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PMID: 18812396 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, U.S. Gov't, Non-P.H.S.

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

Nucleic acids research ·Vol. 37 ·No. Database issue ·2009-01-00 ·Pages D279-83

Fu F, Sander JD, Maeder M, Thibodeau-Beganny S, Joung JK, Dobbs D, Miller L, Voytas DF

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.

MeSH Terms
Binding Sites DNA/chemistry DNA-Binding Proteins/chemistry,genetics Databases, Protein Oligonucleotide Array Sequence Analysis Protein Engineering Transcription Factors/chemistry,genetics User-Computer Interface Zinc Fingers
Chemicals
DNA-Binding Proteins Transcription Factors DNA
Authors & Affiliations
8 authors, click to expand affiliations / ORCID
Fu Fengli
Department of Genetics, Development & Cell Biology, 1043 Roy J. Carver Co-Laboratory, Iowa State University, Ames, Iowa 50011, USA.
Sander Jeffry D
Maeder Morgan
Thibodeau-Beganny Stacey
Joung J Keith
Dobbs Drena
Miller Leslie
Voytas Daniel F
References (21)
21 references, click to expand
  1. A bacterial two-hybrid selection system for studying protein-DNA and protein-protein interactions.
    Proc Natl Acad Sci U S A. 2000 Jun 20;97(13):7382-7 PMID: 10852947
  2. Zinc-finger nucleases: the next generation emerges.
    Mol Ther. 2008 Jul;16(7):1200-7 PMID: 18545224
  3. Insights into the molecular recognition of the 5'-GNN-3' family of DNA sequences by zinc finger domains.
    J Mol Biol. 2000 Nov 3;303(4):489-502 PMID: 11054286
  4. Synthetic zinc finger transcription factor action at an endogenous chromosomal site. Activation of the human erythropoietin gene.
    J Biol Chem. 2000 Oct 27;275(43):33850-60 PMID: 10913152
  5. Regulation of an endogenous locus using a panel of designed zinc finger proteins targeted to accessible chromatin regions. Activation of vascular endothelial growth factor A.
    J Biol Chem. 2001 Apr 6;276(14):11323-34 PMID: 11145970
  6. Development of zinc finger domains for recognition of the 5'-ANN-3' family of DNA sequences and their use in the construction of artificial transcription factors.
    J Biol Chem. 2001 Aug 3;276(31):29466-78 PMID: 11340073
  7. Validated zinc finger protein designs for all 16 GNN DNA triplet targets.
    J Biol Chem. 2002 Feb 8;277(6):3850-6 PMID: 11726671
  8. Rational design of artificial zinc-finger proteins using a nondegenerate recognition code table.
    Biochemistry. 2002 Jun 4;41(22):7074-81 PMID: 12033941
  9. Human zinc fingers as building blocks in the construction of artificial transcription factors.
    Nat Biotechnol. 2003 Mar;21(3):275-80 PMID: 12592413
  10. Highly specific zinc finger proteins obtained by directed domain shuffling and cell-based selection.
    Proc Natl Acad Sci U S A. 2003 Oct 14;100(21):12271-6 PMID: 14527993
  11. Toward rules relating zinc finger protein sequences and DNA binding site preferences.
    Proc Natl Acad Sci U S A. 1992 Aug 15;89(16):7345-9 PMID: 1502144
  12. A general strategy for selecting high-affinity zinc finger proteins for diverse DNA target sites.
    Science. 1997 Jan 31;275(5300):657-61 PMID: 9005850
  13. Synergy between adjacent zinc fingers in sequence-specific DNA recognition.
    Proc Natl Acad Sci U S A. 1997 May 27;94(11):5617-21 PMID: 9159121
  14. Toward controlling gene expression at will: selection and design of zinc finger domains recognizing each of the 5'-GNN-3' DNA target sequences.
    Proc Natl Acad Sci U S A. 1999 Mar 16;96(6):2758-63 PMID: 10077584
  15. Development of zinc finger domains for recognition of the 5'-CNN-3' family DNA sequences and their use in the construction of artificial transcription factors.
    J Biol Chem. 2005 Oct 21;280(42):35588-97 PMID: 16107335
  16. Zinc Finger Tools: custom DNA-binding domains for transcription factors and nucleases.
    Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W516-23 PMID: 16845061
  17. Standardized reagents and protocols for engineering zinc finger nucleases by modular assembly.
    Nat Protoc. 2006;1(3):1637-52 PMID: 17406455
  18. Zinc Finger Targeter (ZiFiT): an engineered zinc finger/target site design tool.
    Nucleic Acids Res. 2007 Jul;35(Web Server issue):W599-605 PMID: 17526515
  19. Unexpected failure rates for modular assembly of engineered zinc fingers.
    Nat Methods. 2008 May;5(5):374-5 PMID: 18446154
  20. Rapid "open-source" engineering of customized zinc-finger nucleases for highly efficient gene modification.
    Mol Cell. 2008 Jul 25;31(2):294-301 PMID: 18657511
  21. DNA recognition by Cys2His2 zinc finger proteins.
    Annu Rev Biophys Biomol Struct. 2000;29:183-212 PMID: 10940247
Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/gkn606
Published
2009-01-00
Epub
2008-00-23
Pages
D279-83
Language
English
Region
England
NLM ID
0411011
PMCID
PMC2686427
Subset
IM
Grants
NIH HHS · DP1 OD006862 · United States
NIGMS NIH HHS · GM069906 · United States
NIGMS NIH HHS · GM078369 · United States
External Links
PubMed source DOI: 10.1093/nar/gkn606 PMC Full Text View journal details
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