Homing endonuclease I-CreI derivatives with novel DNA target specificities

Nucleic Acids Research

Volumn 34, Issue 17, 2006, Pages 4791-4800

  Rosen, Laura E ^a,b   Morrison, Holly A ^a   Masri, Selma ^a   Brown, Michael J ^a   Springstubb, Brendan ^a   Sussman, Django ^b   Stoddard, Barry L ^b   Seligman, Lenny M ^a  

^a POMONA COLLEGE   (United States)

^b Fred Hutchinson Cancer Research Center   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DEOXYRIBONUCLEASE I; DEOXYRIBONUCLEASE I CREI DERIVATIVE; DNA; UNCLASSIFIED DRUG;

ALLELE; AMINO ACID SUBSTITUTION; ARTICLE; CONTROLLED STUDY; CRYSTAL STRUCTURE; DNA CLEAVAGE; DNA SEQUENCE; ENZYME SPECIFICITY; GENE INACTIVATION; GENE TARGETING; GENETIC ANALYSIS; GENETIC MANIPULATION; IN VIVO STUDY; MOLECULAR RECOGNITION; PRIORITY JOURNAL; PROTEIN DNA INTERACTION; PROTEIN FAMILY;

AMINO ACID SUBSTITUTION; DNA; DNA RESTRICTION ENZYMES; MODELS, MOLECULAR; PROTEIN ENGINEERING; SUBSTRATE SPECIFICITY; WATER;

EID: 33750209424     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkl645     Document Type: Article

References (31)

