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

Fengli Fu, Jeffry D. Sander, Morgan Maeder, Stacey Thibodeau-Beganny, J. Keith Joung, Drena Dobbs, Leslie Miller, Daniel F. Voytas

Research output: Contribution to journalArticlepeer-review

61 Scopus citations

Abstract

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.

Original languageEnglish (US)
Pages (from-to)D279-D283
JournalNucleic acids research
Volume37
Issue numberSUPPL. 1
DOIs
StatePublished - 2009

Bibliographical note

Funding Information:
The National Science Foundation (0501678 and 0209818 to D.F.V.); National Institutes of Health (GM069906 and GM078369 to J.K.J.). Funding for open access charge: National Science Foundation 0501678.

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