Structures of large RNA molecules and their complexes
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| Format: | Buch |
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| Sprache: | English |
| Veröffentlicht: |
Amsterdam [u.a.]
Elesevier, Acad. Press
2015
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| Ausgabe: | 1. ed. |
| Schriftenreihe: | Methods in enzymology
558 |
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Datensatz im Suchindex
| _version_ | 1804174784553025536 |
|---|---|
| adam_text | Titel: Structures of large RNA molecules and their complexes
Autor: Woodson, Sarah A
Jahr: 2015
CONTENTS
Contributors
Preface
Section I
RNA Structure and Dynamics
1. Native Purification and Analysis of Long RNAs
Isabel Chillön, Marco Marcia, Michal Legiewicz, Fei Liu, Srinivas Somarowthu,
and Anna Marie Pyle
1. Introduction
2. Native Purification of Long Noncoding RNAs
3. Study of the RNA Tertiary Folding by Sedimentation Velocity
Analytical Ultracentrifugation
4. Analysis of the RNA Tertiary Folding by Analytical Size-Exclusion
Chromatography
5. Determination of the Secondary Structure of LncRNAs by
Chemical Probing
Acknowledgments
References
2. Characterizing RNA Excited States Using NMR Relaxation
Dispersion
Yi Xue, Dawn Kellogg, Isaac J. Kimsey, Bharathwaj Sathyamoorthy,
Zachary W. Stein, Mitchell McBrairty, and Hashim M. Al-Hashimi
1. Introduction
2. NMR Relaxation Dispersion
3. General Protocol for Characterizing RNA ESs Using Low-to-High
SL Field 13C and 15N Off-Resonance NMR R]p and Uniformly
Labeled Nucleic Acid Samples
Acknowledgments
References
3. Quantifying Nucleic Acid Ensembles with X-ray Scattering
Interferometry
Xuesong Shi, Steve Bonilla, Daniel Herschlag, and Pehr Harbury
1. Ensembles and Energy Surfaces
xiii
xix
3
4
6
13
20
22
35
35
39
40
43
50
68
69
75
76
vi
Contents
2. The Experimental Challenge 77
3. Conceptual Framework for XSI 80
4. A General Protocol for XSI Measurement of Nucleic Acid Constructs 84
Acknowledgments 96
References 96
4.2-Aminopurine Fluorescence as a Probe of Local RNA
Structure and Dynamics and Global Folding 99
Michael J. Rau and Kathleen B. Hall
1. Introduction 100
2. Conclusions: GAC Folding—Local and Global Events 121
Acknowledgments 122
References 122
5. Mod-seq: A High-Throughput Method for Probing RNA
Secondary Structure 125
Yizhu Lin, Gemma E. May, and C. Joel McManus
1. Theory 127
2. Equipment 128
3. Materials 129
4. Protocol 133
5. Step 1: RNA Fragmentation 135
6. Step 2: Phosphatase and Kinase the RNA 135
7. Step 3: Ligate the 3 Linker 136
8. Step 4: Ligate the 5 Linker 137
9. Step 5: 5 Linker Selection 138
10. Step 6: Reverse Transcription 140
11. Step 7: PAGE Purification 141
12. Step 8: Ethanol Precipitation 143
13. Step 9: Circularization 143
14. Step 10: Subtractive Hybridization 144
15. Step 11: PCR Amplification 146
16. Step 12: Purification and Analysis 147
17. Step 13: Data Analysis Using Mod-Seeker 148
References 151
6. Reproducible Analysis of Sequencing-Based RNA Structure
Probing Data with User-Friendly Tools 153
Lukasz Jan Kielpinski, Nikolaos Sidiropoulos, and Jeppe Vinther
1. Introduction 154
Contents
vii
2. Data Analysis 159
3. Concluding Remarks 177
Acknowledgments 177
References 177
7. Computational Methods for RNA Structure Validation
and Improvement 181
Swati Jain, David C. Richardson, and Jane S. Richardson
1. Introduction 182
