Includes cutting-edge methods and protocols
Provides step-by-step detail essential for reproducible results
Contains key notes and implementation advice from the experts
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 from standard 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.
1. Investigating CRISPR RNA Biogenesis and Function using RNA-seq
Nadja Heidrich, Gaurav Dugar, Jörg Vogel, and Cynthia M. Sharma
2. In vitro Co-reconstitution of Cas Protein Complexes
André Plagens and Lennart Randau
3. Analysis of CRISPR pre-crRNA Cleavage
Erin L. Garside and Andrew M. MacMillan
4. Annotation and Classification of CRISPR-Cas Systems
Kira S. Makarova and Eugene V. Koonin
5. Computational Detection of CRISPR/crRNA Targets
Ambarish Biswas, Peter C. Fineran, and Chris M. Brown
6. High-throughput CRISPR typing of Mycobacterium tuberculosis Complex and Salmonella enterica Serotype Typhimurium
Christophe Sola, Edgar Abadia, Simon Le Hello, and François-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 CRISPR
Alexandra 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
Cristóbal Almendros and Francisco J.M. Mojica
11. Electrophoretic Mobility Shift Assay of DNA and CRISPR-Cas Ribonucleoprotein Complexes
Tim Künne, 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 White
13. Procedures for Generating CRISPR Mutants With Novel Spacers Acquired from Viruses Or Plasmids
Marie-Ève Dupuis, Rodolphe Barrangou, and Sylvain Moineau
14. Archaeal Viruses of the Sulfolobales: Isolation, Infection, and CRISPR Spacer Acquisition
Susanne Erdmann and Roger A. Garrett
15. Using the CRISPR-Cas system to Positively Select Mutants In Genes Essential for its Function
Ido Yosef, Moran G. Goren, Rotem Edgar, and Udi Qimron
16. Analysis of Nuclease Activity of Cas1 Proteins Against Complex DNA Substrates
Natalia Beloglazova, Sofia Lemak, Robert Flick, and Alexander F. Yakunin
17. Characterizing Metal-Dependent Nucleases of CRISPR-Cas prokaryotic Adaptive Immunity Systems
Ki H. Nam, Matthew P. DeLisa, and Ailong Ke
18. Cas3 Nuclease-Helicase Activity Assays
Tomas Sinkunas, Giedrius Gasiunas, and Virginijus Siksnys
19. Chemical and Enzymatic Footprint Analyses of R-loop Formation by Cascade-crRNA Complex
Ümit Pul
20. Creation and Analysis of a Virome: Using CRISPR Spacers
Michelle Davison and Devaki Bhaya
21. Targeted Mutagenesis in Zebrafish using CRISPR RNA-guided Nucleases
Woong 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 Cas9
Scott J. Gratz, Melissa M. Harrison, Jill Wildonger, and Kate M. O´Connor-Giles
23. Targeted Tranillegalscriptional Repression in Bacteria using CRISPR Interference (CRISPRi)
John S. Hawkins, Spencer Wong, Jason M. Peters, Ricardo Almeida, and Lei S. Qi
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 from standard 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.
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 from standard 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.
Investigating CRISPR RNA Biogenesis and Function using RNA-seq.- In vitro Co-reconstitution of Cas Protein Complexes.- Analysis of CRISPR pre-crRNA Cleavage.- Annotation and Classification of CRISPR-Cas Systems.- Computational Detection of CRISPR/crRNA Targets.- High-throughput CRISPR typing of Mycobacterium tuberculosis Complex and Salmonella enterica Serotype Typhimurium.- Spacer-based Macroarrays for CRISPR Genotyping.- Analysis of crRNA using Liquid Chromatography Electrospray Ionisation Mass Spectrometry (LC ESI MS).- Rapid Multiplex Creation of Escherichia coli Strains Capable of Interfering with Phage Infection through CRISPR.- Exploring CRISPR Interference by Transformation with Plasmid Mixtures: Identification Of Target Interference Motifs in Escherichia coli.- Electrophoretic Mobility Shift Assay of DNA and CRISPR-Cas Ribonucleoprotein Complexes.- Expression and Purification of the CMR (Type III-B) Complex in Sulfolobus solfataricus.- Procedures for Generating CRISPR Mutants With Novel Spacers Acquired from Viruses Or Plasmids .- Archaeal Viruses of the Sulfolobales: Isolation, Infection, and CRISPR Spacer Acquisition.- Using the CRISPR-Cas system to Positively Select Mutants In Genes Essential for its Functionl.- Analysis of Nuclease Activity of Cas1 Proteins Against Complex DNA Substrates.- Characterizing Metal-Dependent Nucleases of CRISPR-Cas prokaryotic Adaptive Immunity Systems.- Cas3 Nuclease-Helicase Activity Assays.- Chemical and Enzymatic Footprint Analyses of R-loop Formation by Cascade-crRNA Complex.- Creation andAnalysis of a Virome: Using CRISPR Spacers.- Targeted Mutagenesis in Zebrafish using CRISPR RNA-guided Nucleases.- Precise Genome Editing of Drosophila with CRISPR RNA-guided Cas9.- Targeted Tranillegalscriptional Repression in Bacteria using CRISPR Interference (CRISPRi).
