Unexpected failure rates for modular assembly of engineered zinc fingers

@article{Ramirez2008UnexpectedFR,
  title={Unexpected failure rates for modular assembly of engineered zinc fingers},
  author={Cherie Lynn Ramirez and Jonathan E. Foley and David A. Wright and Felix M{\"u}ller-Lerch and Shamim H. Rahman and Tatjana I. Cornu and Ronnie J Winfrey and Jeffry D. Sander and Fengli Fu and Jeffrey A. Townsend and Toni Cathomen and Daniel F. Voytas and J. Keith Joung},
  journal={Nature Methods},
  year={2008},
  volume={5},
  pages={374-375}
}
Nat. Methods 5, 374–375 (2008); corrected after print 29 May 2008. In the version of this correspondence initially published, the two previously published datasets analyzed were labeled with incorrect references in Figure 1b. Reference 2 should be associated with the second column (80 sites), and reference 3 should be associated with the third column (96 sites). 
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Evaluation of a modular strategy for the construction of novel polydactyl zinc finger DNA-binding proteins.
TLDR
This report is the first report of target site selection for designed, well characterized 6-finger proteins and has important implications for the design of proteins that can recognize extended DNA sequences, as well as provide insights into the general rules of recognition for naturally occurring zinc finger proteins.
Validated Zinc Finger Protein Designs for All 16 GNN DNA Triplet Targets*
TLDR
A systematic specificity study reveals that the in vivo functionality of these zinc finger proteins in a reporter assay depends on their binding affinities to their target sequences, thus giving a better understanding of how these zinc Finger proteins might function inside cells.
A rapid, generally applicable method to engineer zinc fingers illustrated by targeting the HIV-1 promoter
TLDR
A rapid and convenient method that can be used to design zinc finger proteins against a variety of DNA-binding sites and yields proteins that bind sequence-specifically to DNA with Kd values in the nanomolar range is presented.
A General Strategy for Selecting High-Affinity Zinc Finger Proteins for Diverse DNA Target Sites
TLDR
A method is described for selecting DNA-binding proteins that recognize desired sequences by gradually extending a new zinc finger protein across the desired 9- or 10-base pair target site, adding and optimizing one finger at a time.
Standardized reagents and protocols for engineering zinc finger nucleases by modular assembly
TLDR
A comprehensive, publicly available archive of plasmids encoding more than 140 well-characterized zinc finger modules together with complementary web-based software for identifying potential zinc finger target sites in a gene of interest is described.
Zinc Finger Targeter (ZiFiT): an engineered zinc finger/target site design tool
TLDR
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.
Human zinc fingers as building blocks in the construction of artificial transcription factors
TLDR
The results show that the human genome encodes zinc fingers with diverse DNA-binding specificities and that these domains can be used to design sequence-specific DNA- binding proteins and artificial transcription factors.
Zinc Finger Tools: custom DNA-binding domains for transcription factors and nucleases
TLDR
A user-friendly utility called Zinc Finger Tools (ZF Tools) is created that can be accessed at the URL and the amino acid sequence for a ZFP expected to bind to any chosen target site can be generated.
Gene targeting using zinc finger nucleases
TLDR
Zinc finger nucleases show promise in improving the efficiency of gene targeting by introducing DNA double-strand breaks in target genes, which then stimulate the cell's endogenous homologous recombination machinery.
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