RNA Structure and Folding (eBook)

Biophysical Techniques and Prediction Methods

Dagmar Klostermeier, Christian Hammann (Herausgeber)

eBook Download: PDF

2013
430 Seiten
De Gruyter (Verlag)
978-3-11-028495-9 (ISBN)

Infos

While structure-function relationships of proteins have been studied for a long time, structural studies of RNA face additional challenges. Nevertheless, with the continuous discovery of novel RNA molecules with key cellular functions and of novel pathways and interaction networks, the need for structural information of RNA is still increasing. This volume provides an introduction into techniques to assess structure and folding of RNA. Each chapter explains the theoretical background of one technique, and illustrates possibilities and limitations in selected application examples.

Dagmar Klostermeier, University of Münster, Germany; Christian Hammann, School of Engineering and Science, Jacobs University Bremen, Germany.

Autor

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Dagmar Klostermeier, University of Münster, Germany; Christian Hammann, School of Engineering and Science, Jacobs University Bremen, Germany.

Inhalt

Preface 5
List of contributing authors 7
Contents 13
1 Optical spectroscopy and calorimetry 23
1.1 Introduction 23
1.2 Absorption spectroscopy 23
1.3 Fluorescence 30
1.4 Circular dichroism 30
1.5 Transient electric birefringence 35
1.6 Calorimetry 39
1.6.1 Isothermal titration calorimetry 40
1.6.2 Differential scanning calorimetry 43
1.7 Acknowledgments 46
References 46
2 Footprinting methods for mapping RNA-protein and RNA-RNA interactions 51
2.1 Introduction 51
2.2 Principles and applications of footprinting 52
2.3 Tools for footprinting: what should we know about probes? 54
2.3.1 RNases 54
2.3.2 Chemicals 57
2.3.2.1 Base-specific reagents 57
2.3.2.2 Ribose-phosphate backbone–specific reagents 57
2.4 Examples of RNP or RNA-RNA complexes analyzed by footprinting 59
2.4.1 Determination of the mRNA-binding site of Crc by SHAPE footprinting 59
2.4.2 Footprinting mapping of sRNA-mRNA interaction 61
2.4.3 Footprinting reveals mimicry of mRNA and tRNA for regulation 63
2.4.4 Difficulties in probing transient interactions by footprinting: the case of ribosomal protein S1-RNA complex 65
2.5 Concluding remarks 67
2.6 Acknowledgments 68
References 68
3 Chemical approaches to the structural investigation of RNA in solution 73
3.1 Introduction 73
3.2 Similar chemistry in different concepts: sequencing, probing, and interference 74
3.3 Sequencing and probing by Maxam and Gilbert chemistry 75
3.4 Application of Sanger sequencing to probing 79
3.5 Further electrophilic small molecule probes 80
3.6 Probing agents with nuclease activity 81
3.7 Probing agents involving radical chemistry 83
3.8 Matching suitable probes to structural features 83
3.9 Chemical modification interference 84
3.10 Nucleotide analog interference mapping 85
3.11 Combination and interplay with other methods 87
3.12 Application to an artificial ribozyme 88
3.13 Conclusion and outlook 91
References 91
4 Bioorthogonal modifications and cycloaddition reactions for RNA chemical biology 97
4.1 Introduction 97
4.2 Bioorthogonal conjugation strategies 98
4.2.1 1,3-dipolar cycloaddition reactions ([3+2] cycloaddition) 98
4.2.1.1 Copper-catalyzed azide-alkyne cycloaddition 98
4.2.1.2 Strain-promoted azide-alkyne cycloaddition 99
4.2.1.3 Nitrile oxides as 1,3-dipoles for metal-free cycloadditions 100
4.2.1.4 Photoactivated 1,3-dipolar cycloadditions 102
4.2.2 Inverse electron demand Diels-Alder reaction ([4+2] cycloaddition) 102
4.2.3 Staudinger reaction of azides and phosphines 103
4.3 Synthetic strategies for RNA functionalization: installation of reactive groups for cycloadditions 103
4.3.1 Chemical synthesis of modified RNA 104
4.3.1.1 Alkyne-containing phosphoramidites for solid-phase synthesis 104
4.3.1.2 Solid-phase synthesis of azide-containing RNA 105
4.3.1.3 Postsynthetic modification of RNA with azides and alkynes 105
4.3.1.4 Functionality transfer reaction using s6G-modified DNA 106
