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Nucleic Acids Research Advance Access originally published online on May 25, 2007
Nucleic Acids Research 2007 35(Web Server issue):W599-W605; doi:10.1093/nar/gkm349
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Nucleic Acids Research, 2007, Vol. 35, No. suppl_2 W599-W605
© 2007 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.

Articles

Zinc Finger Targeter (ZiFiT): an engineered zinc finger/target site design tool

Jeffry D. Sander1,*, Peter Zaback1, J. Keith Joung2,3, Daniel F. Voytas1 and Drena Dobbs1

1Department of Genetics, Development & Cell Biology; Bioinformatics & Computational Biology Program, Iowa State University, Ames, IA 50011, USA, 2Molecular Pathology Unit, Center for Cancer Research, and Center for Computational and Integrative Biology, Massachusetts General Hospital, 149 13th Street, Charlestown, MA 02129, USA and 3Department of Pathology, Harvard Medical School, Boston, MA 02115, USA

*To whom correspondence should be addressed. Tel: +1 515 294 4991; Fax: +1 515 294 6790; Email: jdsander{at}iastate.edu

Received January 29, 2007. Revised April 16, 2007. Accepted April 23, 2007.

Zinc Finger Targeter (ZiFiT) is a simple and intuitive web-based tool that facilitates the design of zinc finger proteins (ZFPs) that can bind to specific DNA sequences. The current version of ZiFiT is based on a widely employed method of ZFP design, the ‘modular assembly’ approach, in which pre-existing individual zinc fingers are linked together to recognize desired target DNA sequences. Several research groups have described experimentally characterized zinc finger modules that bind many of the 64 possible DNA triplets. ZiFiT leverages the combined capabilities of three of the largest and best characterized module archives by enabling users to select fingers from any of these sets. ZiFiT searches a query DNA sequence for target sites for which a ZFP can be designed using modules available in one or more of the three archives. In addition, ZiFiT output facilitates identification of specific zinc finger modules that are publicly available from the Zinc Finger Consortium. ZiFiT is freely available at http://bindr.gdcb.iastate.edu/ZiFiT/.


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