E-Book, Englisch, 430 Seiten
Klostermeier / Hammann RNA Structure and Folding
1. Auflage 2013
ISBN: 978-3-11-028495-9
Verlag: De Gruyter
Format: PDF
Kopierschutz: Adobe DRM (»Systemvoraussetzungen)
Biophysical Techniques and Prediction Methods
E-Book, Englisch, 430 Seiten
ISBN: 978-3-11-028495-9
Verlag: De Gruyter
Format: PDF
Kopierschutz: Adobe DRM (»Systemvoraussetzungen)
Zielgruppe
Researchers and advanced students in the life sciences
Autoren/Hrsg.
Fachgebiete
Weitere Infos & Material
1;Preface;5
2;List of contributing authors;7
3;Contents;13
4;1 Optical spectroscopy and calorimetry;23
4.1;1.1 Introduction;23
4.2;1.2 Absorption spectroscopy;23
4.3;1.3 Fluorescence;30
4.4;1.4 Circular dichroism;30
4.5;1.5 Transient electric birefringence;35
4.6;1.6 Calorimetry;39
4.6.1;1.6.1 Isothermal titration calorimetry;40
4.6.2;1.6.2 Differential scanning calorimetry;43
4.7;1.7 Acknowledgments;46
4.7.1;References;46
5;2 Footprinting methods for mapping RNA-protein and RNA-RNA interactions;51
5.1;2.1 Introduction;51
5.2;2.2 Principles and applications of footprinting;52
5.3;2.3 Tools for footprinting: what should we know about probes?;54
5.3.1;2.3.1 RNases;54
5.3.2;2.3.2 Chemicals;57
5.3.2.1;2.3.2.1 Base-specific reagents;57
5.3.2.2;2.3.2.2 Ribose-phosphate backbone–specific reagents;57
5.4;2.4 Examples of RNP or RNA-RNA complexes analyzed by footprinting;59
5.4.1;2.4.1 Determination of the mRNA-binding site of Crc by SHAPE footprinting;59
5.4.2;2.4.2 Footprinting mapping of sRNA-mRNA interaction;61
5.4.3;2.4.3 Footprinting reveals mimicry of mRNA and tRNA for regulation;63
5.4.4;2.4.4 Difficulties in probing transient interactions by footprinting: the case of ribosomal protein S1-RNA complex;65
5.5;2.5 Concluding remarks;67
5.6;2.6 Acknowledgments;68
5.6.1;References;68
6;3 Chemical approaches to the structural investigation of RNA in solution;73
6.1;3.1 Introduction;73
6.2;3.2 Similar chemistry in different concepts: sequencing, probing, and interference;74
6.3;3.3 Sequencing and probing by Maxam and Gilbert chemistry;75
6.4;3.4 Application of Sanger sequencing to probing;79
6.5;3.5 Further electrophilic small molecule probes;80
6.6;3.6 Probing agents with nuclease activity;81
6.7;3.7 Probing agents involving radical chemistry;83
6.8;3.8 Matching suitable probes to structural features;83
6.9;3.9 Chemical modification interference;84
6.10;3.10 Nucleotide analog interference mapping;85
6.11;3.11 Combination and interplay with other methods;87
6.12;3.12 Application to an artificial ribozyme;88
6.13;3.13 Conclusion and outlook;91
6.13.1;References;91
7;4 Bioorthogonal modifications and cycloaddition reactions for RNA chemical biology;97
7.1;4.1 Introduction;97
7.2;4.2 Bioorthogonal conjugation strategies;98
7.2.1;4.2.1 1,3-dipolar cycloaddition reactions ([3+2] cycloaddition);98
7.2.1.1;4.2.1.1 Copper-catalyzed azide-alkyne cycloaddition;98
7.2.1.2;4.2.1.2 Strain-promoted azide-alkyne cycloaddition;99
7.2.1.3;4.2.1.3 Nitrile oxides as 1,3-dipoles for metal-free cycloadditions;100
7.2.1.4;4.2.1.4 Photoactivated 1,3-dipolar cycloadditions;102
