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Nucleic Acids Research Advance Access originally published online on September 23, 2008
Nucleic Acids Research 2009 37(Database issue):D279-D283; doi:10.1093/nar/gkn606
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Nucleic Acids Research, 2009, Vol. 37, Database issue D279-D283
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

This article appears in the following Nucleic Acids Research issue: Database issue [View the issue table of contents]

Articles

Zinc Finger Database (ZiFDB): a repository for information on C2H2 zinc fingers and engineered zinc-finger arrays

Fengli Fu1,2, Jeffry D. Sander1,2, Morgan Maeder3, Stacey Thibodeau-Beganny3, J. Keith Joung3,4, Drena Dobbs1,2, Leslie Miller2,5 and Daniel F. Voytas6,*

1Department of Genetics, Development & Cell Biology, 1043 Roy J. Carver Co-Laboratory, 2Interdepartmental Graduate Program in Bioinformatics & Computational Biology, 2114 Molecular Biology Building, Iowa State University, Ames, Iowa 50011, 3Molecular Pathology Unit, Center for Cancer Research and Center for Computational and Integrative Biology, Massachusetts General Hospital, 149 13th Street, Charlestown, MA 02129, 4Department of Pathology, Harvard Medical School, Boston, MA 02115, 5Department of Computer Science, 227 Atanasoff Hall, Iowa State University, Ames, IA 50011 and 6Department of Genetics, Cell Biology & Development and Center for Genome Engineering, 321 Church Street SE, University of Minnesota, MN 55455, USA

*To whom correspondence should be addressed. Tel: +1 515 294 1963; Fax: +1 515 294 7155; Email: voytas{at}iastate.edu

Received August 15, 2008. Accepted September 6, 2008.

Zinc fingers are the most abundant DNA-binding motifs encoded by eukaryotic genomes and one of the best understood DNA-recognition domains. Each zinc finger typically binds a 3-nt target sequence, and it is possible to engineer zinc-finger arrays (ZFAs) that recognize extended DNA sequences by linking together individual zinc fingers. Engineered zinc-finger proteins have proven to be valuable tools for gene regulation and genome modification because they target specific sites in a genome. Here we describe ZiFDB (Zinc Finger Database; http://bindr.gdcb.iastate.edu/ZiFDB), a web-accessible resource that compiles information on individual zinc fingers and engineered ZFAs. To enhance its utility, ZiFDB is linked to the output from ZiFiT—a software package that assists biologists in finding sites within target genes for engineering zinc-finger proteins. For many molecular biologists, ZiFDB will be particularly valuable for determining if a given ZFA (or portion thereof) has previously been constructed and whether or not it has the requisite DNA-binding activity for their experiments. ZiFDB will also be a valuable resource for those scientists interested in better understanding how zinc-finger proteins recognize target DNA.


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