Inhaltsverzeichnis
1. Investigating CRISPR RNA Biogenesis and Function using RNA-seq
Nadja Heidrich, Gaurav Dugar, Jörg Vogel, and Cynthia M. Sharma
2. In vitro Co-reconstitution of Cas Protein Complexes
André Plagens and Lennart Randau
3. Analysis of CRISPR pre-crRNA Cleavage
Erin L. Garside and Andrew M. MacMillan
4. Annotation and Classification of CRISPR-Cas Systems
Kira S. Makarova and Eugene V. Koonin
5. Computational Detection of CRISPR/crRNA Targets
Ambarish Biswas, Peter C. Fineran, and Chris M. Brown
6. High-throughput CRISPR typing of Mycobacterium tuberculosis Complex and Salmonella enterica Serotype Typhimurium
Christophe Sola, Edgar Abadia, Simon Le Hello, and François-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 CRISPR
Alexandra 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
Cristóbal Almendros and Francisco J.M. Mojica
11. Electrophoretic Mobility Shift Assay of DNA and CRISPR-Cas Ribonucleoprotein Complexes
Tim Künne, 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 White
13. Procedures for Generating CRISPR Mutants With Novel Spacers Acquired from Viruses Or Plasmids
Marie-Ève Dupuis, Rodolphe Barrangou, and Sylvain Moineau
14. Archaeal Viruses of the Sulfolobales: Isolation, Infection, and CRISPR Spacer Acquisition
Susanne Erdmann and Roger A. Garrett
15. Using the CRISPR-Cas system to Positively Select Mutants In Genes Essential for its Function
Ido Yosef, Moran G. Goren, Rotem Edgar, and Udi Qimron
16. Analysis of Nuclease Activity of Cas1 Proteins Against Complex DNA Substrates
Natalia Beloglazova, Sofia Lemak, Robert Flick, and Alexander F. Yakunin
17. Characterizing Metal-Dependent Nucleases of CRISPR-Cas prokaryotic Adaptive Immunity Systems
Ki H. Nam, Matthew P. DeLisa, and Ailong Ke
18. Cas3 Nuclease-Helicase Activity Assays
Tomas Sinkunas, Giedrius Gasiunas, and Virginijus Siksnys
19. Chemical and Enzymatic Footprint Analyses of R-loop Formation by Cascade-crRNA Complex
Ümit Pul
20. Creation and Analysis of a Virome: Using CRISPR Spacers
Michelle Davison and Devaki Bhaya
21. Targeted Mutagenesis in Zebrafish using CRISPR RNA-guided Nucleases
Woong 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 Cas9
Scott J. Gratz, Melissa M. Harrison, Jill Wildonger, and Kate M. O'Connor-Giles
23. Targeted Tranillegalscriptional Repression in Bacteria using CRISPR Interference (CRISPRi)
John S. Hawkins, Spencer Wong, Jason M. Peters, Ricardo Almeida, and Lei S. Qi
Klappentext
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 from standard 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.
Includes cutting-edge methods and protocols
Provides step-by-step detail essential for reproducible results
Contains key notes and implementation advice from the experts
