Selection-Free Zinc-Finger Nuclease Engineering by Context-Dependent Assembly (CoDA)

Engineered zinc-finger nucleases (ZFNs) enable targeted genome modification. Here we describe context-dependent assembly (CoDA), a platform for engineering ZFNs using only standard cloning techniques or custom DNA synthesis. Using CoDA-generated ZFNs, we rapidly altered 20 genes in Danio rerio, Arabidopsis thaliana and Glycine max. The simplicity and efficacy of CoDA will enable broad adoption of ZFN technology and make possible large-scale projects focused on multigene pathways or genome-wide alterations.

• Publication year

  2010

• Venue

  Nature Methods

• Publication date

  2010-12-10

• Fields of study

  Biology, Medicine, Engineering

• Identifiers
  DOI 10.1038/nmeth.1542PMID 21151135PMCID 3018472
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Genome editing with modularly assembled zinc-finger nucleases

  2010cited by this paper
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• Targeted chromosomal deletions in human cells using zinc finger nucleases.

  2010cited by this paper
• High frequency targeted mutagenesis in Arabidopsis thaliana using zinc finger nucleases

  2010influential reference
• Expanding or restricting the target site repertoire of zinc-finger nucleases: the inter-domain linker as a major determinant of target site selectivity.

  2009cited by this paper
• Gene targeting of a disease-related gene in human induced pluripotent stem and embryonic stem cells.

  2009cited by this paper
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  2009cited by this paper
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  2009cited by this paper
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  2009cited by this paper
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  2009cited by this paper
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  2009cited by this paper
• High frequency modification of plant genes using engineered zinc finger nucleases

  2009cited by this paper
• Protein engineering: The fate of fingers

  2008cited by this paper
• Zinc-finger Nucleases: The Next Generation Emerges.

  2008cited by this paper
• Rapid "open-source" engineering of customized zinc-finger nucleases for highly efficient gene modification.

  2008cited by this paper
• Targeted gene inactivation in zebrafish using engineered zinc-finger nucleases

  2008cited by this paper
• Heritable Targeted Gene Disruption in Zebrafish Using Designed Zinc Finger Nucleases

  2008cited by this paper
• Unexpected failure rates for modular assembly of engineered zinc fingers

  2008cited by this paper
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  2008cited by this paper
• Evaluation of constitutive viral promoters in transgenic soybean roots and nodules.

  2008cited by this paper
• MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0.

  2007cited by this paper
• Cell stem cell.

  2007cited by this paper
• Standardized reagents and protocols for engineering zinc finger nucleases by modular assembly

  2006cited by this paper
• Zinc Finger Tools: custom DNA-binding domains for transcription factors and nucleases

  2006cited by this paper
• Human zinc fingers as building blocks in the construction of artificial transcription factors

  2003cited by this paper
• Agents.

  2002cited by this paper
• Validated Zinc Finger Protein Designs for All 16 GNN DNA Triplet Targets*

  2002cited by this paper
• Requirements for double-strand cleavage by chimeric restriction enzymes with zinc finger DNA-recognition domains.

  2000cited by this paper
• Comprehensive DNA recognition through concerted interactions from adjacent zinc fingers.

  1998cited by this paper
• Synergy between adjacent zinc fingers in sequence-specific DNA recognition.

  1997cited by this paper

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