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Full Description
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 transcription 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.
Contents
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 Transcription Factors.- Generation of Cell-Permeable Artificial Zinc Finger Protein Variants.- Inhibition of Viral Transcription Using Designed Zinc Finger Proteins.- Modulation of Gene Expression Using Zinc Finger-Based Artificial Transcription Factors.- Construction of Combinatorial Libraries that Encode Zinc Finger-Based Transcription Factors.- Silencing of Gene Expression by Targeted DNA Methylation: Concepts and Approaches.- Remodeling Genomes with Artificial Transcription 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 Transcription 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 Transcription Factors.- Crystallization of Zinc Finger Proteins Bound to DNA.- Beyond DNA: Zinc Finger Domains as RNA-Binding Modules.
