-Chapters from nearly all of the top research groups in the field-Sections on zinc finger nucleases, one of the most exciting tools for gene therapy and genome engineering in the past decade
Among the many types of DNA binding domains, C2H2 zinc finger proteins (ZFPs) have proven to be the most malleable for creating custom DNA-binding proteins. In Engineered Zinc Finger Proteins: Methods and Protocols, expert researchers from some of the most active laboratories in this field present detailed methods, guidance, and perspectives. The volume contains sections covering the engineering of ZFPs, methods for the creation, evaluation, and delivery of artificial tranillegalscription factors (ATFs), methods for the creation and evaluation of zinc finger nucleases (ZFNs), and a collection of the several applications and assays beyond ATFs and ZFNs, including zinc finger transposases and ChIP-seq methodology amongst other subjects. Written in the highly successful Methods in Molecular Biology™ series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting and avoiding known pitfalls.Comprehensive and cutting-edge, Engineered Zinc Finger Proteins: Methods and Protocols aims to aid both seasoned practitioners and new investigators with its vital methods and insights as they seek to create the next generation of engineered ZFPs and applications.
Part I: Engineering Zinc Finger Proteins1. The Generation of Zinc Finger Proteins by Modular AssemblyMital S. Bhakta and David J. Segal2. Engineering Single Cys2His2 Zinc Finger Domains using a Bacterial Cell-Based Two-Hybrid Selection SystemStacey Thibodeau-Beganny, Morgan L. Maeder, and J. Keith Joung3. Bipartite Selection of Zinc Fingers by Phage Display for Any 9-bp DNA Target SiteJia-Ching Shieh4. Structure-Based DNA Binding Prediction and DesignAndreu Alibés, Luis Serrano, and Alejandro D. NadraPart II: Artificial Tranillegalscription Factors5. Generation of Cell-Permeable Artificial Zinc Finger Protein VariantsTakashi Sera6. Inhibition of Viral Tranillegalscription Using Designed Zinc Finger ProteinsKimberley A. Hoeksema and D. Lorne J. Tyrrell7. Modulation of Gene Expression Using Zinc Finger Based Artificial Tranillegalscription FactorsSabine Stolzenburg, Alan Bilsland, W. Nicol Keith, and Marianne G. Rots8. Construction of Combinatorial Libraries that Encode Zinc Finger–Based Tranillegalscription FactorsSeokjoong Kim, Eun Ji Kim, and Jin-Soo Kim9. Silencing of Gene Expression by Targeted DNA Methylation: Concepts and ApproachesRenata Z. Jurkowska and Albert Jeltsch10. Remodeling Genomes with Artificial Tranillegalscription Factors (ATFs)Adriana S. Beltran and Pilar Blancafort11. Transgenic Mice Expressing an Artificial Zinc Finger Regulator Targeting an Endogenous GeneClaudio Passananti, Nicoletta Corbi, Annalisa Onori, Maria Grazia Di Certo, and Elisabetta MatteiPart III: Zinc Finger Nucleases12. Artificial Zinc Finger Nucleases for DNA CloningVardit Zeevi, Andriy Tovkach, and Tzvi Tzfira13. In Vitro Assessment of Zinc-Finger Nuclease ActivityToni Cathomen and Cem Söllü14. Assessing Zinc Finger Nuclease-Associated ToxicityTatjana I. Cornu and Toni Cathomen15. A Rapid and General Assay for Monitoring Endogenous Gene ModificationDmitry Y. Guschin, Adam J. Waite, George E. Katibah, Jeffrey C. Miller, Michael C. Holmes, andEdward J. Rebar16. Engineered Zinc Finger Proteins for Manipulation of the Human Mitochondrial GenomeMichal Minczuk17. High Efficiency Gene Targeting in Drosophila with Zinc Finger NucleasesDana Carroll, Kelly J. Beumer, and Jonathan K. Trautman18. Using Zinc Finger Nucleases for Efficient and Heritable Gene Disruption in ZebrafishJasmine M. McCammon and Sharon L. Amacher19. A Transient Assay for Monitoring Zinc Finger Nuclease Activity at Endogenous Plant Gene TargetsJustin P. Hoshaw, Erica Unger-Wallace, Feng Zhang, and Daniel F. Voytas20. Validation and Expression of Zinc Finger Nucleases in Plant CellsAndriy Tovkach, Vardit Zeevi, and Tzvi Tzfira21. Non-FokI-Based Zinc Finger NucleasesMiki Imanishi, Shigeru Negi, and Yukio SugiuraPart IV: Beyond Tranillegalscription and Cleavage22. Designing and Testing Chimeric Zinc Finger TransposasesMatthew 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 Ghosh24. Zinc Finger-Mediated Live Cell Imaging in Arabidopsis RootsBeatrice I. Lindhout, Tobias Meckel, and Bert J. van der Zaal25. Biophysical Analysis of the Interaction of Toxic Metal Ions and Oxidants with the Zinc Finger Domain of XPAAndrea Hartwig, Tanja Schwerdtle, and Wojciech Bal26. Preparation and Zinc-Binding Properties of Multi-Fingered Zinc-Sensing DomainsJohn H. Laity and Linda S. Feng27. Using ChIP-seq Technology to Identify Targets of Zinc Finger Tranillegalscription FactorsHenriette O´Geen, Seth Frietze, and Peggy J. Farnham28. Crystallization of Zinc Finger Proteins Bound to DNANancy C. Horton and Chad K. Park29. Beyond DNA: Zinc Finger Domains as RNA-Binding ModulesJosep Font and Joel P. Mackay
In this book, experts from some of the most active laboratories present detailed methods, guidance, and perspectives. It includes coverage of zinc finger nucleases, one of the most exciting tools for gene therapy and genome engineering in the past decade.