1. Belfort,M. and Roberts,R.J. (1997) Homing endonucleases: Keeping the house in order. Nucleic Acids Res., 25, 3379-3388.
2. Chevalier,B.S. and Stoddard,B.L. (2001) Homing endonucleases: Structural and functional insight into the catalysts of intron/intein mobility. Nucleic Acids Res., 29, 3757-3774.
3. Gimble,F.S. (2000) Invasion of a multitude of genetic niches by mobile endonuclease genes. FEMS Microbiol. Lett., 185, 99-107.
4. Burt,A. and Koufopanou,V. (2004) Homing endonuclease genes: The rise and fall and rise again of a selfish element. Curr. Opin. Genet. Dev., 14, 609-615.
5. Seligman,L.M., Stephens,K.M., Savage,J.H. and Monnat,R.J., Jr (1997) Genetic analysis of the Chlamydomonas reinhardtii I-CreI mobile intron homing system in Escherichia coli. Genetics, 147, 1653-1664.
6. Donoho,G., Jasin,M. and Berg,P. (1998) Analysis of gene targeting and intrachromosomal homologous recombination stimulated by genomic double-strand breaks in mouse embryonic stem cells. Mol. Cell. Biol., 18, 4070-4078.
7. Posfai,G., Kolisnychenko,V., Bereczki,Z. and Blattner,F.R. (1999) Markerless gene replacement in Escherichia coli stimulated by a double-strand break in the chromosome. Nucleic Acids Res., 27, 4409-4415.
8. Monnat,R.J., Jr, Hackmann,A.F. and Cantrell,M.A. (1999) Generation of highly site-specific DNA double-strand breaks in human cells by the homing endonucleases I-PpoI and I-CreI. Biochem. Biophys. Res. Commun., 255, 88-93.
9. Kirik,A., Salomon,S. and Puchta,H. (2000) Species-specific double-strand break repair and genome evolution in plants. EMBO J., 19, 5562-5566.
10. Rong,Y.S. and Golic,K.G. (2000) Gene targeting by homologous recombination in Drosophila. Science, 288, 2013-2018.
11. Jurica,M.S., Monnat,R.J., Jr and Stoddard,B.L. (1998) DNA recognition and cleavage by the LAGLIDADG homing endonuclease I-CreI. Mol. Cell, 2, 469-476.
12. Chevalier,B., Turmel,M., Lemieux,C., Monnat,R.J., Jr and Stoddard,B.L. (2003) Flexible DNA target site recognition by divergent homing endonuclease isoschizomers I-CreI and I-MsoI. J. Mol. Biol., 329, 253-269.
13. Seligman,L.M., Chisholm,K.M., Chevalier,B.S., Chadsey,M.S., Edwards,S.T., Savage,J.H. and Veillet,A.L. (2002) Mutations altering the cleavage specificity of a homing endonuclease. Nucleic Acids Res., 30, 3870-3879.
14. Sussman,D., Chadsey,M., Fauce,S., Engel,A., Bruett,A., Monnat,R., Jr, Stoddard,B.L. and Seligman,L.M. (2004) Isolation and characterization of new homing endonuclease specificities at individual target site positions. J. Mol. Biol., 342, 31-41.
15. Arnould,S., Chames,P., Perez,C., Lacroix,E., Duclert,A., Epinat,J.C., Stricher,F., Petit,A.S., Patin,A., Guillier,S. et al. (2006) Engineering of large numbers of highly specific homing endonucleases that induce recombination on novel DNA targets. J. Mol. Biol., 355, 443-458.
16. Miller,J.H. (1992) A Short Course in Bacterial Genetics: A Laboratory Manual and Handbook for Escherichia coli and Related Bacteria, 1st edn. Cold Spring Harbor Laboratory Press, Plainview, NY.
17. Otwinowski,Z. and Minor,W. (1997) Processing of X-ray diffraction data collected in oscillation mode. Meth. Enzymol., 276, 307-326.
18. Kissinger,C.R., Gehlhaar,D.K. and Fogel,D.B. (1999) Rapid automated molecular replacement by evolutionary search. Acta Crystallogr. D Biol. Crystallogr., 55, 484-491.
19. McRee,D.E. (1999) XtalView/Xfit--a versatile program for manipulating atomic coordinates and electron density. J. Struct. Biol., 125, 156-165.
20. Brunger,A.T., Adams,P.D., Clore,G.M., DeLano,W.L., Gros,P., Grosse-Kunstleve,R.W., Jiang,J.S., Kuszewski,J., Nilges,M., Pannu,N.S. et al. (1998) Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr. D Biol. Crystallogr., 54, 905-921.
21. Brunger,A.T. (1993) Assessment of phase accuracy by cross validation: the free R value. Methods and applications. Acta Crystallogr. D Biol. Crystallogr., 49, 24-36.
22. Laskowski,R.A., MacArthur,M.W., Moss,D.S. and Thornton,J.M. (1993) PROCHECK: A program to check the stereochemical quality of protein structures. J. Appl. Crystallog., 26, 291-294.
23. Burt,A. (2003) Site-specific selfish genes as tools for the control and genetic engineering of natural populations. Proc. Biol. Sci., 270, 921-928.
24. Chevalier,B.S., Kortemme,T., Chadsey,M.S., Baker,D., Monnat,R.J. and Stoddard,B.L. (2002) Design, activity, and structure of a highly specific artificial endonuclease. Mol. Cell, 10, 895-905.
25. Epinat,J.C., Arnould,S., Chames,P., Rochaix,P., Desfontaines,D., Puzin,C., Patin,A., Zanghellini,A., Paques,F. and Lacroix,E. (2003) A novel engineered meganuclease induces homologous recombination in yeast and mammalian cells. Nucleic Acids Res., 31, 2952-2962.
26. Chames,P., Epinat,J.C., Guillier,S., Patin,A., Lacroix,E. and Paques,F. (2005) In vivo selection of engineered homing endonucleases using double-strand break induced homologous recombination. Nucleic Acids Res., 33, e178.
27. Spiegel,P.C., Chevalier,B., Sussman,D., Turmel,M., Lemieux,C. and Stoddard,B.L. (2006) The Structure of I-CeuI homing endonuclease: evolving asymmetric DNA recognition from a symmetric protein scaffold. Structure, 14, 869-880.
28. Argast,G.M., Stephens,K.M., Emond,M.J. and Monnat,R.J., Jr (1998) I-PpoI and I-CreI homing site sequence degeneracy determined by random mutagenesis and sequential in vitro enrichment. J. Mol. Biol., 280, 345-353.
29. Chen,Z. and Zhao,H. (2005) A highly sensitive selection method for directed evolution of homing endonucleases. Nucleic Acids Res., 33, e154.
30. Doyon,J.B., Pattanayak,V., Meyer,C.B. and Liu,D.R. (2006) Directed evolution and substrate specificity profile of homing endonuclease I-SceI. J. Am. Chem. Soc., 128, 2477-2484.
31. Ashworth,J., Havranek,J.J., Duarte,C.M., Sussman,D., Monnat,R.J., Jr, Stoddard,B.L. and Baker,D. (2006) Computational redesign of endonuclease DNA binding and cleavage specificity. Nature, 441, 656-659.