4.3.2 Enzymatic incorporation of functional groups for click chemistry 107
4.3.2.1 In vitro transcription using modified nucleotides 108
4.3.2.2 Enzymatic posttranscriptional modification 108
4.4 Case studies for applications of click chemistry in RNA chemical biology 110
4.4.1 Synthesis of chemically modified ribozymes 110
4.4.2 Monitoring RNA synthesis and turnover by metabolic labeling and click chemistry 112
4.4.3 Bioorthogonal modification of siRNAs for detection, improved stability, and delivery 113
4.5 Summary and conclusions 115
4.6 Acknowledgments 115
References 116
5 Analysis of RNA conformation using comparative gel electrophoresis 123
5.1 The principle behind the analysis of the structure of branched nucleic acids by gel electrophoresis 123
5.2 Helical discontinuities in duplex RNA 125
5.3 The direction of a helical bend 126
5.4 Comparative gel electrophoresis of branched nucleic acids 126
5.5 Comparative gel electrophoresis of four-way DNA junctions 130
5.6 Analysis of the structure of four-way RNA junctions 133
5.7 The 4H junctions of the U1 snRNA and the hairpin ribozyme 134
5.8 A more complex junction found in the HCV IRES 134
5.9 Analysis of the structure of three-way RNA junctions 137
5.9.1 A three-way junction of the HCV IRES element 137
5.9.2 Three-way junctions are the key architectural elements of the VS ribozyme 138
5.9.3 The hammerhead ribozyme is a complex three-way helical junction 140
5.10 Some final thoughts 140
5.11 Acknowledgments 142
References 142
6 Virus RNA structure deduced by combining X-ray diffraction and atomic force microscopy 147
6.1 Introduction 147
6.2 Why don’t we learn more about RNA from X-ray crystallography? 147
6.3 X-ray studies revealing RNA 148
6.4 Secondary structure prediction 150
6.5 Generalized ssRNA secondary structural motifs 151
6.6 The folding of RNA in STMV 153
6.7 Atomic force microscopy 155
6.8 Preparation of viral RNA samples for AFM 158
6.9 Atomic force microscopy of viral ssRNAs 159
6.10 AFM results for extended STMV RNA 162
6.11 ssRNA in T = 3 icosahedral viruses 166
6.12 A model for assembly of STMV inspired by crystallography and AFM 169
6.13 AFM of large ssRNA viruses 172
References 174
7 Investigating RNA structure and folding with optical tweezers 179
7.1 Introduction 179
7.2 Single-RNA force measurements with optical tweezers 180
7.3 Probing RNA and RNA-protein interactions: selected examples 182
7.3.1 Probing the structure and the folding dynamics of RNA hairpins 182
7.3.2 Exploring the folding dynamics of complex RNA structures in presence of proteins 194
7.4 Conclusion 200
7.5 Acknowledgments 200
References 200
8 Fluorescence resonance energy transfer as a tool to investigate RNA structure and folding 203
8.1 An introduction to fluorescence resonance energy transfer 203
8.2 Introduction of donor and acceptor fluorophores into RNAs and RNA/protein complexes 205
8.3 Ensemble FRET 206
8.3.1 Steady-state FRET 206
8.3.2 Time-resolved FRET 208
8.4 Single-molecule FRET 211
8.4.1 Instrumentation and experimental procedure 213
8.4.2 Data analysis 215
8.4.2.1 Identifying single-molecule events 215
8.4.2.2 Correction for instrument nonnonideality 215
8.4.2.3 The Förster distance R0 217
8.4.2.4 The orientation factor k2 218
8.4.2.5 Analysis of FRET histograms 219
8.4.3 FRET data and RNA folding 220
8.4.4 From FRET data to structural models of RNA and RNA/protein complexes 220
8.5 Selected examples 221
8.5.1 Steady-state FRET: ribozymes, rRNA, and RNA polymerase transcription complexes 221
8.5.2 Time-resolved FRET: the hairpin ribozyme 226
8.5.3 Single-molecule FRET: folding of large ribozymes and transcription by RNA polymerases 228
8.5.4 Single-molecule FRET and modeling of complex structures 229
8.6 Perspectives 230
8.7 Acknowledgments 231
References 231
9 RNA studies by small angle X-ray scattering in solution 237
9.1 Introduction to SAXS 237
9.2 SAXS experiment 238
9.2.1 Sample preparation 238
9.2.2 Form and structure factor: particle interactions 239
