Effects of DNA binding of the zinc finger and linkers for domain fusion on the catalytic activity of sequence-specific chimeric recombinases determined by a facile fluorescent system

Biochemistry

Volumn 51, Issue 7, 2012, Pages 1510-1517

  Nomura, Wataru ^a   Masuda, Akemi ^a   Ohba, Kenji ^b   Urabe, Arisa ^a   Ito, Nobutoshi ^a   Ryo, Akihide ^c   Yamamoto, Naoki ^b   Tamamura, Hirokazu ^a  

^a Tokyo Medical and Dental University ^*  (Japan)

^b NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

^c YOKOHAMA CITY UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING DOMAIN; CATALYTIC DOMAINS; CLINICAL TRIAL; DNA BINDING; DNA BINDING AFFINITY; DNA CLEAVAGE; DNA TARGETS; FLUORESCENT SYSTEMS; GENE MANIPULATION; GENOME MODIFICATION; LINKER SEQUENCE; MAMMALIAN CELLS; MODEL ORGANISMS; NONHOMOLOGOUS END JOINING; RECOMBINASES; RECOMBINATION EFFICIENCY; RESTRICTION ENZYMES; SEQUENCE SPECIFICITY; TARGET SITES; THERAPEUTIC GENES; ZINC FINGER; ZINC FINGER DOMAINS; ZINC FINGER NUCLEASE; ZINC FINGER PROTEIN; ZINC IONS;

AMINO ACIDS; BINDING ENERGY; CATALYST ACTIVITY; DESIGN; DNA; DNA SEQUENCES; ENZYMES; ESCHERICHIA COLI; FLUORESCENCE; GENE THERAPY;

ZINC;

RECOMBINASE; UNCLASSIFIED DRUG; ZINC FINGER PROTEIN; ZINC FINGER RECOMBINASE;

ANIMAL CELL; ARTICLE; BACTERIAL CELL; BINDING AFFINITY; CATALYSIS; CHIMERA; DNA BINDING; DNA MODIFICATION; ENZYME MODIFICATION; ESCHERICHIA COLI; FLUORESCENCE; GENETIC RECOMBINATION; GENOME ANALYSIS; MAMMAL CELL; NONHUMAN; PLASMID; PRIORITY JOURNAL; ZINC FINGER MOTIF;

AMINO ACID SEQUENCE; ANIMALS; CATALYSIS; CELL SEPARATION; CHO CELLS; CRICETINAE; DNA; ESCHERICHIA COLI; FLOW CYTOMETRY; FLUORESCENT DYES; HUMANS; MOLECULAR CONFORMATION; MOLECULAR SEQUENCE DATA; MUTAGENESIS; PROTEIN BINDING; PROTEIN STRUCTURE, TERTIARY; RECOMBINATION, GENETIC; SEQUENCE HOMOLOGY, AMINO ACID; ZINC FINGERS;

EID: 84857418823     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi201878x     Document Type: Article

References (34)