2. General Validation Criteria 186
3. Criteria Specific to RNA Conformation 189
4. How to Interpret Validation Results 195
5. Correcting the Problems 201
6. What s Coming Next 207
Acknowledgments 208
References 209
8. Structures of Large RNAs and RNA-Protein Complexes:
Toward Structure Determination of Riboswitches 213
Jason C. Grigg and Ailong Ke
1. Introduction 214
2. Rational Construct Design for Structure Determination 215
3. Crystallization and Structure Determination 223
4. Structure-Function Validation 225
5. Conclusions 227
Acknowledgments 227
References 227
Section II
RNA-Protein Interactions
9. One, Two, Three, Four! How Multiple RRMs Read the
Genome Sequence 235
Tariq Afroz, Zuzana Cienikova, Antoine Cléry, and Frédéric H.T. Allain
1. Introduction 236
2. Structural Investigations of RRMs: How Many? 236
3. The RRM Fold and Its Numerous Variations 237
4. Single RRMs Recognize a Large Repertoire of RNA Sequences:
Is There a Recognition Code? 239
viii
Contents
5. Increasing Specificity and Affinity by Recognition of Longer RNA
Sequences 251
6. RNA Recognition by Tandem RRMs 254
7. Assembly of Higher Order Ribonucleoprotein Complexes by
Multi RRM-RNA and Multi Protein-RNA Interactions 258
8. Structural and Genome-Wide Approaches: How do They Match? 260
9. Conclusions and Perspectives 267
Acknowledgments 268
References 268
10. Combining NMR and EPR to Determine Structures
of Large RNAs and Protein-RNA Complexes in Solution 279
Olivier Duss, Maxim Yulikov, Frédéric H.T. Allain, and Gunnar Jeschke
1. Introduction 280
2. Limitations of Current Techniques to Solve Structures of Large
RNAs and Protein-RNA Complexes in Solution 282
3. EPR Theory 285
4. EPR-Aided Approach for Structure Determination of Large RNAs
and Protein-RNA Complexes in Solution 292
5. Future Challenges and Implications 322
Acknowledgments 324
References 324
11. Structural Analysis of Protein-RNA Complexes in Solution
Using NMR Paramagnetic Relaxation Enhancements 333
Janosch Hennig, Lisa R. Warner, Bernd Simon, Arie Geerlof,
Cameron D. Mackereth, and Michael Sattler
1. Introduction 334
2. Spin Labeling of Protein-RNA Complexes 336
3. Choice of Spin Label and Attachment Sites 337
4. Spin Labeling Protocol and Sample Handling 340
5. Measurement and Analysis of PRE Data 342
6. Structure Calculation Using PRE-Derived Distance Restraints 345
7. Case Study I: Structure of the U2AF65 RRM1.2-U9 RNA Complex 347
8. Case Study II: Conformational Dynamics of RRM Domains
in Apo U2AF65-RRMT2 351
9. Case Study III: Use of NMR and PRE Data for Validation of the
Sxl-Unr mRNA Complex 353
10. Outlook 355
Contents
ix
Acknowledgments 355
References 356
12. Resolving Individual Components in Protein-RNA Complexes
Using Small-Angle X-ray Scattering Experiments 363
Robert P. Rambo
1. Introduction 364
2. Technical Requirements 365
3. Theoretical Considerations 365
4. Assessing SAXS Sample Quality 374
5. Case Studies 375
6. Considerations 387
Acknowledgments 388
References 388
13. Small-Angle Neutron Scattering for Structural Biology
of Protein-RNA Complexes 391
Frank Gabel
1. Small-Angle Neutron Scattering: A Powerful Tool for Structural
Biology of Protein-RNA Complexes 392
2. Principles of SANS 393
3. Practical Aspects of SANS and Requirements on the Sample State 396
4. Model-Free Parameters: Molecular Mass and Radius of Gyration 397
