Includes cutting-edge methods and protocols
Provides step-by-step detail essential for reproductible results
Contains key notes and implementation advice from the experts
This volume provides readers with current methods to study RNA remodeling proteins. The methods, ranging from basic to complex, help the scientific community understand the role and fate of RNA species in cells, and their structures and interactions with other biomolecules. The book begins with two introductory chapters, followed by chapters where readers will find procedures to identify RNA remodeling proteins and their cofactors, physiological RNA targets and biological functions, and complex molecular mechanisms of action using purified components. Written in the highly successful Methods of 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 key tips on troubleshooting and avoiding known pitfalls.
Authoritative and practical, RNA Remodeling Proteins: Methods and Protocols seeks to aid scientists in the further study of this ever evolving field of proteins and mechanisms.
1. Key Points to Consider When Studying RNA Remodeling by Proteins
W. Luke Ward and Rick Russell
2. Happy Birthday: 25 years of DEAD-box Proteins
Patrick Linder and Frances Fuller-Pace
3. In vivo Cross-linking Followed by polyA Enrichment to Identify Yeast mRNA Binding Proteins
Sarah F. Mitchell and Roy Parker
4. Dynamics of the Spb4 Interactome Monitored by Affinity Purification
Juan José García-Gómez, Simon Lebaron, Yves Henry, and Jesús de la Cruz
5. Using EMOTE to Map the Exact 5'-ends of Processed RNA on a Tranillegalscriptome-wide Scale
Peter Redder
6. Cellular Localization of RNA Degradation and Processing Components in Escherichia coli
Véronique Arluison and Aziz Taghbalout
7. Recombineering Applications for the Mutational Analysis of Bacterial RNA-binding Proteins and Their Sites of Action
Nara Figueroa-Bossi and Lionello Bossi
8. Determination of RNA Chaperone Activity Using an Escherichia coli Mutant
Myung-Hee Kim and Ryozo Imai
9. Biochemical Characterization of G4 Quadruplex Telomerase RNA Unwinding by the RNA Helicase RHAU
Evan P. Booy, Ewan K.S. McRae, and Sean A. McKenna
10. ATPase Site Configuration of the RNA Helicase DbpA Probed by ENDOR Spectroscopy
Ilia Kaminker and Daniella Goldfarb
11. Bioinformatics and Biochemical Methods to Study the Structural and Functional Elements of DEAD-box RNA Helicases
Josette Banroques and N. Kyle Tanner
12. Measuring Helicase Inhibition of the DEAD-box Protein Dbp2 by Yra1
Wai Kit Ma and Elizabeth J. Tran
13. A FRET-based, Continuous Assay for the Helicase Activity of DEAD-box Proteins
Thierry Bizebard and Marc Dreyfus
14. A Fluorescence-Based Screening Assay for Identification of Hepatitis C Virus NS3 Helicase Inhibitors and Characterization of Their Inhibitory Mechanism
Atsushi Furuta, Kazi Abdus Salam, Hidenori Tani, Satoshi Tsuneda, Yuji Sekiguchi, Nobuyoshi Akimitsu, and Naohiro Noda
15. Mechanisms of HCV NS3 Helicase Monitored by Optical Tweezers
Wei Cheng
16. Constructing a Magnetic Tweezers to Monitor RNA Translocation at the Single-molecule Level
Desiree Salas, Veronika Gocheva, and Marcelo Nöllmann
17. Probing RNA Translocases with DNA
Kimberly A. Reynolds and Kevin D. Raney
18. Monitoring RNA Unwinding by the Tranillegalscription Termination Factor Rho From Mycobacterium Tuberculosis
François D´Heygère, Annie Schwartz, Franck Coste, Bertrand Castaing, and Marc Boudvillain
19. Characterization of the Mechanisms of Tranillegalscription Termination by the Helicase Sen1
Odil Porrua and Domenico Libri
20. Characterization of TRAP-mediated Regulation of the B. subtilis trp Operon Using in vitro Tranillegalscription and Tranillegalscriptional Reporter Fusions in vivo
Natalie M. McAdams and Paul Gollnick
21. Single-molecule FRET Characterization of RNA Remodeling Induced by an Antitermination Protein
Soraya Ait-Bara, Caroline Clerté, and Emmanuel Margeat
22. Fluorescence Reporters for Hfq Oligomerization and RNA Annealing
Subrata Panja and Sarah A. Woodson
23. Fluorescence Anisotropy-based Salt-titration Approach to Characterize Protein-Nucleic Acid Interactions
Tiffiny Rye-McCurdy, Ioulia Rouzina, and Karin Musier-Forsyth
24. Probing Hfq:RNA Interactions with Hydroxyl Radical and RNase Footprinting
Michael J. Ellis, Ryan S. Trussler, Joseph A. Ross, and David B. Haniford
25. Purification of Eukaryotic Exoribonucleases Following Heterologous Expression in Bacteria and Analysis of Their Biochemical Properties by in vitro Enzymatic Assays
Rafal Tomecki, Karolina Drazkowska, Antonina Krawczyk, Katarzyna Kowalska, and Andrzej Dziembowski
26. Tips and Tricks to Probe the RNA-degrading Activities of Hyperthermophilic Archaeal ?-CASP Ribonucleases
Duy Khanh Phung and Béatrice Clouet-d´Orval
This volume provides readers with current methods to study RNA remodeling proteins. The methods, ranging from basic to complex, help the scientific community understand the role and fate of RNA species in cells, and their structures and interactions with other biomolecules. The book begins with two introductory chapters, followed by chapters where readers will find procedures to identify RNA remodeling proteins and their cofactors, physiological RNA targets and biological functions, and complex molecular mechanisms of action using purified components. Written in the highly successful Methods of 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 key tips on troubleshooting and avoiding known pitfalls.
