Boudvillain RNA Remodeling Proteins

Methods and Protocols
2015
ISBN: 978-1-4939-2214-7
Verlag: Springer US
Format: PDF
Kopierschutz: 1 - PDF Watermark

E-Book, Englisch, Band 1259, 470 Seiten, eBook

Reihe: Methods in Molecular Biology

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.

Zielgruppe

Professional/practitioner

Autoren/Hrsg.

Boudvillain, Marc

Inhaltsverzeichnis

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 Transcriptome-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 Transcription Termination Factor Rho From Mycobacterium Tuberculosis.- Characterization of the Mechanisms of Transcription Termination by the Helicase Sen1.- Characterization of TRAP-mediated Regulation of the B. subtilis trp Operon Using in vitro Transcription and Transcriptional 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 ß-CASP Ribonucleases.