5. Neutron Scattering Length Densities of Proteins and RNAs and
Implications on Model Building 399
6. Possibilities and Limits of Ab Initio Models (Shape Envelopes) 402
7. Present State-of-the-Art Examples 405
8. Conclusions and Future Perspectives 409
Acknowledgments 411
References 411
14. Studying RNA-Protein Interactions of Pre-mRNA Complexes
by Mass Spectrometry 417
Saadia Qamar, Katharina Kramer, and Henning Urlaub
1. Background 419
2. Equipment 421
3. Materials 423
4. Protocol 433
5. Step 1—In Vitro Transcription 434
X
Contents
6. Step 2—HeLa Nuclear Extract Preparation 438
7. Step 3—RNA-Protein Complex Assembly and Purification 441
8. Step 4—UV Cross-Linking 443
9. Step 5—Dissociation and Hydrolysis of Proteins 445
10. Step 6—Isolation of Cross-Links 446
11. Step 7—Hydrolysis of RNA and Proteins 450
12. Step 8—Desalting and Removal of RNA Fragments 451
13. Step 9—Enrichment of RNA-Protein Cross-Links 453
14. Step 10—Analysis by LC-Coupled ESI MS 455
15. Step 11—MS Data Analysis 457
16. Pros and Cons of the Presented Protocol 459
Acknowledgments 460
References 460
15. RNA Bind-n-Seq: Measuring the Binding Affinity Landscape
of RNA-Binding Proteins 465
Nicole J. Lambert, Alex D. Robertson, and Christopher B. Bürge
1. Introduction 466
2. Experimental Method 468
3. Preparation of RBNS Reagents 469
4. RBNS Assay 472
5. Computational Analysis 477
6. Pipeline Inputs 482
7. k-mer Analysis 482
8. Streaming k-mer Assignment 484
9. Presence Fractions 487
10. Relative Binding Affinity Determination 487
11. RBNS Quality Control 489
12. Conclusions 491
References 492
Section III
Large RNA-Protein Assemblies
16. Using Molecular Simulation to Model High-Resolution
Cryo-EM Reconstructions 497
Serdal Kirmizialtin, Justus Loerke, Elmar Behrmann, Christian M.T. Spahn,
and Karissa Y. Sanbonmatsu
1. Introduction
2. Theory
498
501
Contents xi
3. Methods 503
4. Results 505
5. Summary 508
Acknowledgments 510
References 510
17. In Vitro Reconstitution and Crystallization of Cas9
Endonuclease Bound to a Guide RNA and a DNA Target 515
Carolin Anders, Ole Niewoehner, and Martin Jinek
1. Introduction 516
2. Electrophoretic Mobility Shift Assay 518
3. Fluorescence-Detection Size Exclusion Chromatography Assay 523
4. Crystallization of Cas9-RNA-DNA Complexes 530
5. Concluding Remarks 534
Acknowledgments 535
References 535
18. Single-Molecule Pull-Down FRET to Dissect the
Mechanisms of Biomolecular Machines 539
Matthew L. Kahlscheuer, Julia Widom, and Nils G. Walter
1. Introduction 540
2. Experimental Methods 543
3. Data Analysis 559
4. The Spliceosome as a Biased Brownian Ratchet Machine 562
5. Conclusions and Outlook 566
Acknowledgment 567
References 567
19. Single-Molecule Imaging of RNA Splicing in Live Cells 571
José Ri no, Robert M. Martin, Célia Carvalho, Ana C. de Jesus,
and Maria Carmo-Fonseca
1. Introduction 572
2. Overview of the Method 574
3. Detailed Protocol 575
4. Concluding Remarks 583
Acknowledgments 584
References 584
Author Index
Subject Index
587
619
|
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| classification_rvk | VK 8700 |
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| format | Book |
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| id | DE-604.BV042612704 |
| illustrated | Illustrated |
| indexdate | 2024-07-10T07:05:54Z |
| institution | BVB |
| isbn | 9780128019344 |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-028045554 |