Authoritative and practical, RNA Remodeling Proteins: Methods and Protocols seeks to aid scientists in the further study of this ever evolving field of proteins and mechanisms.
Key Points to Consider When Studying RNA Remodeling by Proteins.- Happy Birthday: 25 years of DEAD-box Proteins.- In vivo Cross-linking Followed by polyA Enrichment to Identify Yeast mRNA Binding Proteins.- Dynamics of the Spb4 Interactome Monitored by Affinity Purification.- Using EMOTE to Map the Exact 5'-ends of Processed RNA on a Tranillegalscriptome-wide Scale.- Cellular Localization of RNA Degradation and Processing Components in Escherichia coli.- Recombineering Applications for the Mutational Analysis of Bacterial RNA-binding Proteins and Their Sites of Action.- Determination of RNA Chaperone Activity Using an Escherichia coli Mutant.- Biochemical Characterization of G4 Quadruplex Telomerase RNA Unwinding by the RNA Helicase RHAU.- ATPase Site Configuration of the RNA Helicase DbpA Probed by ENDOR Spectroscopy.- Bioinformatics and Biochemical Methods to Study the Structural and Functional Elements of DEAD-box RNA Helicases.- Measuring Helicase Inhibition of the DEAD-box Protein Dbp2 by Yra1.- A FRET-based, Continuous Assay for the Helicase Activity of DEAD-box Proteins.- A Fluorescence-Based Screening Assay for Identification of Hepatitis C Virus NS3 Helicase Inhibitors and Characterization of Their Inhibitory Mechanism.- Mechanisms of HCV NS3 Helicase Monitored by Optical Tweezers.- Constructing a Magnetic Tweezers to Monitor RNA Translocation at the Single-molecule Level.- Probing RNA Translocases with DNA.- Monitoring RNA Unwinding by the Tranillegalscription Termination Factor Rho From Mycobacterium Tuberculosis.- Characterization of the Mechanisms of Tranillegalscription Termination by the Helicase Sen1.- Characterization of TRAP-mediated Regulation of the B. subtilis trp Operon Using in vitro Tranillegalscription and Tranillegalscriptional Reporter Fusions in vivo.- Single-molecule FRET Characterization of RNA Remodeling Induced by an Antitermination Protein.- Fluorescence Reporters for Hfq Oligomerization and RNA Annealing.- Fluorescence Anisotropy-based Salt-titration Approach to Characterize Protein-Nucleic Acid Interactions.- Probing Hfq:RNA Interactions with Hydroxyl Radical and RNase Footprinting.- Purification of Eukaryotic Exoribonucleases Following Heterologous Expression in Bacteria and Analysis of Their Biochemical Properties by in vitro Enzymatic Assays.- Tips and Tricks to Probe the RNA-degrading Activities of Hyperthermophilic Archaeal beta-CASP Ribonucleases.
