title: ZFN-site searches genomes for zinc finger nuclease target sites and off-target sites.
abstract: BACKGROUND
  Zinc Finger Nucleases (ZFNs) are man-made restriction enzymes useful for manipulating genomes by cleaving target DNA sequences. ZFNs allow therapeutic gene correction or creation of genetically modified model organisms. ZFN specificity is not absolute; therefore, it is essential to select ZFN target sites without similar genomic off-target sites. It is important to assay for off-target cleavage events at sites similar to the target sequence.
  
  
  RESULTS
  ZFN-Site is a web interface that searches multiple genomes for ZFN off-target sites. Queries can be based on the target sequence or can be expanded using degenerate specificity to account for known ZFN binding preferences. ZFN off-target sites are outputted with links to genome browsers, facilitating off-target cleavage site screening. We verified ZFN-Site using previously published ZFN half-sites and located their target sites and their previously described off-target sites. While we have tailored this tool to ZFNs, ZFN-Site can also be used to find potential off-target sites for other nucleases, such as TALE nucleases.
  
  
  CONCLUSIONS
  ZFN-Site facilitates genome searches for possible ZFN cleavage sites based on user-defined stringency limits. ZFN-Site is an improvement over other methods because the FetchGWI search engine uses an indexed search of genome sequences for all ZFN target sites and possible off-target sites matching the half-sites and stringency limits. Therefore, ZFN-Site does not miss potential off-target sites.
authors.affiliation: University of Iowa School of Medicine, Department of Internal Medicine, Iowa City, Iowa 52245, USA. tj@alum.mit.edu
authors.forename: Thomas J
authors.initials: TJ
authors.lastname: Cradick
authors.forename: Giovanna
authors.initials: G
authors.lastname: Ambrosini
authors.forename: Christian
authors.initials: C
authors.lastname: Iseli
authors.forename: Philipp
authors.initials: P
authors.lastname: Bucher
authors.forename: Anton P
authors.initials: AP
authors.lastname: McCaffrey
mesh_terms: D001483:Base Sequence; D004720:Endonucleases / Q000378:metabolism*; D016678:Genome; D006801:Humans; D011485:Protein Binding; D019713:Receptors, CCR5 / Q000235:genetics; D014584:User-Computer Interface; D016335:Zinc Fingers
chemical_list: D019713:Receptors, CCR5; D004720:Endonucleases