HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS		QUICK SEARCH:   [advanced] Author: Keyword(s): Year:  Vol:  Page:

J. Biol. Chem., Vol. 280, Issue 42, 35588-35597, October 21, 2005

This Article Full Text Full Text (PDF) All Versions of this Article: 280/42/35588    most recent M506654200v1 Submit a Letter to Editor Alert me when this article is cited Alert me when eLetters are posted Alert me if a correction is posted Citation Map Services Email this article to a friend Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Request Permissions Citing Articles Citing Articles via HighWire Citing Articles via Google Scholar Google Scholar Articles by Dreier, B. Articles by Barbas, C. F. Search for Related Content PubMed PubMed Citation Articles by Dreier, B. Articles by Barbas, C. F., III Social Bookmarking                      What's this?

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^*

Birgit Dreier1, Roberta P. Fuller, David J. Segal, Caren V. Lund, Pilar Blancafort, Adrian Huber, Beate Koksch¶, and Carlos F. Barbas, III2

From the The Skaggs Institute for Chemical Biology and the Departments of Molecular Biology and Chemistry, The Scripps Research Institute, La Jolla, California 92037, University of California, University of California Davis Genome Center and Departments of Medical Pharmacology and Toxicology, Davis, California 95616, and ^¶Freie Universität Berlin, Institut für Chemie, Takustrasse 3, 14195 Berlin, Germany

Considerable progress has been made in recent years in the design of transcription factors for the directed regulation of endogenous genes. Although many strategies involve selection methods that must be applied for each new target sequence, we have developed an approach based on linkage of predefined zinc finger domains that each recognize a three-base pair DNA sequence to construct artificial transcription factors that bind to a desired sequence. These domains can be assembled to recognize unique 18-base pair DNA sequences with high specificity. Here we report the development and characterization of zinc finger domains that bind to 15 of the 16 5'-CNN-3' subsites. These domains were created through a combination of phage display selection, site-directed mutagenesis, and de novo design. Furthermore, these domains were used to generate a highly specific six-finger protein targeting the ERBB-2 promoter. When fused to regulatory domains, this protein was capable of up- and down-regulating the expression of the endogenous ERBB-2 gene. With the addition of this collection of predefined zinc finger domains, most 5'-CNN-3'-, 5'-GNN-3'-, and 5'-ANN-3'-containing sequences can now be rapidly targeted for directed gene regulation and nuclease cleavage.

Received for publication, June 20, 2005 , and in revised form, August 16, 2005.

The nucleotide sequence(s) reported in this paper has been submitted to the GenBank^TM/EBI Data Bank with accession number(s) DQ160159 and DQ160160

^* This study was supported by National Institutes of Health Grants CA086258 and GM065059 (to C. F. B.). The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

¹ Recipient of a postdoctoral fellowship from the Deutsche Forschungsgemeinschaft. Present address: University of Zurich, Dept. of Biochemistry, Winterthurerstrasse 190, 8057 Zurich, Switzerland.

² To whom correspondence should be addressed: The Scripps Research Institute, BCC-550, North Torrey Pines Rd., La Jolla, CA 92037. Tel.: 858-784-9098; Fax: 858-784-2583; E-mail: carlos{at}scripps.edu.

CiteULike    Complore    Connotea    Del.icio.us    Digg    Reddit    Technorati    What's this?

This article has been cited by other articles:

				H. J. Kim, H. J. Lee, H. Kim, S. W. Cho, and J.-S. Kim Targeted genome editing in human cells with zinc finger nucleases constructed via modular assembly Genome Res., July 1, 2009; 19(7): 1279 - 1288. [Abstract] [Full Text] [PDF]

				D. Mittelman, C. Moye, J. Morton, K. Sykoudis, Y. Lin, D. Carroll, and J. H. Wilson Zinc-finger directed double-strand breaks within CAG repeat tracts promote repeat instability in human cells PNAS, June 16, 2009; 106(24): 9607 - 9612. [Abstract] [Full Text] [PDF]

				R. M. Gordley, C. A. Gersbach, and C. F. Barbas III Synthesis of programmable integrases PNAS, March 31, 2009; 106(13): 5053 - 5058. [Abstract] [Full Text] [PDF]