Inhaltsverzeichnis
1. Key Points to Consider When Studying RNA Remodeling by Proteins
W. Luke Ward and Rick Russell
2. Happy Birthday: 25 years of DEAD-box Proteins
Patrick Linder and Frances Fuller-Pace
3. In vivo Cross-linking Followed by polyA Enrichment to Identify Yeast mRNA Binding Proteins
Sarah F. Mitchell and Roy Parker
4. Dynamics of the Spb4 Interactome Monitored by Affinity Purification
Juan José García-Gómez, Simon Lebaron, Yves Henry, and Jesús de la Cruz
5. Using EMOTE to Map the Exact 5'-ends of Processed RNA on a Tranillegalscriptome-wide Scale
Peter Redder
6. Cellular Localization of RNA Degradation and Processing Components in Escherichia coli
Véronique Arluison and Aziz Taghbalout
7. Recombineering Applications for the Mutational Analysis of Bacterial RNA-binding Proteins and Their Sites of Action
Nara Figueroa-Bossi and Lionello Bossi
8. Determination of RNA Chaperone Activity Using an Escherichia coli Mutant
Myung-Hee Kim and Ryozo Imai
9. Biochemical Characterization of G4 Quadruplex Telomerase RNA Unwinding by the RNA Helicase RHAU
Evan P. Booy, Ewan K.S. McRae, and Sean A. McKenna
10. ATPase Site Configuration of the RNA Helicase DbpA Probed by ENDOR Spectroscopy
Ilia Kaminker and Daniella Goldfarb
11. Bioinformatics and Biochemical Methods to Study the Structural and Functional Elements of DEAD-box RNA Helicases
Josette Banroques and N. Kyle Tanner
12. Measuring Helicase Inhibition of the DEAD-box Protein Dbp2 by Yra1
Wai Kit Ma and Elizabeth J. Tran
13. A FRET-based, Continuous Assay for the Helicase Activity of DEAD-box Proteins
Thierry Bizebard and Marc Dreyfus
14. A Fluorescence-Based Screening Assay for Identification of Hepatitis C Virus NS3 Helicase Inhibitors and Characterization of Their Inhibitory Mechanism
Atsushi Furuta, Kazi Abdus Salam, Hidenori Tani, Satoshi Tsuneda, Yuji Sekiguchi, Nobuyoshi Akimitsu, and Naohiro Noda
15. Mechanisms of HCV NS3 Helicase Monitored by Optical Tweezers
Wei Cheng
16. Constructing a Magnetic Tweezers to Monitor RNA Translocation at the Single-molecule Level
Desiree Salas, Veronika Gocheva, and Marcelo Nöllmann
17. Probing RNA Translocases with DNA
Kimberly A. Reynolds and Kevin D. Raney
18. Monitoring RNA Unwinding by the Tranillegalscription Termination Factor Rho From Mycobacterium Tuberculosis
François D'Heygère, Annie Schwartz, Franck Coste, Bertrand Castaing, and Marc Boudvillain
19. Characterization of the Mechanisms of Tranillegalscription Termination by the Helicase Sen1
Odil Porrua and Domenico Libri
20. Characterization of TRAP-mediated Regulation of the B. subtilis trp Operon Using in vitro Tranillegalscription and Tranillegalscriptional Reporter Fusions in vivo
Natalie M. McAdams and Paul Gollnick
21. Single-molecule FRET Characterization of RNA Remodeling Induced by an Antitermination Protein
Soraya Ait-Bara, Caroline Clerté, and Emmanuel Margeat
22. Fluorescence Reporters for Hfq Oligomerization and RNA Annealing
Subrata Panja and Sarah A. Woodson
23. Fluorescence Anisotropy-based Salt-titration Approach to Characterize Protein-Nucleic Acid Interactions
Tiffiny Rye-McCurdy, Ioulia Rouzina, and Karin Musier-Forsyth
24. Probing Hfq:RNA Interactions with Hydroxyl Radical and RNase Footprinting
Michael J. Ellis, Ryan S. Trussler, Joseph A. Ross, and David B. Haniford
25. Purification of Eukaryotic Exoribonucleases Following Heterologous Expression in Bacteria and Analysis of Their Biochemical Properties by in vitro Enzymatic Assays
Rafal Tomecki, Karolina Drazkowska, Antonina Krawczyk, Katarzyna Kowalska, and Andrzej Dziembowski
26. Tips and Tricks to Probe the RNA-degrading Activities of Hyperthermophilic Archaeal ß-CASP Ribonucleases
Duy Khanh Phung and Béatrice Clouet-d'Orval
Klappentext
This volume provides readers with current methods to study RNA remodeling proteins. The methods, ranging from basic to complex, help the scientific community understand the role and fate of RNA species in cells, and their structures and interactions with other biomolecules. The book begins with two introductory chapters, followed by chapters where readers will find procedures to identify RNA remodeling proteins and their cofactors, physiological RNA targets and biological functions, and complex molecular mechanisms of action using purified components. Written in the highly successful Methods of 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 key tips on troubleshooting and avoiding known pitfalls.nAuthoritative and practical, RNA Remodeling Proteins: Methods and Protocols seeks to aid scientists in the further study of this ever evolving field of proteins and mechanisms.
Includes cutting-edge methods and protocols
Provides step-by-step detail essential for reproductible results
Contains key notes and implementation advice from the experts
Includes supplementary material: sn.pub/extras
