RNA - Ligand Interactions, Part A: Structural Biology Methods: Structural Biology Methods
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Table of contents
- Table of Contentsv
- Contributors to Volume 317ix
- Prefacexiii
- Volumes in Seriesxv
- Section I: Semisynthetic Methodologies1
- A. RNA Synthetic Methods1
- Chapter 1. Advanced 5' -Silyl-2' -Orthoester Approach to RNA Oligonucleotide Synthesis3
- Chapter 2. Preparation of Specifically 2H- and 13C-Labeled Ribonucleotides18
- Chapter 3. Base-Modified Phosphoramidite Analogs of Pyrimidine Ribonucleosides for RNA Structure–39
- B. Derivatization of RNA1
- Chapter 4. Use of T7 RNA Polymerase and Its Mutants for Incorporation of Nucleoside Analogs into RNA65
- Chapter 5. Phosphorothioate Modification of RNA for Stereochemical and Interference Analyses74
- Chapter 6. Chemical Probing of RNA by Nucleotide Analog Interference Mapping92
- Chapter 7. Joining of RNAs by Splinted Ligation109
- Chapter 8. Heavy Atom Derivatives of RNA124
- Chapter 9. Site-Specific Cleavage of Transcript RNA132
- Chapter 10. Using DNAzymes to Cut, Process, and Map RNA Molecules for Structural Studies or Modifica140
- Section II: RNA Structure Determination147
- A. X-Ray Crystallography149
- Chapter 11. Purification, Crystallization, and X-Ray Diffraction Analysis of Small Ribozymes149
- Chapter 12. Solving Large RNA Structures by X-Ray Crystallography169
- Chapter 13. Conventional and Time-Resolved Ribozyme X-Ray Crystallography180
- B. Nuclear Magnetic Resonance Spectroscopy198
- Chapter 14. Nuclear Magnetic Resonance Methods to Study RNA–Protein Complexes198
- Chapter 15. Filamentous Bacteriophage for Aligning RNA, DNA, and Proteins for Measurement of Nuclear220
- Chapter 16. Biochemical and Nuclear Magnetic Resonance Studies of Aminoglycoside–RNA Complexes240
- C. Electron Microscopy261
- Chapter 17. Experimental Prerequisites for Determination of tRNA Binding to Ribosomes from Escherich261
- Chapter 18. Three-Dimensional Cryoelectron Microscopy of Ribosomes276
- Chapter 19. Preparation of Functional Ribosomal Complexes and Effect of Buffer Conditions on tRNA Po292
- Section III: Techniques for Monitoring RNA Conformation and Dynamics311
- A. Solution Methods313
- Chapter 20. Probing RNA Structure and Function by Circular Permutation313
- Chapter 21. Kinetic Oligonucleotide Hybridization for Monitoring Kinetic Folding of Large RNAs330
- Chapter 22. Time-Resolved Synchrotron X-Ray Footprinting and Its Application to RNA Folding353
- B. Electrophoretic and Spectroscopic Methods368
- Chapter 23. Analysis of Global Conformation of Branched RNA Species Using Electrophoresis and Fluore368
- Chapter 24. Application of Circular Dichroism to Study RNA Folding Transitions393
- Chapter 25. Fluorescence Assays to Study Structure, Dynamics, and Function of RNA and RNA–Ligand C409
- Chapter 26. Transient Electric Birefringence for Determining Global Conformations of Nonhelix Elemen440
- Section IV: Modeling Tertiary Structure455
- Chapter 27. Structure–Function Relationships of RNA: A Modeling Approach457
- Chapter 28. Computational Modeling of Structural Experimental Data470
- Chapter 29. Modeling RNA Tertiary Structure from Patterns of Sequence Variation491
- Author Index511
- Subject Index533
RNA-Ligand Interactions, Part A focuses on structural biology methods. Major topics covered include semisynthetic methodologies (RNA synthetic methods and derivatization of RNA); RNA structure determination (X-ray crystallography, NMR, EM); techniques for monitoring RNA conformation and dynamics (solution methods and electrophoretic and spectroscopic methods); and modeling tertiary structure: Part B, its companion Volume 318 of Methods in Enzymology, focuses on molecular biology methods.
The critically acclaimed laboratory standard for more than forty years, Methods in Enzymology is one of the most highly respected publications in the field of biochemistry. Since 1955, each volume has been eagerly awaited, frequently consulted, and praised by researchers and reviewers alike. Now with more than 300 volumes (all of them still in print), the Series contains much material still relevant today--truly an essential publication for researchers in all fields of life sciences.
The critically acclaimed laboratory standard for more than forty years, Methods in Enzymology is one of the most highly respected publications in the field of biochemistry. Since 1955, each volume has been eagerly awaited, frequently consulted, and praised by researchers and reviewers alike. Now with more than 300 volumes (all of them still in print), the Series contains much material still relevant today--truly an essential publication for researchers in all fields of life sciences.