				J. D. Sander, P. Zaback, J. K. Joung, D. F. Voytas, and D. Dobbs An affinity-based scoring scheme for predicting DNA-binding activities of modularly assembled zinc-finger proteins Nucleic Acids Res., February 1, 2009; 37(2): 506 - 515. [Abstract] [Full Text] [PDF]

				A. V. Persikov, R. Osada, and M. Singh Predicting DNA recognition by Cys2His2 zinc finger proteins Bioinformatics, January 1, 2009; 25(1): 22 - 29. [Abstract] [Full Text] [PDF]

				F. Fu, J. D. Sander, M. Maeder, S. Thibodeau-Beganny, J. K. Joung, D. Dobbs, L. Miller, and D. F. Voytas Zinc Finger Database (ZiFDB): a repository for information on C2H2 zinc fingers and engineered zinc-finger arrays Nucleic Acids Res., January 1, 2009; 37(suppl_1): D279 - D283. [Abstract] [Full Text] [PDF]

				K. J. Beumer, J. K. Trautman, A. Bozas, J.-L. Liu, J. Rutter, J. G. Gall, and D. Carroll Efficient gene targeting in Drosophila by direct embryo injection with zinc-finger nucleases PNAS, December 16, 2008; 105(50): 19821 - 19826. [Abstract] [Full Text] [PDF]

				K. A. Zimmerman, K. P. Fischer, M. A. Joyce, and D. L. J. Tyrrell Zinc Finger Proteins Designed To Specifically Target Duck Hepatitis B Virus Covalently Closed Circular DNA Inhibit Viral Transcription in Tissue Culture J. Virol., August 15, 2008; 82(16): 8013 - 8021. [Abstract] [Full Text] [PDF]

				J. D. Sander, P. Zaback, J. K. Joung, D. F. Voytas, and D. Dobbs Zinc Finger Targeter (ZiFiT): an engineered zinc finger/target site design tool Nucleic Acids Res., July 13, 2007; 35(suppl_2): W599 - W605. [Abstract] [Full Text] [PDF]

				J. R. Newton, Y. Miao, S. L. Deutscher, and T. P. Quinn Melanoma Imaging with Pretargeted Bivalent Bacteriophage J. Nucl. Med., March 1, 2007; 48(3): 429 - 436. [Abstract] [Full Text] [PDF]

				M. Heinemann and S. Panke Synthetic biology--putting engineering into biology Bioinformatics, November 15, 2006; 22(22): 2790 - 2799. [Abstract] [Full Text] [PDF]

				J. Morton, M. W. Davis, E. M. Jorgensen, and D. Carroll Induction and repair of zinc-finger nuclease-targeted double-strand breaks in Caenorhabditis elegans somatic cells PNAS, October 31, 2006; 103(44): 16370 - 16375. [Abstract] [Full Text] [PDF]

				J. G. Mandell and C. F. Barbas III Zinc Finger Tools: custom DNA-binding domains for transcription factors and nucleases. Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W516 - W523. [Abstract] [Full Text] [PDF]

				K. Beumer, G. Bhattacharyya, M. Bibikova, J. K. Trautman, and D. Carroll Efficient Gene Targeting in Drosophila With Zinc-Finger Nucleases Genetics, April 1, 2006; 172(4): 2391 - 2403. [Abstract] [Full Text] [PDF]

				S. R. Eberhardy, J. Goncalves, S. Coelho, D. J. Segal, B. Berkhout, and C. F. Barbas III Inhibition of Human Immunodeficiency Virus Type 1 Replication with Artificial Transcription Factors Targeting the Highly Conserved Primer-Binding Site J. Virol., March 15, 2006; 80(6): 2873 - 2883. [Abstract] [Full Text] [PDF]

				P. Chames, J.-C. Epinat, S. Guillier, A. Patin, E. Lacroix, and F. Paques In vivo selection of engineered homing endonucleases using double-strand break induced homologous recombination Nucleic Acids Res., November 23, 2005; 33(20): e178 - e178. [Abstract] [Full Text] [PDF]