Creating designed zinc-finger nucleases with minimal cytotoxicity

Sivaprakash Ramalingam, Karthikeyan Kandavelou, Raja Rajenderan, Srinivasan Chandrasegaran

Research output: Contribution to journalArticlepeer-review

54 Scopus citations


Zinc-finger nucleases (ZFNs) have emerged as powerful tools for delivering a targeted genomic double-strand break (DSB) to either stimulate local homologous recombination with investigator-provided donor DNA or induce gene mutations at the site of cleavage in the absence of a donor by nonhomologous end joining both in plant cells and in mammalian cells, including human cells. ZFNs are formed by fusing zinc-finger proteins to the nonspecific cleavage domain of the FokI restriction enzyme. ZFN-mediated gene targeting yields high gene modification efficiencies (> 10%) in a variety of cells and cell types by delivering a recombinogenic DSB to the targeted chromosomal locus, using two designed ZFNs. The mechanism of DSB by ZFNs requires (1) two ZFN monomers to bind to their adjacent cognate sites on DNA and (2) the FokI nuclease domains to dimerize to form the active catalytic center for the induction of the DSB. In the case of ZFNs fused to wild-type FokI cleavage domains, homodimers may also form; this could limit the efficacy and safety of ZFNs by inducing off-target cleavage. In this article, we report further refinements to obligate heterodimer variants of the FokI cleavage domain for the creation of custom ZFNs with minimal cellular toxicity. The efficacy and efficiency of the reengineered obligate heterodimer variants of the FokI cleavage domain were tested using the green fluorescent protein gene targeting reporter system. The three-finger and four-finger zinc-finger protein fusions to the REL-DKK pair among the newly generated FokI nuclease domain variants appear to eliminate or greatly reduce the toxicity of designer ZFNs to human cells.

Original languageEnglish (US)
Pages (from-to)630-641
Number of pages12
JournalJournal of molecular biology
Issue number3
StatePublished - Jan 21 2011
Externally publishedYes


  • Genome engineering
  • Homologous recombination
  • Non-homologous end-joining
  • Site-Specific modification
  • Targeted cleavage

ASJC Scopus subject areas

  • Structural Biology
  • Molecular Biology


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