9.3 Methods 241
9.3.1 Distance distribution function 241
9.3.2 Overall parameters: radius of gyration, molecular mass, and volume 241
9.4 Modeling 243
9.4.1 Ab initio modeling 243
9.4.1.1 Bead models 243
9.4.1.2 Dummy residue models 244
9.4.1.3 Multiphase models 244
9.4.1.4 Comparison of multi ple models 245
9.4.2 SAXS and complementary methods 245
9.4.2.1 High-resolution models 245
9.4.2.2 Rigid body modeling 246
9.4.3 Flexible systems 247
9.4.4 Mixtures 247
9.5 Resolution and ambiguity of SAXS data interpretation 248
9.6 Practical applications 249
9.6.1 Ab initio shape determination 249
9.6.2 Analysis of RNA flexibility 251
9.6.3 Nonstochiometric RNA-protein mixtures and complex formation 253
9.6.4 Structural studies of spliceosome function assisted by SAXS measurements 254
9.6.5 How SAXS helps elucidate riboswitch structure-function relationships 255
9.6.6 Use of SAXS and ASAXS to study the influences of counterions on RNA folding 258
9.6.7 Quantitation of free-energy changes estimated from SAXS 3-D reconstructions 258
9.7 Conclusions and outlook 259
9.8 Acknowledgments 260
References 260
10 Integrative structure-function analysis of large nucleoprotein complexes 265
10.1 Summary 265
10.2 Integrative structure-function analysis of nucleoprotein complexes, example 1: translation complexes 272
10.3 Integrative structure-function analysis of nucleoprotein complexes, example 2: transcription complexes 275
10.4 Outlook 277
10.5 Acknowledgments 278
References 279
11 Structure and conformational dynamics of RNA determined by pulsed EPR 283
11.1 Introduction 283
11.2 Pulse EPR spectroscopy on RNA 286
11.2.1 Spin labeling of nucleic acids 286
11.2.2 Theoretical description of the PELDOR experiment 288
11.2.3 Practical aspects of the PELDOR experiment 292
11.2.4 PELDOR experiments with rigid spin labels 293
11.2.5 Data analysis and interpretation 296
11.3 Application examples 298
11.3.1 Applications on dsRNA and DNA 299
11.3.2 Application on RNA with more complex structure 299
11.3.3 Applications on DNA with rigid spin labels 301
11.4 Outlook and summary 302
11.5 Acknowledgments 303
References 304
12 NMR-based characterization of RNA structure and dynamics 309
12.1 Introduction 309
12.2 Part I: RNA structure 310
12.2.1 Primary structure 310
12.2.1.1 RNA sequence determinants on structure 310
12.2.1.2 Unusual nucleotides 310
12.2.1.3 Torsion angles in the polynucleotide sequence 310
12.2.2 Secondary structure: base pairing and helices 311
12.2.2.1 Regular structure and base pairing 311
12.2.2.2 Helical secondary structure 313
12.3 Part II: NMR studies of RNA 313
12.3.1 NMR sample preparation and labeling 313
12.3.1.1 Sample preparation 313
12.3.1.2 Labeling schemes 314
12.3.1.3 RNA purification 314
12.3.2 NMR parameters to characterize RNA structure 315
12.3.2.1 Sequence-specific assignment of NMR resonances 315
12.3.2.2 NMR measurements for torsion angle restraints 319
12.3.2.3 NMR measurements for distance restraints 320
12.3.2.4 Scalar couplings across hydrogen bonds 320
12.3.2.5 Residual dipolar couplings 321
12.3.2.6 NMR-based structure calculation 323
12.3.3 NMR parameters to characterize RNA dynamics 323
12.3.3.1 NMR measurements for RNA dynamics 324
12.3.3.2 Dynamics probed by relaxation parameters 325
12.3.3.3 Dynamics probed by residual dipolar couplings 325
12.4 Part III: examples of RNA tertiary structure 326
12.4.1 Helix-helix interactions 326
12.4.1.1 Coaxial stacking 326
12.4.1.2 A-platform and A-C platform 327
12.4.2 Helix-strand interactions 327
12.4.2.1 Base triples and A-minor motifs 327
12.4.2.2 Tetraloops 328
12.4.3 Loop-loop interactions 329
12.4.3.1 Kissing loop 329
12.4.3.2 Pseudoknot 329
12.5 Conclusion 330
12.6 Acknowledgments 330
References 330
13 Crystallization of RNA for structure determination by X-ray crystallography 341
13.1 Introduction 341
13.2 General strategy for crystallization 341
13.2.1 Oligonucleotides and duplex termini 342
13.2.2 Loop engineering and RNP formation and topological permutation 344
