CRISPR: Methods and Protocols - Methods in Molecular Biology 2015 edition

Jacket Description/Back: This volume presents a list of cutting-edge protocols for the study of CRISPR-Cas defense systems and their applications at the genomic, genetic, biochemical and structural levels."CRISPR: Methods and Protocols"guides readers through techniques that have been developed specifically for the analysis of CRISPR-Cas and techniques adapted fromstandard protocols of DNA, RNA and protein biology. 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 tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, """CRISPR: Methods and Protocols"provides a broad list of tools and techniques to study the interdisciplinary aspects of the prokaryotic CRISPR-Cas defense systems."Table of Contents:1. Investigating CRISPR RNA Biogenesis and Function using RNA-seqNadja Heidrich, Gaurav Dugar, Jorg Vogel, and Cynthia M. Sharma 2. "In vitro" Co-reconstitution of Cas Protein ComplexesAndre Plagens and Lennart Randau 3. Analysis of CRISPR pre-crRNA CleavageErin L. Garside and Andrew M. MacMillan 4. Annotation and Classification of CRISPR-Cas SystemsKira S. Makarova and Eugene V. Koonin 5. Computational Detection of CRISPR/crRNA TargetsAmbarish Biswas, Peter C. Fineran, and Chris M. Brown 6. High-throughput CRISPR typing of "Mycobacterium tuberculosis" Complex and "Salmonella enterica" Serotype TyphimuriumChristophe Sola, Edgar Abadia, Simon Le Hello, and Francois-Xavier Weill 7. Spacer-based Macroarrays for CRISPR Genotyping Igor Mokrousov and Nalin Rastogi 8. Analysis of crRNA using Liquid Chromatography Electrospray Ionisation Mass Spectrometry (LC ESI MS) Sakharam P. Waghmare, Alison O. Nwokeoji, and Mark J. Dickman 9. Rapid Multiplex Creation of "Escherichia coli "Strains Capable of Interfering with Phage Infection through CRISPRAlexandra Strotskaia, Ekaterina Semenova, Ekaterina Savitskaya, and Konstantin Severinov 10. Exploring CRISPR Interference by Transformation with Plasmid Mixtures: Identification Of Target Interference Motifs in "Escherichia coli"Cristobal Almendros and Francisco J. M. Mojica 11. Electrophoretic Mobility Shift Assay of DNA and CRISPR-Cas Ribonucleoprotein ComplexesTim Kunne, Edze R. Westra, and Stan J. J. Brouns 12. Expression and Purification of the CMR (Type III-B) Complex in "Sulfolobus solfataricus"Jing Zhang and Malcolm F White13. Procedures for Generating CRISPR Mutants With Novel Spacers Acquired from Viruses Or Plasmids Marie-Eve Dupuis, Rodolphe Barrangou, and Sylvain Moineau 14. Archaeal Viruses of the Sulfolobales: Isolation, Infection, and CRISPR Spacer AcquisitionSusanne Erdmann and Roger A. Garrett15. Using the CRISPR-Cas system to Positively Select Mutants In Genes Essential for its FunctionIdo Yosef, Moran G. Goren, Rotem Edgar, and Udi Qimron 16. Analysis of Nuclease Activity of Cas1 Proteins Against Complex DNA SubstratesNatalia Beloglazova, Sofia Lemak, Robert Flick, and Alexander F. Yakunin 17. Characterizing Metal-Dependent Nucleases of CRISPR-Cas prokaryotic Adaptive Immunity SystemsKi H. Nam, Matthew P. DeLisa, and Ailong Ke 18. Cas3 Nuclease-Helicase Activity AssaysTomas Sinkunas, Giedrius Gasiunas, and Virginijus Siksnys 19. Chemical and Enzymatic Footprint Analyses of R-loop Formation by Cascade-crRNA ComplexUmit Pul 20. Creation and Analysis of a Virome: Using CRISPR SpacersMichelle Davison and Devaki Bhaya 21. Targeted Mutagenesis in Zebrafish using CRISPR RNA-guided NucleasesWoong Y Hwang, Yanfang Fu, Deepak Reyon, Andrew PW Gonzales, J Keith Joung, and Jing-Ruey Joanna Yeh 22. Precise Genome Editing of Drosophila with CRISPR RNA-guided Cas9Scott J. Gratz, Melissa M. Harrison, Jill Wildonger, and Kate M. O Connor-Giles 23. Targeted Transcriptional Repression in Bacteria using CRISPR Interference (CRISPRi) John S. Hawkins, Spencer Wong, Jason M. Peters, Ricardo Almeida, and Lei S. Qi"