ZiFiT Targeter Version 4.2

The ZiFiT Targeter software package is designed to aid research in the application of gene editing and expression technologies. ZiFiT identifies potential target sites in DNA sequences for several DNA binding platforms using publicly available reagents and protocols including:

1. CRISPR/Cas clustered regularly interspaced short palindromic repeats/CRISPR-associated systems
2. TALEs transcription activator-like effector proteins
3. ZFs zinc finger proteins

ZiFiT was originally developed by the Zinc Finger Consortium as a tool for enabling identification of potential zinc finger nulcease (ZFN) sites in specific target sequences. In this update of ZiFiT, we provide support for the identification of CRISPR/Cas taget sites and reagents and user-friendly guidance for construction of guide RNA plasmids as well as updated support for TALE engineering including FLASH TALE assembly and sequence analysis (Hwang and Fu et al., Nat Biotechnol. 2013)

As in previous versions of ZiFiT (Version 4.1), we continue to provide support for TALEs using assembly protocols described by the Joung lab (Sander et al., Nat Biotechnol. 2012, Reyon et al. 2012 Nat Biotechnol, Reyon et al. 2012 Current Protocols in Molecular Biology). ZiFiT generates intuitive and easy-to-follow graphical overviews that guide users through an assembly process for TALEN-encoding plasmids that requires only standard restriction digestion and ligation to practice. All plasmids required to practice this method are available on a dedicated webpage provided by the non-profit plasmid distribution service Addgene (http://www.addgene.org/talengineering). ZiFiT also continues to support Zinc Finger Engineering (Versions 3.2 & 3.3) for the CoDA (Context-Dependent Assembly; Sander et al., Nat. Methods 2011) and OPEN (Oligomerized Pool Engineering; Maeder et al., Mol Cell 2008) design methods developed by Keith Joung's lab at the Massachusetts General Hospital and Harvard Medical School.

ZiFiT Targeter is necessarily dynamic, and we encourage you to check back as the software improves. Furthermore, after trying your hand at ZiFiT, we welcome feedback to improve the program and its ease of use. For questions or suggestions pertaining to this website and ZiFiT, please contact: Deepak.Reyon@gmail.com, JSander@alumni.iastate.edu (or) JJoung@mgh.harvard.edu

If you use ZiFiT please reference:

Sander, J.D., Zaback, P.Z., Joung, J.K., Voytas, D.F., Dobbs, D. (2007) Zinc Finger Targeter (ZiFiT): an engineered zinc finger/target site design tool. Nucleic Acids Research, 35, W599-605;

Sander, J.D., Maeder, M.L., Reyon, D., Voytas, D.F., Joung, J.K., Dobbs, D. (2010) ZiFiT (Zinc Finger Targeter): an updated zinc finger engineering tool. Nucleic Acids Research, 38:W462-468;

This material is based upon work supported by:

The National Institutes of Health (DP1OD006862, T32CA009216, R01 GM088040, R01 GM069906)

The National Science Foundation under Grant No. DBI0501678 and DBI 0923827

Iowa State University: Center for Integrated Animal Genomics (CIAG)

Any opinions, findings and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Institutes of Health or the National Science Foundation.