7.2.2;4.2.2 Inverse electron demand Diels-Alder reaction ([4+2] cycloaddition);102
7.2.3;4.2.3 Staudinger reaction of azides and phosphines;103
7.3;4.3 Synthetic strategies for RNA functionalization: installation of reactive groups for cycloadditions;103
7.3.1;4.3.1 Chemical synthesis of modified RNA;104
7.3.1.1;4.3.1.1 Alkyne-containing phosphoramidites for solid-phase synthesis;104
7.3.1.2;4.3.1.2 Solid-phase synthesis of azide-containing RNA;105
7.3.1.3;4.3.1.3 Postsynthetic modification of RNA with azides and alkynes;105
7.3.1.4;4.3.1.4 Functionality transfer reaction using s6G-modified DNA;106
7.3.2;4.3.2 Enzymatic incorporation of functional groups for click chemistry;107
7.3.2.1;4.3.2.1 In vitro transcription using modified nucleotides;108
7.3.2.2;4.3.2.2 Enzymatic posttranscriptional modification;108
7.4;4.4 Case studies for applications of click chemistry in RNA chemical biology;110
7.4.1;4.4.1 Synthesis of chemically modified ribozymes;110
7.4.2;4.4.2 Monitoring RNA synthesis and turnover by metabolic labeling and click chemistry;112
7.4.3;4.4.3 Bioorthogonal modification of siRNAs for detection, improved stability, and delivery;113
7.5;4.5 Summary and conclusions;115
7.6;4.6 Acknowledgments;115
7.6.1;References;116
8;5 Analysis of RNA conformation using comparative gel electrophoresis;123
8.1;5.1 The principle behind the analysis of the structure of branched nucleic acids by gel electrophoresis;123
8.2;5.2 Helical discontinuities in duplex RNA;125
8.3;5.3 The direction of a helical bend;126
8.4;5.4 Comparative gel electrophoresis of branched nucleic acids;126
8.5;5.5 Comparative gel electrophoresis of four-way DNA junctions;130
8.6;5.6 Analysis of the structure of four-way RNA junctions;133
8.7;5.7 The 4H junctions of the U1 snRNA and the hairpin ribozyme;134
8.8;5.8 A more complex junction found in the HCV IRES;134
8.9;5.9 Analysis of the structure of three-way RNA junctions;137
8.9.1;5.9.1 A three-way junction of the HCV IRES element;137
8.9.2;5.9.2 Three-way junctions are the key architectural elements of the VS ribozyme;138
8.9.3;5.9.3 The hammerhead ribozyme is a complex three-way helical junction;140
8.10;5.10 Some final thoughts;140
8.11;5.11 Acknowledgments;142
8.11.1;References;142
9;6 Virus RNA structure deduced by combining X-ray diffraction and atomic force microscopy;147
9.1;6.1 Introduction;147
9.2;6.2 Why don’t we learn more about RNA from X-ray crystallography?;147
9.3;6.3 X-ray studies revealing RNA;148
9.4;6.4 Secondary structure prediction;150
9.5;6.5 Generalized ssRNA secondary structural motifs;151
9.6;6.6 The folding of RNA in STMV;153
9.7;6.7 Atomic force microscopy;155
9.8;6.8 Preparation of viral RNA samples for AFM;158
9.9;6.9 Atomic force microscopy of viral ssRNAs;159
9.10;6.10 AFM results for extended STMV RNA;162
9.11;6.11 ssRNA in T = 3 icosahedral viruses;166
9.12;6.12 A model for assembly of STMV inspired by crystallography and AFM;169
9.13;6.13 AFM of large ssRNA viruses;172
9.13.1;References;174
10;7 Investigating RNA structure and folding with optical tweezers;179
10.1;7.1 Introduction;179