13.2.3 An example of success through construct engineering 345
13.3 Purity and monodispersity 347
13.4 Postcrystallization treatments 348
13.5 Construct design and structure determination 350
13.6 Conclusion 351
13.7 Acknowledgments 352
References 352
14 RNA structure prediction 357
14.1 The thermodynamic model of RNA folding 358
14.1.1 Free energy and partition function 358
14.1.2 Abstract shapes 359
14.1.3 Free-energy computation of an RNA structure 360
14.1.4 Influence of solvent 362
14.2 MFE structure 362
14.3 Partition folding 363
14.3.1 Suboptimal structures 365
14.3.2 Mean and sampled structures 366
14.3.3 Shape representative structures and shape probabilities 367
14.4 Structure prediction and multiple alignment 367
14.5 Beyond secondary structure prediction 371
14.5.1 Pseudoknots 371
14.5.2 RNA-RNA hybridization 375
14.6 Acknowledgments 379
References 379
15 Analyzing, searching, and annotating recurrent RNA three-dimensional motifs 385
15.1 Characteristics of structured RNAs 385
15.1.1 RNA molecules are structurally diverse 385
15.1.2 “Loops” in RNA secondary structures and RNA 3D motifs 386
15.1.3 The 3D motifs and hierarchical organization of RNA 388
15.1.4 Linker regions and 3D motifs 388
15.2 Structural diversity of RNA 3D motifs 390
15.2.1 Contribution of RNA chain flexibility to motif diversity 390
15.2.2 Contribution of internucleotide interactions to motif diversity 391
15.3 Pairwise nucleotide interactions that stabilize RNA 3D motifs 392
15.3.1 Base-pairing interactions and 3D motifs 392
15.3.1.1 Occurrence frequencies of base pairs is context dependent 392
15.3.1.2 Base-pair isostericity and structure conservation during evolution 393
15.3.2 Base-stacking interactions and 3D motifs 394
15.3.3 Base-phosphate interactions and 3D motifs 394
15.4 Defining RNA 3D motifs 395
15.4.1 Role of induced fit in RNA motif structure 395
15.4.2 Definition of “classic” RNA 3D motifs 396
15.4.2.1 Definition of modular motifs 396
15.4.2.2 Conservation of motif sequence and structure 397
15.4.3 Recurrent RNA 3D motifs 397
15.5 Tools for searching for RNA 3D motifs in atomic-resolution RNA structures 397
15.5.1 MC-Search 398
15.5.2 NASSAM 398
15.5.3 PRIMOS 398
15.5.4 FR3D and WebFR3D 400
15.5.5 Apostolico et al., 2009 400
15.5.6 RNAMotifScan 400
15.5.7 FRMF 401
15.5.8 RNA FRABASE 2.0 401
15.5.9 FASTR3D 401
15.5.10 FRASS 402
15.5.11 R3D-BLAST 402
15.5.12 Comparison of 3D search methods 402
15.6 Classifying RNA 3D motifs 403
15.6.1 Why classify RNA 3D motifs? 403
15.6.2 How to classify RNA 3D motifs? 403
15.6.3 Criteria for grouping motif instances in the same recurrent family 404
15.6.4 Evaluating 3D motif similarity 405
15.6.5 Application of motif classification criteria 405
15.6.6 Automatic classification of RNA 3D motifs 406
15.7 RNA 3D motif collections 406
15.7.1 Motif-oriented collections 406
15.7.1.1 SCOR 406
15.7.1.2 Comparative RNA Web Site 408
15.7.1.3 K-turn database 408
15.7.1.4 RNAMotifScan 408
15.7.1.5 FRMF 408
15.7.1.6 RNA 3D Motif Atlas 409
15.7.2 Loop-oriented collections 409
15.7.2.1 RNAJunction 409
15.7.2.2 RNA STRAND 409
15.7.2.3 RLooM 410
15.7.2.4 RNA CoSSMos 410
15.7.3 Comparing RNA 3D motif collections 410
15.8 RNA 3D motifs that “break the rules” 412
15.8.1 The 3D motifs that contain isolated cWW base pairs 412
15.8.2 Composite 3D motifs: 3D motifs composed of more than one loop 414
15.8.3 Motifs comprising linker strands 415
15.8.4 Motifs interacting with adjacent helices 416
15.9 Conclusions 417
15.10 Acknowledgments 417
References 418
Index 421

Produkt-Details

• Erscheint lt. Verlag: 14.10.2013
• Zusatzinfo: 50 col. ill.
• Verlagsort: Berlin/Boston
• Sprache: englisch
• Themenwelt: Naturwissenschaften ► Biologie ► Biochemie
• Themenwelt: Naturwissenschaften ► Biologie ► Genetik / Molekularbiologie
• Themenwelt: Naturwissenschaften ► Physik / Astronomie ► Angewandte Physik
• Themenwelt: Technik
• Schlagworte: Biophysics • experimental techniques • prediction methods • RNA
• ISBN-10: 3-11-028495-2 / 3110284952
• ISBN-13: 978-3-11-028495-9 / 9783110284959