1. Beerli, R. R., Dreier, B., and Barbas, C. F., III (2000) Positive and negative regulation of endogenous genes by designed transcription factors Proc. Natl. Acad. Sci. U.S.A. 97, 1495-1500
2. Pabo, C. O., Peisach, E., and Grant, R. A. (2001) Design and selection of novel Cys2His2 zinc-finger proteins Annu. Rev. Biochem. 70, 313-340
3. Beerli, R. R. and Barbas, C. F., III (2002) Engineering polydactyl zinc-finger transcription factors Nat. Biotechnol. 20, 135-141
4. Jamieson, A. C., Miller, J. C., and Pabo, C. O. (2003) Drug discovery with engineered zinc-finger proteins Nat. Rev. Drug Discovery 2, 361-368
5. Blancafort, P., Segal, D. J., and Barbas, C. F., III (2004) Designing transcription factor architectures for drug discovery Mol. Pharmacol. 66, 1361-1371
6. Carroll, D. (2008) Progress and prospects: Zinc-finger nucleases as gene therapy agents Gene Ther. 15, 1463-1468
7. Akopian, A., He, J., Boocock, M. R., and Stark, W. M. (2003) Chimeric recombinases with designed DNA sequence recognition Proc. Natl. Acad. Sci. U.S.A. 100, 8688-8691
8. Gordley, R. M., Smith, J. D., Gräslund, T., and Barbas, C. F., III (2007) Evolution of programmable zinc-finger-recombinases with activity in human cells J. Mol. Biol. 367, 802-813
9. Gordley, R. M., Gersbach, C. A., and Barbas, C. F., III (2009) Synthesis of programmable integrases Proc. Natl. Acad. Sci. U.S.A. 106, 5053-5058
10. Gersbach, C. A., Gaj, T., Gordley, R. M., and Barbas, C. F., III (2010) Directed evolution of recombinase specificity by split gene reassembly Nucleic Acids Res. 38, 4198-4206
11. Gaj, T., Mercer, A. C., Gersbach, C. A., Gordley, R. M., and Barbas, C. F., III (2011) Structure-Guided Reprogramming of Serine Recombinase DNA Sequence Specificity Proc. Natl. Acad. Sci. U.S.A. 108, 498-503
12. Gersbach, C. A., Gaj, T., Gordley, R. M., Mercer, A. C., and Barbas, C. F., III (2011) Targeted plasmid integration into the human genome by an engineered zinc-finger recombines Nucleic Acids Res. 39, 7868-7878
13. Xu, G.-L. and Bestor, T. H. (1997) Cytosine methylation targeted to predetermined sequences Nat. Genet. 17, 376-378
14. McNamara, A. R., Hurd, P. J., Smith, A. E., and Ford, K. G. (2002) Characterisation of site-biased DNA methyltransferases: Specificity, affinity and subsite relationships Nucleic Acids Res. 30, 3818-3130
15. Carvin, C. D., Parr, R. D., and Kladde, M. P. (2003) Site-selective in vivo targeting of cytosine-5 DNA methylation by zinc-finger proteins Nucleic Acids Res. 31, 6493-6501
16. Minczuk, M., Papworth, M. A., Kolasinska, P., Murphy, M. P., and Klug, A. (2006) Sequence-specific modification of mitochondrial DNA using a chimeric zinc-finger methylase Proc. Natl. Acad. Sci. U.S.A. 103, 19689-19694
17. Li, F., Papworth, M., Minczuk, M., Rohde, C., Zhang, Y., Ragozin, S., and Jeltsch, A. (2007) Chimeric DNA methyltransferases target DNA methylation to specific DNA sequences and repress expression of target genes Nucleic Acids Res. 35, 100-112
18. Smith, A. E. and Ford, K. G. (2007) Specific targeting of cytosine methylation to DNA sequences in vivo Nucleic Acids Res. 35, 740-754
19. Smith, A. E., Hurd, P. J., Bannister, A. J., Kouzarides, T., and Ford, K. G. (2008) Heritable Gene Repression through the Action of a Directed DNA Methyltransferase at a Chromosomal Locus J. Biol. Chem. 283, 9878-9885
20. Nomura, W. and Barbas, C. F., III (2007) In vivo site-specific DNA methylation with a designed sequence-enabled DNA methylase J. Am. Chem. Soc. 129, 8676-8677
21. Grindley, N. D., Whiteson, K. L., and Rice, P. A. (2006) Mechanisms of site-specific recombination Annu. Rev. Biochem. 75, 567-605
22. Yang, W. and Steitz, T. A. (1995) Crystal structure of the site-specific recombinase gamma delta resolvase complexed with a 34 bp cleavage site Cell 82, 193-207
23. Arnold, P. H., Blake, D. G., Grindley, N. D., Boocock, M. R., and Stark, W. M. (1999) Mutants of Tn3 resolvase which do not require accessory binding sites for recombination activity EMBO J. 18, 1407-1414
24. Li, W., Kamtekar, S., Xiong, Y., Sarkis, G. J., Grindley, N. D., and Steitz, T. A. (2005) Structure of a synaptic γδ resolvase tetramer covalently linked to two cleaved DNAs Science 309, 1210-1215
25. Olorunniji, F. J., He, J., Wenwieser, S. V., Boocock, M. R., and Stark, W. M. (2008) Synapsis and catalysis by activated Tn3 resolvase mutants Nucleic Acids Res. 36, 7181-7191
26. Gonzalez, B., Schwimmer, L. J., Fuller, R. P., Ye, Y., Asawapornmongkol, L., and Barbas, C. F., III (2010) Modular system for the construction of zinc-finger libraries and proteins Nat. Protoc. 5, 791-810
27. Mandell, J. G. and Barbas, C. F., III (2006) Zinc Finger Tools: Custom DNA-binding domains for transcription factors and nucleases Nucleic Acids Res. 34, W516-W523
28. Kim, C. A. and Berg, J. M. (1996) A 2.2 Angstroms resolution crystal structure of a designed zinc finger protein bound to DNA Nat. Struct. Mol. Biol. 3, 940-945
29. Segal, D. J., Dreier, B., Beerli, R. R., and Barbas, C. F., III (1999) Toward controlling gene expression at will: Selection and design of zinc finger domains recognizing each of the 5′-GNN-3′ DNA target sequences Proc. Natl. Acad. Sci. U.S.A. 96, 2758-2763
30. Dreier, B., Segal, D. J., and Barbas, C. F., III (2000) Insights into the molecular recognition of the 5′-GNN-3′ family of DNA sequences by zinc-finger domains J. Mol. Biol. 303, 489-502
31. Dreier, B., Beerli, R. R., Segal, D. J., Flippin, J. D., and Barbas, C. F., III (2001) Development of zinc finger domains for recognition of the 5′-ANN-3′ family of DNA sequences and their use in the construction of artificial transcription factors J. Biol. Chem. 276, 29466-29478
32. Dreier, B., Fuller, R. P., Segal, D. J., Lund, C., Blancafort, P., Huber, A., Koksch, B., and Barbas, C. F., III (2005) Development of zinc finger domains for recognition of the 5′-CNN-3′ family DNA sequences and their use in the construction of artificial transcription factors J. Biol. Chem. 280, 35588-35597
33. Kamiuchi, T., Abe, E., Imanishi, M., Kaji, T., Nagaoka, M., and Sugiura, Y. (1998) Artificial nine zinc-finger peptide with 30 base pair binding sites Biochemistry 37, 13827-13834
34. Guo, J., Gaj, T., and Barbas, C. F., III (2010) Directed evolution of an enhanced and highly efficient FokI cleavage domain for zinc finger nuclease J. Mol. Biol. 400, 96-107