Among the many types of DNA binding domains, C2H2 zinc finger proteins (ZFPs) have proven to be the most malleable for creating custom DNA-binding proteins. In Engineered Zinc Finger Proteins: Methods and Protocols, expert researchers from some of the most active laboratories in this field present detailed methods, guidance, and perspectives. The volume contains sections covering the engineering of ZFPs, methods for the creation, evaluation, and delivery of artificial tranillegalscription factors (ATFs), methods for the creation and evaluation of zinc finger nucleases (ZFNs), and a collection of the several applications and assays beyond ATFs and ZFNs, including zinc finger transposases and ChIP-seq methodology amongst other subjects. Written in the highly successful Methods in Molecular Biology(TM) series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting and avoiding known pitfalls.Comprehensive and cutting-edge, Engineered Zinc Finger Proteins: Methods and Protocols aims to aid both seasoned practitioners and new investigators with its vital methods and insights as they seek to create the next generation of engineered ZFPs and applications.
Engineering Zinc Finger Proteins.- The Generation of Zinc Finger Proteins by Modular Assembly.- Engineering Single Cys2His2 Zinc Finger Domains Using a Bacterial Cell-Based Two-Hybrid Selection System.- Bipartite Selection of Zinc Fingers by Phage Display for Any 9-bp DNA Target Site.- Structure-Based DNA-Binding Prediction and Design.- Artificial Tranillegalscription Factors.- Generation of Cell-Permeable Artificial Zinc Finger Protein Variants.- Inhibition of Viral Tranillegalscription Using Designed Zinc Finger Proteins.- Modulation of Gene Expression Using Zinc Finger-Based Artificial Tranillegalscription Factors.- Construction of Combinatorial Libraries that Encode Zinc Finger-Based Tranillegalscription Factors.- Silencing of Gene Expression by Targeted DNA Methylation: Concepts and Approaches.- Remodeling Genomes with Artificial Tranillegalscription Factors (ATFs).- Transgenic Mice Expressing an Artificial Zinc Finger Regulator Targeting an Endogenous Gene.- Zinc Finger Nucleases.- Artificial Zinc Finger Nucleases for DNA Cloning.- In Vitro Assessment of Zinc Finger Nuclease Activity.- Quantification of Zinc Finger Nuclease-Associated Toxicity.- A Rapid and General Assay for Monitoring Endogenous Gene Modification.- Engineered Zinc Finger Proteins for Manipulation of the Human Mitochondrial Genome.- High-Efficiency Gene Targeting in Drosophila with Zinc Finger Nucleases.- Using Zinc Finger Nucleases for Efficient and Heritable Gene Disruption in Zebrafish.- A Transient Assay for Monitoring Zinc Finger Nuclease Activity at Endogenous Plant Gene Targets.- Validation and Expression of Zinc Finger Nucleases in Plant Cells.- Non-FokI-Based Zinc Finger Nucleases.- Beyond Tranillegalscription and Cleavage.- Designing and Testing Chimeric Zinc Finger Transposases.- Seeing Genetic and Epigenetic Information Without DNA Denaturation Using Sequence-Enabled Reassembly (SEER).- Zinc Finger-Mediated Live Cell Imaging in Arabidopsis Roots.- Biophysical Analysis of the Interaction of Toxic Metal Ions and Oxidants with the Zinc Finger Domain of XPA.- Preparation and Zinc-Binding Properties of Multi-Fingered Zinc-Sensing Domains.- Using ChIP-seq Technology to Identify Targets of Zinc Finger Tranillegalscription Factors.- Crystallization of Zinc Finger Proteins Bound to DNA.- Beyond DNA: Zinc Finger Domains as RNA-Binding Modules.
Inhaltsverzeichnis
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 Alibés, Luis Serrano, and Alejandro D. Nadra
Part II: Artificial Tranillegalscription Factors
5. Generation of Cell-Permeable Artificial Zinc Finger Protein Variants
Takashi Sera
6. Inhibition of Viral Tranillegalscription Using Designed Zinc Finger Proteins
Kimberley A. Hoeksema and D. Lorne J. Tyrrell
7. Modulation of Gene Expression Using Zinc Finger Based Artificial Tranillegalscription Factors
Sabine Stolzenburg, Alan Bilsland, W. Nicol Keith, and Marianne G. Rots
8. Construction of Combinatorial Libraries that Encode Zinc Finger-Based Tranillegalscription 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 Tranillegalscription 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 Söllü
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 Tranillegalscription 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 Tranillegalscription 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
Klappentext
Among the many types of DNA binding domains, C2H2 zinc finger proteins (ZFPs) have proven to be the most malleable for creating custom DNA-binding proteins. In Engineered Zinc Finger Proteins: Methods and Protocols, expert researchers from some of the most active laboratories in this field present detailed methods, guidance, and perspectives. The volume contains sections covering the engineering of ZFPs, methods for the creation, evaluation, and delivery of artificial tranillegalscription factors (ATFs), methods for the creation and evaluation of zinc finger nucleases (ZFNs), and a collection of the several applications and assays beyond ATFs and ZFNs, including zinc finger transposases and ChIP-seq methodology amongst other subjects. Written in the highly successful Methods in Molecular Biology(TM) series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting and avoiding known pitfalls.
Comprehensive and cutting-edge, Engineered Zinc Finger Proteins: Methods and Protocols aims to aid both seasoned practitioners and new investigators with its vital methods and insights as they seek to create the next generation of engineered ZFPs and applications.
Chapters from nearly all of the top research groups in the field
Sections on zinc finger nucleases, one of the most exciting tools for gene therapy and genome engineering in the past decade
Includes supplementary material: sn.pub/extras
