Engineered Zinc Finger Proteins: Methods and Protocols

Part I: Engineering Zinc Finger Proteins 1. The Generation of Zinc Finger Proteins by Modular Assembly Mital S. Bhakta and David J. Segal 2. Engineering Single Cys2His2 Zinc Finger Domains using a Bacterial Cell-Based Two-Hybrid Selection System Stacey Thibodeau-Beganny, Morgan L. Maeder, and J. Keith Joung 3. Bipartite Selection of Zinc Fingers by Phage Display for Any 9-bp DNA Target Site Jia-Ching Shieh 4. Structure-Based DNA Binding Prediction and Design Andreu Alib?s, Luis Serrano, and Alejandro D. Nadra Part II: Artificial Transcription Factors 5. Generation of Cell-Permeable Artificial Zinc Finger Protein Variants Takashi Sera 6. Inhibition of Viral Transcription Using Designed Zinc Finger Proteins Kimberley A. Hoeksema and D. Lorne J. Tyrrell 7. Modulation of Gene Expression Using Zinc Finger Based Artificial Transcription Factors Sabine Stolzenburg, Alan Bilsland, W. Nicol Keith, and Marianne G. Rots 8. Construction of Combinatorial Libraries that Encode Zinc Finger-Based Transcription Factors Seokjoong Kim, Eun Ji Kim, and Jin-Soo Kim 9. Silencing of Gene Expression by Targeted DNA Methylation: Concepts and Approaches Renata Z. Jurkowska and Albert Jeltsch 10. Remodeling Genomes with Artificial Transcription Factors (ATFs) Adriana S. Beltran and Pilar Blancafort 11. Transgenic Mice Expressing an Artificial Zinc Finger Regulator Targeting an Endogenous Gene Claudio Passananti, Nicoletta Corbi, Annalisa Onori, Maria Grazia Di Certo, and Elisabetta Mattei Part III: Zinc Finger Nucleases 12. Artificial Zinc Finger Nucleases for DNA Cloning Vardit Zeevi, Andriy Tovkach, and Tzvi Tzfira 13. In Vitro Assessment of Zinc-Finger Nuclease Activity Toni Cathomen and Cem S?ll? 14. Assessing Zinc Finger Nuclease-Associated Toxicity Tatjana I. Cornu and Toni Cathomen 15. A Rapid and General Assay for Monitoring Endogenous Gene Modification Dmitry Y. Guschin, Adam J. Waite, George E. Katibah, Jeffrey C. Miller, Michael C. Holmes, andEdward J. Rebar 16. Engineered Zinc Finger Proteins for Manipulation of the Human Mitochondrial Genome Michal Minczuk 17. High Efficiency Gene Targeting in Drosophila with Zinc Finger Nucleases Dana Carroll, Kelly J. Beumer, and Jonathan K. Trautman 18. Using Zinc Finger Nucleases for Efficient and Heritable Gene Disruption in Zebrafish Jasmine M. McCammon and Sharon L. Amacher 19. A Transient Assay for Monitoring Zinc Finger Nuclease Activity at Endogenous Plant Gene Targets Justin P. Hoshaw, Erica Unger-Wallace, Feng Zhang, and Daniel F. Voytas 20. Validation and Expression of Zinc Finger Nucleases in Plant Cells Andriy Tovkach, Vardit Zeevi, and Tzvi Tzfira 21. Non-FokI-Based Zinc Finger Nucleases Miki Imanishi, Shigeru Negi, and Yukio Sugiura Part IV: Beyond Transcription and Cleavage 22. Designing and Testing Chimeric Zinc Finger Transposases Matthew H. Wilson and Alfred L. George, Jr. 23. Seeing Genetic and Epigenetic Information without DNA Denaturation Using Sequence Enabled Reassembly (SEER) Jason R. Porter, Sarah H. Lockwood, Mital S. Bhakta, David J. Segal, and Indraneel Ghosh 24. Zinc Finger-Mediated Live Cell Imaging in Arabidopsis Roots Beatrice I. Lindhout, Tobias Meckel, and Bert J. van der Zaal 25. Biophysical Analysis of the Interaction of Toxic Metal Ions and Oxidants with the Zinc Finger Domain of XPA Andrea Hartwig, Tanja Schwerdtle, and Wojciech Bal 26. Preparation and Zinc-Binding Properties of Multi-Fingered Zinc-Sensing Domains John H. Laity and Linda S. Feng 27. Using ChIP-seq Technology to Identify Targets of Zinc Finger Transcription Factors Henriette O'Geen, Seth Frietze, and Peggy J. Farnham 28. Crystallization of Zinc Finger Proteins Bound to DNA Nancy C. Horton and Chad K. Park 29. Beyond DNA: Zinc Finger Domains as RNA-Binding Modules Josep Font and Joel P. Mackay