Zinc Finger Database (ZiFDB): a repository for information on C2H2 zinc fingers and engineered zinc-finger arrays.
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.
Fu
Fengli
F
Department of Genetics, Development & Cell Biology, 1043 Roy J. Carver Co-Laboratory, Iowa State University, Ames, Iowa 50011, USA.
Sander
Jeffry D
JD
Maeder
Morgan
M
Thibodeau-Beganny
Stacey
S
Joung
J Keith
JK
Dobbs
Drena
D
Miller
Leslie
L
Voytas
Daniel F
DF
D001665:Binding Sites; D004247:DNA / Q000737:chemistry; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000235:genetics*; D030562:Databases, Protein; D020411:Oligonucleotide Array Sequence Analysis; D015202:Protein Engineering; D014157:Transcription Factors / Q000737:chemistry* / Q000235:genetics*; D014584:User-Computer Interface; D016335:Zinc Fingers
D004268:DNA-Binding Proteins; D014157:Transcription Factors; D004247:DNA