This volume provides the most current methods to study RNA remodeling proteins. Chapters detail methods, ranging from basic to complex, 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 in Molecular Biology series format, chapters include introductions to their respective topics, application details for both the expert and non-expert reader, and tips on troubleshooting and avoiding known pitfalls. Authoritative…mehr
This volume provides the most current methods to study RNA remodeling proteins. Chapters detail methods, ranging from basic to complex, 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 in Molecular Biology series format, chapters include introductions to their respective topics, application details for both the expert and non-expert reader, and tips on troubleshooting and avoiding known pitfalls.
Authoritative and cutting-edge, RNA Remodeling Proteins: Methods and Protocols, Second Edition aims to ensure successful results in the further study of this vital field.
Key Points to Consider when Studying RNA Remodeling by Proteins.- Happy Birthday : 30 Years of RNA Helicases.- Known Inhibitors of RNA Helicases and their Therapeutic Potential.- Identifying RNA Helicase Inhibitors Using Duplex Unwinding Assays.- Thermal Shift Assay for Characterizing the Stability of RNA Helicases and their Interaction with Ligands.- SRCD and FTIR Spectroscopies to Monitor Protein-induced Nucleic Acid Remodeling.- High throughput Protein-Nucleic Acid Interaction Assay Based on Protein Induced Fluorescence Enhancement.- Probing RNA Helicase Conformational Changes by Single-molecule FRET Microscopy.- A Fluorescent Assay to Monitor Ligand-Dependent Closure of the Hexameric Rho Helicase Ring.- A Simple Fluorescence Microplate Assay to Monitor RNA-DNA Hybrid Unwinding by the Bacterial Transcription Termination Factor Rho.- Monitoring Enzymatic RNA G-quadruplex Unwinding Activities by Nuclease Sensitivity and Reverse Transcription Stop Assays.- Using Magnetic Tweezers to Unravel the Mechanism of the G-quadruplex Binding and Unwinding Activities of DHX36 Helicase.- Characterization of the Brr2 RNA Helicase and its Regulation by other Spliceosomal Proteins using Gel-based U4/U6 di-snRNA Binding and Unwinding Assays.- Monitoring Acetylation of the RNA-helicase DDX3X, a Protein Critical for Formation of Stress Granules.- In vivo cross-linking Followed by polyA Enrichment to Identify Yeast mRNA Binding Proteins.- Deciphering the Dynamic Landscape of Transcription-associated mRNP quality Control Components over the Whole Yeast Genome.- Probing the Conformational State of mRNPs using smFISH and SIM.- Probing Transcriptome-wide RNA Structural Changes Dependent on the DEAD-box Helicase Dbp2.- In situ hybridization - Proximity Ligation Assay (ISH-PLA) to Study the Interaction of HIV-1 RNA and Remodeling Proteins.- RNAi Screening to Identify Factors that Control Circular RNA Localization.- A Cell-Free System for Investigating Human MARF1 Endonuclease Activity.- Monitoring eIF4E-dependent Nuclear 3' end mRNA Cleavage.- An In Vitro Approach To Study RNase III Activities Of Plant RTL Proteins.- Analysis of Bacillus subtilisRibonuclease Activity In Vivo.- Assay of Bacillus subtilis Ribonuclease Activity in vitro.- Protein Pulldown Assays to Monitor the Composition of the Bacterial RNA Degradosome.
Key Points to Consider when Studying RNA Remodeling by Proteins.- Happy Birthday : 30 Years of RNA Helicases.- Known Inhibitors of RNA Helicases and their Therapeutic Potential.- Identifying RNA Helicase Inhibitors Using Duplex Unwinding Assays.- Thermal Shift Assay for Characterizing the Stability of RNA Helicases and their Interaction with Ligands.- SRCD and FTIR Spectroscopies to Monitor Protein-induced Nucleic Acid Remodeling.- High throughput Protein-Nucleic Acid Interaction Assay Based on Protein Induced Fluorescence Enhancement.- Probing RNA Helicase Conformational Changes by Single-molecule FRET Microscopy.- A Fluorescent Assay to Monitor Ligand-Dependent Closure of the Hexameric Rho Helicase Ring.- A Simple Fluorescence Microplate Assay to Monitor RNA-DNA Hybrid Unwinding by the Bacterial Transcription Termination Factor Rho.- Monitoring Enzymatic RNA G-quadruplex Unwinding Activities by Nuclease Sensitivity and Reverse Transcription Stop Assays.- Using Magnetic Tweezers to Unravel the Mechanism of the G-quadruplex Binding and Unwinding Activities of DHX36 Helicase.- Characterization of the Brr2 RNA Helicase and its Regulation by other Spliceosomal Proteins using Gel-based U4/U6 di-snRNA Binding and Unwinding Assays.- Monitoring Acetylation of the RNA-helicase DDX3X, a Protein Critical for Formation of Stress Granules.- In vivo cross-linking Followed by polyA Enrichment to Identify Yeast mRNA Binding Proteins.- Deciphering the Dynamic Landscape of Transcription-associated mRNP quality Control Components over the Whole Yeast Genome.- Probing the Conformational State of mRNPs using smFISH and SIM.- Probing Transcriptome-wide RNA Structural Changes Dependent on the DEAD-box Helicase Dbp2.- In situ hybridization - Proximity Ligation Assay (ISH-PLA) to Study the Interaction of HIV-1 RNA and Remodeling Proteins.- RNAi Screening to Identify Factors that Control Circular RNA Localization.- A Cell-Free System for Investigating Human MARF1 Endonuclease Activity.- Monitoring eIF4E-dependent Nuclear 3' end mRNA Cleavage.- An In Vitro Approach To Study RNase III Activities Of Plant RTL Proteins.- Analysis of Bacillus subtilisRibonuclease Activity In Vivo.- Assay of Bacillus subtilis Ribonuclease Activity in vitro.- Protein Pulldown Assays to Monitor the Composition of the Bacterial RNA Degradosome.
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