzymatically active Cas9 (eaCas9) molecule selected from the group consisting of a wild-type Cas9 molecule, a Cas9 nickase molecule, a split Cas9 molecule, and an inducible Cas9 molecule; and

wherein the template nucleic acid comprises a double stranded nucleic acid or a single stranded nucleic acid.

2. The Cas9 fusion molecule of claim 1 , wherein the Cas9 molecule comprises at least one surface exposed cysteine residue.

3. The Cas9 fusion molecule of claim 2 , wherein

(i) the Cas9 molecule comprises a surface exposed thiol group;

(ii) the template nucleic acid comprises a maleimide modification; and/or

(iii) the template nucleic acid comprises an acrydite modification.

4. The Cas9 fusion molecule of claim 1 , wherein the Cas9 molecule comprises succinimidyl-6-hydrazino-nicotinamide (S-HyNic); or the Cas9 molecule comprises a tag linked to the Cas9 molecule.

5. The Cas9 fusion molecule of claim 4 , wherein the Cas9 molecule comprises a tag linked to the Cas9 molecule, and the template nucleic acid comprises a haloalkane.

6. The Cas9 fusion molecule of claim 1 , wherein the polypeptide linker is between 3 and 100 amino acids in length.

7. The Cas9 fusion molecule of claim 1 , wherein the polypeptide linker comprises an amino acid sequence selected from the group consisting of SEQ ID NO: 206-214.

8. A gene editing system, comprising at least one Cas9 fusion molecule comprising:

(i) a Cas9 molecule covalently linked to a template nucleic acid by a polypeptide linker, wherein the Cas9 molecule is a polypeptide, and wherein the Cas9 molecule is an enzymatically active Cas9 (eaCas9) molecule selected from the group consisting of a wild-type Cas9 molecule, a Cas9 nickase molecule, a split Cas9 molecule, and an inducible Cas9 molecule; and

(ii) at least one gRNA molecule.

9. The gene editing system of claim 8 ,

i) wherein the at least one gRNA molecule and the Cas9 fusion molecule are designed to associate with a target nucleic acid and generate a double strand break on the target nucleic acid, wherein the double strand break is repaired by at least one DNA repair pathway, thereby producing a modified target nucleic acid; or

ii) wherein the Cas9 molecule is a Cas9 nickase molecule.

10. A pharmaceutical composition comprising the gene editing system of claim 8 .

11. A gene editing system, comprising (i) a first Cas9 fusion molecule, wherein the first Cas9 fusion molecule comprises a first Cas9 nickase molecule covalently linked to a template nucleic acid by a polypeptide linker;

a first gRNA molecule;

a second Cas9 fusion molecule, wherein the second Cas9 fusion molecule comprises a second Cas9 nickase molecule covalently linked to the template nucleic acid by a polypeptide linker; and

a second gRNA molecule; wherein the first Cas9 nickase molecule and the second Cas9 nickase molecule is a polypeptide;

wherein the template nucleic acid comprises a double stranded nucleic acid or a single stranded nucleic acid; or

(ii) a first Cas9 fusion molecule, wherein the first Cas9 fusion molecule comprises a first Cas9 nickase molecule covalently linked to a first template nucleic acid by a polypeptide linker;

a first gRNA molecule;

a second Cas9 fusion molecule, wherein the second Cas9 fusion molecule comprises a second Cas9 nickase molecule covalently linked to a second template nucleic acid by a polypeptide linker; and

a second gRNA molecule; wherein the first Cas9 nickase molecule and the second Cas9 nickase molecule is a polypeptide;

wherein the first template nucleic acid and the second template nucleic acid independently comprise a double stranded nucleic acid or a single stranded nucleic acid.

12. The gene editing system of claim 11 ,

wherein the first gRNA molecule and the first Cas9 fusion molecule are designed to associate with a target nucleic acid and generate a first single strand break on a first strand of the target nucleic acid;

wherein the second gRNA molecule and the second Cas9 fusion molecule are designed to associate with the target nucleic acid and generate a second single strand break on a second strand of the target nucleic acid, thereby forming a double strand break in the target nucleic acid having a first overhang and a second overhang; and

wherein the double strand break is repaired by at least one DNA repair pathway, thereby producing a modified target nucleic acid.

13. The gene editing system of claim 11 , wherein

each Cas9 nickase molecule comprises an amino acid mutation at an amino acid position corresponding to amino acid position 10 or 863 of the Streptococcus pyogenes Cas9 of SEQ ID NO: 2.

14. A method of modifying a target nucleic acid in a cell, the method comprising:

contacting the cell with a gRNA molecule and the Cas9 fusion molecule of claim 1 ;

wherein the gRNA molecule and the Cas9 fusion molecule associate with the target nucleic acid and generate a double strand break in the target nucleic acid; and

wherein the double strand break is repaired by gene correction using the template nucleic acid of the Cas9 fusion molecule.

15. A method of modifying a target nucleic acid in a cell, the method comprising:

contacting the cell with a first gRNA molecule; a first Cas9 molecule; a second gRNA molecule; and a second Cas9 molecule; wherein the first Cas9 molecule and the second Cas9 molecule are polypeptides, and wherein the first Cas9 molecule and the second Cas9 molecule are enzymatically active Cas9 (eaCas9) molecules selected from the group consisting of a wild-type Cas9 molecule, a Cas9 nickase molecule, a split Cas9 molecule, and an inducible Cas9 molecule,

wherein at least one of the first and second Cas9 molecule is covalently linked to a template nucleic acid by a polypeptide linker,

wherein the first gRNA molecule and the first Cas9 molecule associate with the target nucleic acid and generate a first single strand cleavage event on a first strand of the target nucleic acid;

wherein the second gRNA molecule and the second Cas9 molecule associate with the target nucleic acid and generate a second single strand cleavage event on a second strand of the target nucleic acid, thereby forming a double strand break having a first overhang and a second overhang; and

wherein the first overhang and the second overhang in the target nucleic acid are repaired by gene correction using the template nucleic acid.

16. The method of claim 15 , wherein the first Cas9 molecule is covalently linked to the template nucleic acid by a polypeptide linker.

17. The method of claim 15 , wherein both the first Cas9 molecule and the second Cas9 molecule are covalently linked to the template nucleic acid by a polypeptide linker.

18. The method of claim 15 , wherein each Cas9 molecule is a Cas9 nickase molecule that comprises an amino acid mutation at an amino acid position corresponding to amino acid position 10 or 863 of the Streptococcus pyogenes Cas9 of SEQ ID NO: 2.