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Nucleic Acids Research 2006 34(Web Server issue):W516-W523; doi:10.1093/nar/gkl209
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© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Article

Zinc Finger Tools: custom DNA-binding domains for transcription factors and nucleases

Jeffrey G. Mandell1, and Carlos F. Barbas, III1,2,*

1 Department of Molecular Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute La Jolla, CA 92037, USA 2 Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute La Jolla, CA 92037, USA

*To whom correspondence should be addressed. Tel: 858 784 9098; Fax: 858 784 2583; Email: carlos{at}scripps.edu

Received February 14, 2006. Revised March 24, 2006. Accepted March 24, 2006.

Individual zinc finger (ZF) domains that recognize DNA triplets with high specificity and affinity can be used to create designer transcription factors and nucleases that are specific for nearly any site in the genome. These domains can be treated as modular units and assembled to create a polydactyl protein that recognizes extended DNA sequences. Deter-mination of valid target sites and the subsequent design of ZF proteins (ZFPs) is error-prone and not trivial, however. As a result, the use of ZFPs have been restricted primarily to those labs with the appropriate expertise. To address these limitations, we have created a user-friendly utility called Zinc Finger Tools (ZF Tools) that can be accessed at the URL http://www.zincfingertools.org. User-supplied DNA sequences can be searched for target sites appropriate for either gene regulation or nuclease targeting. Using a database of experimentally characterized zinc finger domains, the amino acid sequence for a ZFP expected to bind to any chosen target site can be generated. A reverse engineering utility is provided to predict the binding site for a ZFP of known sequence.


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