10.2;7.2 Single-RNA force measurements with optical tweezers;180
10.3;7.3 Probing RNA and RNA-protein interactions: selected examples;182
10.3.1;7.3.1 Probing the structure and the folding dynamics of RNA hairpins;182
10.3.2;7.3.2 Exploring the folding dynamics of complex RNA structures in presence of proteins;194
10.4;7.4 Conclusion;200
10.5;7.5 Acknowledgments;200
10.5.1;References;200
11;8 Fluorescence resonance energy transfer as a tool to investigate RNA structure and folding;203
11.1;8.1 An introduction to fluorescence resonance energy transfer;203
11.2;8.2 Introduction of donor and acceptor fluorophores into RNAs and RNA/protein complexes;205
11.3;8.3 Ensemble FRET;206
11.3.1;8.3.1 Steady-state FRET;206
11.3.2;8.3.2 Time-resolved FRET;208
11.4;8.4 Single-molecule FRET;211
11.4.1;8.4.1 Instrumentation and experimental procedure;213
11.4.2;8.4.2 Data analysis;215
11.4.2.1;8.4.2.1 Identifying single-molecule events;215
11.4.2.2;8.4.2.2 Correction for instrument nonnonideality;215
11.4.2.3;8.4.2.3 The Förster distance R0;217
11.4.2.4;8.4.2.4 The orientation factor k2;218
11.4.2.5;8.4.2.5 Analysis of FRET histograms;219
11.4.3;8.4.3 FRET data and RNA folding;220
11.4.4;8.4.4 From FRET data to structural models of RNA and RNA/protein complexes;220
11.5;8.5 Selected examples;221
11.5.1;8.5.1 Steady-state FRET: ribozymes, rRNA, and RNA polymerase transcription complexes;221
11.5.2;8.5.2 Time-resolved FRET: the hairpin ribozyme;226
11.5.3;8.5.3 Single-molecule FRET: folding of large ribozymes and transcription by RNA polymerases;228
11.5.4;8.5.4 Single-molecule FRET and modeling of complex structures;229
11.6;8.6 Perspectives;230
11.7;8.7 Acknowledgments;231
11.7.1;References;231
12;9 RNA studies by small angle X-ray scattering in solution;237
12.1;9.1 Introduction to SAXS;237
12.2;9.2 SAXS experiment;238
12.2.1;9.2.1 Sample preparation;238
12.2.2;9.2.2 Form and structure factor: particle interactions;239
12.3;9.3 Methods;241
12.3.1;9.3.1 Distance distribution function;241
12.3.2;9.3.2 Overall parameters: radius of gyration, molecular mass, and volume;241
12.4;9.4 Modeling;243
12.4.1;9.4.1 Ab initio modeling;243
12.4.1.1;9.4.1.1 Bead models;243
12.4.1.2;9.4.1.2 Dummy residue models;244
12.4.1.3;9.4.1.3 Multiphase models;244
12.4.1.4;9.4.1.4 Comparison of multi ple models;245
12.4.2;9.4.2 SAXS and complementary methods;245
12.4.2.1;9.4.2.1 High-resolution models;245
12.4.2.2;9.4.2.2 Rigid body modeling;246
12.4.3;9.4.3 Flexible systems;247
12.4.4;9.4.4 Mixtures;247
12.5;9.5 Resolution and ambiguity of SAXS data interpretation;248
12.6;9.6 Practical applications;249
12.6.1;9.6.1 Ab initio shape determination;249
12.6.2;9.6.2 Analysis of RNA flexibility;251
12.6.3;9.6.3 Nonstochiometric RNA-protein mixtures and complex formation;253
12.6.4;9.6.4 Structural studies of spliceosome function assisted by SAXS measurements;254
12.6.5;9.6.5 How SAXS helps elucidate riboswitch structure-function relationships;255
12.6.6;9.6.6 Use of SAXS and ASAXS to study the influences of counterions on RNA folding;258
12.6.7;9.6.7 Quantitation of free-energy changes estimated from SAXS 3-D reconstructions;258