| oclc_num | 911169898 |
| open_access_boolean | |
| owner | DE-19 DE-BY-UBM DE-188 |
| owner_facet | DE-19 DE-BY-UBM DE-188 |
| physical | XXI, 631 S., [10] Bl. Ill., graph. Darst. |
| publishDate | 2015 |
| publishDateSearch | 2015 |
| publishDateSort | 2015 |
| publisher | Elesevier, Acad. Press |
| record_format | marc |
| series | Methods in enzymology |
| series2 | Methods in enzymology |
| spelling | Structures of large RNA molecules and their complexes ed. by Sarah A. Woodson ... 1. ed. Amsterdam [u.a.] Elesevier, Acad. Press 2015 XXI, 631 S., [10] Bl. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Methods in enzymology 558 Protein (DE-588)16276913-1 gnd rswk-swf Interaktion (DE-588)4027266-7 gnd rswk-swf Dynamik (DE-588)4013384-9 gnd rswk-swf Aggregation (DE-588)4000728-5 gnd rswk-swf Struktur (DE-588)4058125-1 gnd rswk-swf Komplexe (DE-588)4133953-8 gnd rswk-swf RNS (DE-588)4076759-0 gnd rswk-swf Strukturanalyse (DE-588)4183787-3 gnd rswk-swf RNS (DE-588)4076759-0 s Struktur (DE-588)4058125-1 s Dynamik (DE-588)4013384-9 s DE-604 Protein (DE-588)16276913-1 b Interaktion (DE-588)4027266-7 s Aggregation (DE-588)4000728-5 s Strukturanalyse (DE-588)4183787-3 s 1\p DE-604 Komplexe (DE-588)4133953-8 s 2\p DE-604 Woodson, Sarah A. Sonstige oth Methods in enzymology 558 (DE-604)BV000000938 558 HBZ Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=028045554&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis 1\p cgwrk 20201028 DE-101 https://d-nb.info/provenance/plan#cgwrk 2\p cgwrk 20201028 DE-101 https://d-nb.info/provenance/plan#cgwrk |
| spellingShingle | Structures of large RNA molecules and their complexes Methods in enzymology Protein (DE-588)16276913-1 gnd Interaktion (DE-588)4027266-7 gnd Dynamik (DE-588)4013384-9 gnd Aggregation (DE-588)4000728-5 gnd Struktur (DE-588)4058125-1 gnd Komplexe (DE-588)4133953-8 gnd RNS (DE-588)4076759-0 gnd Strukturanalyse (DE-588)4183787-3 gnd |
| subject_GND | (DE-588)16276913-1 (DE-588)4027266-7 (DE-588)4013384-9 (DE-588)4000728-5 (DE-588)4058125-1 (DE-588)4133953-8 (DE-588)4076759-0 (DE-588)4183787-3 |
| title | Structures of large RNA molecules and their complexes |
| title_auth | Structures of large RNA molecules and their complexes |
| title_exact_search | Structures of large RNA molecules and their complexes |
| title_full | Structures of large RNA molecules and their complexes ed. by Sarah A. Woodson ... |
| title_fullStr | Structures of large RNA molecules and their complexes ed. by Sarah A. Woodson ... |
| title_full_unstemmed | Structures of large RNA molecules and their complexes ed. by Sarah A. Woodson ... |
| title_short | Structures of large RNA molecules and their complexes |
| title_sort | structures of large rna molecules and their complexes |
| topic | Protein (DE-588)16276913-1 gnd Interaktion (DE-588)4027266-7 gnd Dynamik (DE-588)4013384-9 gnd Aggregation (DE-588)4000728-5 gnd Struktur (DE-588)4058125-1 gnd Komplexe (DE-588)4133953-8 gnd RNS (DE-588)4076759-0 gnd Strukturanalyse (DE-588)4183787-3 gnd |
| topic_facet | Protein Interaktion Dynamik Aggregation Struktur Komplexe RNS Strukturanalyse |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=028045554&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| volume_link | (DE-604)BV000000938 |
| work_keys_str_mv | AT woodsonsaraha structuresoflargernamoleculesandtheircomplexes |