Alteration of Cre recombinase site specificity by substrate-linked protein evolution (original) (raw)
References
Plückthun, A., Schaffitzel, C., Hanes, J. & Jermutus, L. In vitro selection and evolution of proteins. Adv. Protein Chem.55, 367–403 (2000). Article Google Scholar
Arnold, F.H. & Volkov, A.A. Directed evolution of biocatalysts. Curr. Opin. Chem. Biol.3, 54–59 (1999). ArticleCAS Google Scholar
Wilson, D.S. & Szostak, J.W. In vitro selection of functional nucleic acids. Annu. Rev. Biochem.68, 611–647 (1999). ArticleCAS Google Scholar
Beaudry, A.A. & Joyce, G.F. Directed evolution of an RNA enzyme. Science257, 635–641 (1992). ArticleCAS Google Scholar
Roberts, R.W. Totally in vitro protein selection using mRNA–protein fusions and ribosome display. Curr. Opin. Chem. Biol.3, 268–273 (1999). ArticleCAS Google Scholar
Jermutus, L., Ryabova, L.A. & Plückthun, A. Recent advances in producing and selecting functional proteins by using cell-free translation. Curr. Opin. Biotechnol.9, 534–548 (1998). ArticleCAS Google Scholar
Tawfik, D.S. & Griffiths, A.D. Man-made cell-like compartments for molecular evolution. Nat. Biotechnol.16, 652–656 (1998). ArticleCAS Google Scholar
Buchholz, F., Angrand, P.O. & Stewart, A.F. Improved properties of FLP recombinase evolved by cycling mutagenesis. Nat. Biotechnol.16, 657–662 (1998). ArticleCAS Google Scholar
Hoess, R., Abremski, K., Irwin, S., Kendall, M. & Mack, A. DNA specificity of the Cre recombinase resides in the 25 kDa carboxyl domain of the protein. J. Mol. Biol.216, 873–882 (1990). ArticleCAS Google Scholar
Guo, F., Gopaul, D.N. & van Duyne, G.D. Structure of Cre recombinase complexed with DNA in a site-specific recombination synapse. Nature389, 40–46 (1997). ArticleCAS Google Scholar
Hoess, R.H. & Abremski, K. Mechanism of strand cleavage and exchange in the Cre-lox site-specific recombination system. J. Mol. Biol.181, 351–362 (1985). ArticleCAS Google Scholar
Hoess, R.H., Wierzbicki, A. & Abremski, K. The role of the loxP spacer region in P1 site-specific recombination. Nucleic Acids Res.14, 2287–2300 (1986). ArticleCAS Google Scholar
Rodriguez, C.I. et al. High-efficiency deleter mice show that FLPe is an alternative to Cre-loxP. Nat. Genet.25, 139–140 (2000). ArticleCAS Google Scholar
Drake, J.W. & Holland, J.J. Mutation rates among RNA viruses. Proc. Natl. Acad. Sci. USA96, 13910–13913 (1999). ArticleCAS Google Scholar
Dorgai, L., Yagil, E. & Weisberg, R.A. Identifying determinants of recombination specificity: construction and characterization of mutant bacteriophage integrases. J. Mol. Biol.252, 178–188 (1995). ArticleCAS Google Scholar
Yagil, E., Dorgai, L. & Weisberg, R.A. Identifying determinants of recombination specificity: construction and characterization of chimeric bacteriophage integrases. J. Mol. Biol.252, 163–177 (1995). ArticleCAS Google Scholar
Hennighausen, L. & Furth, P.A. The right time and place for molecular scissors. Nat. Biotechnol.17, 1062–1063 (1999). ArticleCAS Google Scholar
Metzger, D. & Feil, R. Engineering the mouse genome by site-specific recombination. Curr. Opin. Biotechnol.10, 470–476 (1999). ArticleCAS Google Scholar
Nagy, A. Cre recombinase: the universal reagent for genome tailoring. Genesis26, 99–109 (2000). ArticleCAS Google Scholar
Seibler, J., Schübeler, D., Fiering, S., Groudine, M. & Bode, J. DNA cassette exchange in ES cells mediated by Flp recombinase: an efficient strategy for repeated modification of tagged loci by marker-free constructs. Biochemistry37, 6229–6234 (1998). ArticleCAS Google Scholar
Soukharev, S., Miller, J.L. & Sauer, B. Segmental genomic replacement in embryonic stem cells by double lox targeting. Nucleic Acids Res.27, e21 (1999). ArticleCAS Google Scholar
Lee, G. & Saito, I. Role of nucleotide sequences of loxP spacer region in Cre-mediated recombination. Gene216, 55–65 (1998). ArticleCAS Google Scholar
Feng, Y.Q. et al. Site-specific chromosomal integration in mammalian cells: highly efficient CRE recombinase-mediated cassette exchange. J. Mol. Biol.292, 779–785 (1999). ArticleCAS Google Scholar
Lauth, M., Moerl, K., Barski, J.J. & Meyer, M. Characterization of Cre-mediated cassette exchange after plasmid microinjection in fertilized mouse oocytes. Genesis27, 153–158 (2000). ArticleCAS Google Scholar
