Compositions and methods for site specific recombination at asymmetric sites

1. An isolated enzyme comprising two distinct subunits A and B, wherein the A subunit comprises one or more mutations at K25, D29, R32, D33, Q35, E123 and R337 relative to SEQ ID NO:1 and the B subunit comprises one or more mutations at E69, R72, L76, E123, and E308 relative to SEQ ID NO:1, wherein if subunit A comprises E123Q, then subunit B does not comprise E123Q and if subunit B comprises E123Q, then subunit A does not comprise E123Q; wherein subunit A comprises at least 80% identity to SEQ ID NO:2 comprising one or more mutations at K25, D29, R32, D33, Q35, E123 and R337 relative to SEQ ID NO:1 and subunit B comprises at least 80% identity to SEQ ID NO:3 comprising one or more mutations at E69, R72, L76, E123, and E308 relative to SEQ ID NO:1; and wherein the isolated enzyme is a tetramer having Cre recombinase activity.

2. The isolated enzyme of claim 1 , wherein in subunit A, K25 is mutated to another positive amino acid, D29 is mutated to a positive amino acid, R32 is mutated to a negative amino acid, D33 is mutated to a neutral amino acid, Q35 is mutated to a positive amino acid, E123 is mutated to a neutral amino acid, and/or R337 is mutated to a negative amino acid and in subunit B, E69 is mutated to aspartic acid (D), R72 is mutated to histidine (H) or lysine (K), L76 is mutated to a negative amino acid, E123 is mutated to a neutral amino acid, and/or E308 is mutated to a positive amino acid.

3. The isolated enzyme of claim 1 , wherein in subunit A, D29 is mutated to a positive amino acid, R32 is mutated to a negative amino acid, and R337 is mutated to a negative amino acid and in subunit B, E308 is mutated to a positive amino acid.

4. The isolated enzyme of claim 1 , wherein subunit A comprises the mutations: K25R, D29R, R32E, D33L, Q35R, E123L and R337E relative to SEQ ID NO:1 and subunit B comprises E69D, R72K, L76E and E308R relative to SEQ ID NO:1.

5. The isolated enzyme of claim 1 , wherein subunit A comprises at least 90% identity to SEQ ID NO:2.

6. The isolated enzyme of claim 1 , wherein subunit B comprises at least 90% identity to SEQ ID NO:3.

7. The isolated enzyme of claim 1 , wherein the isolated enzyme comprises two A subunits and two B subunits.

8. The isolated enzyme of claim 1 , wherein the isolated enzyme is a Cre recombinase.

9. The isolated enzyme of claim 4 , wherein subunit B further comprises an E123L mutation.

10. The isolated enzyme of claim 1 , wherein the isolated enzyme is capable of mediating a site-specific recombination between two predetermined recombination sites, wherein the recombination sites are asymmetric recombination sites comprising two non-palindromic halves flanking a spacer region.

11. The isolated enzyme of claim 10 , wherein one non-palindromic half is a loxP site.

12. The isolated enzyme of claim 10 , wherein one non-palindromic half is not a loxP site.

13. The isolated enzyme of claim 10 , wherein one non-palindromic half is a loxP site and one non-palindromic half is a M7 site.

14. A recombinant vector encoding at least one polypeptide, the polypeptide comprising subunit A comprising one or more mutations at K25, D29, R32, D33, Q35, E123 and R337 relative to SEQ ID NO:1, subunit B comprising one or more mutations at E69, R72, L76, E123, E308 relative to SEQ ID NO:1, or combinations thereof, wherein if subunit A comprises E123Q, then subunit B does not comprise E123Q and if subunit B comprises E123Q, then subunit A does not comprise E123Q; wherein subunit A comprises at least 80% identity to SEQ ID NO:2 comprising one or more mutations at K25, D29, R32, D33, Q35, E123 and R337 relative to SEQ ID NO:1 and subunit B comprises at least 80% identity to SEQ ID NO:3 comprising one or more mutations at E69, R72, L76, E123, and E308 relative to SEQ ID NO:1; wherein the recombinant vector expresses the polypeptide and is selected from the group consisting of: a naked plasmid, a plasmid within a liposome, a retroviral vector, an AAV vector, or a recombinant adenoviral vector.

15. The isolated polynucleotide of claim 14 , wherein expression of the polypeptide is driven by a promoter selected from the group consisting of the Nrl (rod photoreceptor-specific) promoter and the HBB (haemoglobin beta) promoter.

16. The isolated polynucleotide of claim 15 , wherein expression of the polypeptide is further driven by an enhancer selected from the group consisting of the CMV enhancer and the SP1 enhancer.

17. A host cell comprising the polynucleotide of claim 14 .

18. A composition comprising the polynucleotide of claim 14 .

19. A method for mediating asymmetric site-specific recombination in a nucleic acid, the method comprising contacting an isolated enzyme of claim 1 with a nucleic acid, wherein the isolated enzyme recognizes asymmetric sites on the nucleic acid and cleaves the asymmetric sites, wherein the asymmetric sites are loxp+M7 asymmetric recombination sites and wherein the asymmetric site-specific recombination is selected from the group consisting of inversion, excision, insertion and translocation.

20. A method for mediating recombination-mediated cassette exchange (RMCE) in a cell, the method comprising contacting an isolated enzyme of claim 1 and an exogenous DNA molecule with a cellular endogenous genome, wherein the isolated enzyme recognizes asymmetric sites on the cellular endogenous genome, wherein the asymmetric sites are loxp+M7 asymmetric recombination sites and wherein the RMCE occurs between the cellular endogenous genome and the exogenous DNA molecule such that the exogenous DNA molecule is integrated by recombination between the two asymmetric sites into a predetermined locus within the cellular genome.