Thyagarajan, B., Guimarães, M.J., Groth, A.C. & Calos, M.P. Mammalian genomes contain active recombinase recognition sites. Gene244, 47–54 (2000). ArticleCAS Google Scholar
Thyagarajan, B., Olivares, E.C., Hollis, R.P., Ginsburg, D.S. & Calos, M.P. Site-specific genomic integration in mammalian cells mediated by phage phiC31 integrase. Mol. Cell. Biol.21, 3926–3934 (2001). ArticleCAS Google Scholar
Guo, H. et al. Group II introns designed to insert into therapeutically relevant DNA target sites in human cells. Science289, 452–457 (2000). ArticleCAS Google Scholar
Satoh, W., Hirai, Y., Tamayose, K. & Shimada, T. Site-specific integration of an adeno-associated virus vector plasmid mediated by regulated expression of rep based on Cre-loxP recombination. J. Virol.74, 10631–10638 (2000). ArticleCAS Google Scholar
Logie, C. & Stewart, A.F. Ligand-regulated site-specific recombination. Proc. Natl. Acad. Sci. USA92, 5940–5944 (1995). ArticleCAS Google Scholar
Goff, S.P. Genetics of retroviral integration. Annu. Rev. Genet.26, 527–544 (1992). ArticleCAS Google Scholar
Russ, A.P., Friedel, C., Grez, M. & von Melchner, H. Self-deleting retrovirus vectors for gene therapy. J. Virol.70, 4927–4932 (1996). CASPubMedPubMed Central Google Scholar
Choulika, A., Guyot, V. & Nicolas, J.F. Transfer of single gene-containing long terminal repeats into the genome of mammalian cells by a retroviral vector carrying the cre gene and the loxP site. J. Virol.70, 1792–1798 (1996). CASPubMedPubMed Central Google Scholar
Salmon, P. et al. Reversible immortalization of human primary cells by lentivector-mediated transfer of specific genes. Mol. Ther.2, 404–414 (2000). ArticleCAS Google Scholar
Habu, Y. et al. Development of an HIV-1-dependent expression vector with the Cre/loxP system. Nucleic Acids Symp. Ser.42, 295–296 (1999). ArticleCAS Google Scholar
Flowers, C.C., Woffendin, C., Petryniak, J., Yang, S. & Nabel, G.J. Inhibition of recombinant human immunodeficiency virus type 1 replication by a site-specific recombinase. J. Virol.71, 2685–2692 (1997). CASPubMedPubMed Central Google Scholar
Lee, Y. & Park, J. A novel mutant loxP containing part of long terminal repeat of HIV-1 in spacer region: presentation of possible target site for antiviral strategy using site-specific recombinase. Biochem. Biophys. Res. Commun.253, 588–593 (1998). ArticleCAS Google Scholar
Kim, S.T., Kim, G.W., Lee, Y.S. & Park, J.S. Characterization of Cre-loxP interaction in the major groove: hint for structural distortion of mutant Cre and possible strategy for HIV-1 therapy. J. Cell Biochem.80, 321–327 (2001). ArticleCAS Google Scholar
Guzman, L.M., Belin, D., Carson, M.J. & Beckwith, J. Tight regulation, modulation, and high-level expression by vectors containing the arabinose PBAD promoter. J. Bacteriol.177, 4121–4130 (1995). ArticleCAS Google Scholar
Stemmer, W.P. Rapid evolution of a protein in vitro by DNA shuffling. Nature370, 389–391 (1994). ArticleCAS Google Scholar
Zhao, H., Giver, L., Shao, Z., Affholter, J.A. & Arnold, F.H. Molecular evolution by staggered extension process (StEP) in vitro recombination. Nat. Biotechnol.16, 258–261 (1998). ArticleCAS Google Scholar
Buchholz, F., Ringrose, L., Angrand, P.O., Rossi, F. & Stewart, A.F. Different thermostabilities of FLP and Cre recombinases: implications for applied site-specific recombination. Nucleic Acids Res.24, 4256–4262 (1996). ArticleCAS Google Scholar
Zhang, Y. et al. Inducible site-directed recombination in mouse embryonic stem cells. Nucleic Acids Res.24, 543–548 (1996). ArticleCAS Google Scholar
Gopaul, D.N., Guo, F. & Van Duyne, G.D. Structure of the Holliday junction intermediate in Cre-loxP site-specific recombination. EMBO J.17, 4175–4187 (1998). ArticleCAS Google Scholar
Guo, F., Gopaul, D.N. & Van Duyne, G.D. Asymmetric DNA bending in the Cre-loxP site-specific recombination synapse. Proc. Natl. Acad. Sci. USA96, 7143–7148 (1999). ArticleCAS Google Scholar
Kellendonk, C. et al. Regulation of Cre recombinase activity by the synthetic steroid RU 486. Nucleic Acids Res.24, 1404–1411 (1996). ArticleCAS Google Scholar