12.7;9.7 Conclusions and outlook;259
12.8;9.8 Acknowledgments;260
12.8.1;References;260
13;10 Integrative structure-function analysis of large nucleoprotein complexes;265
13.1;10.1 Summary;265
13.2;10.2 Integrative structure-function analysis of nucleoprotein complexes, example 1: translation complexes;272
13.3;10.3 Integrative structure-function analysis of nucleoprotein complexes, example 2: transcription complexes;275
13.4;10.4 Outlook;277
13.5;10.5 Acknowledgments;278
13.5.1;References;279
13.6;11 Structure and conformational dynamics of RNA determined by pulsed EPR;283
13.6.1;11.1 Introduction;283
13.6.2;11.2 Pulse EPR spectroscopy on RNA;286
13.6.2.1;11.2.1 Spin labeling of nucleic acids;286
13.6.2.2;11.2.2 Theoretical description of the PELDOR experiment;288
13.6.2.3;11.2.3 Practical aspects of the PELDOR experiment;292
13.6.2.4;11.2.4 PELDOR experiments with rigid spin labels;293
13.6.2.5;11.2.5 Data analysis and interpretation;296
13.6.3;11.3 Application examples;298
13.6.3.1;11.3.1 Applications on dsRNA and DNA;299
13.6.3.2;11.3.2 Application on RNA with more complex structure;299
13.6.3.3;11.3.3 Applications on DNA with rigid spin labels;301
13.6.4;11.4 Outlook and summary;302
13.6.5;11.5 Acknowledgments;303
13.6.5.1;References;304
14;12 NMR-based characterization of RNA structure and dynamics;309
14.1;12.1 Introduction;309
14.2;12.2 Part I: RNA structure;310
14.2.1;12.2.1 Primary structure;310
14.2.1.1;12.2.1.1 RNA sequence determinants on structure;310
14.2.1.2;12.2.1.2 Unusual nucleotides;310
14.2.1.3;12.2.1.3 Torsion angles in the polynucleotide sequence;310
14.2.2;12.2.2 Secondary structure: base pairing and helices;311
14.2.2.1;12.2.2.1 Regular structure and base pairing;311
14.2.2.2;12.2.2.2 Helical secondary structure;313
14.3;12.3 Part II: NMR studies of RNA;313
14.3.1;12.3.1 NMR sample preparation and labeling;313
14.3.1.1;12.3.1.1 Sample preparation;313
14.3.1.2;12.3.1.2 Labeling schemes;314
14.3.1.3;12.3.1.3 RNA purification;314
14.3.2;12.3.2 NMR parameters to characterize RNA structure;315
14.3.2.1;12.3.2.1 Sequence-specific assignment of NMR resonances;315
14.3.2.2;12.3.2.2 NMR measurements for torsion angle restraints;319
14.3.2.3;12.3.2.3 NMR measurements for distance restraints;320
14.3.2.4;12.3.2.4 Scalar couplings across hydrogen bonds;320
14.3.2.5;12.3.2.5 Residual dipolar couplings;321
14.3.2.6;12.3.2.6 NMR-based structure calculation;323
14.3.3;12.3.3 NMR parameters to characterize RNA dynamics;323
14.3.3.1;12.3.3.1 NMR measurements for RNA dynamics;324
14.3.3.2;12.3.3.2 Dynamics probed by relaxation parameters;325
14.3.3.3;12.3.3.3 Dynamics probed by residual dipolar couplings;325
14.4;12.4 Part III: examples of RNA tertiary structure;326
14.4.1;12.4.1 Helix-helix interactions;326
14.4.1.1;12.4.1.1 Coaxial stacking;326
14.4.1.2;12.4.1.2 A-platform and A-C platform;327
14.4.2;12.4.2 Helix-strand interactions;327
14.4.2.1;12.4.2.1 Base triples and A-minor motifs;327
14.4.2.2;12.4.2.2 Tetraloops;328
14.4.3;12.4.3 Loop-loop interactions;329
14.4.3.1;12.4.3.1 Kissing loop;329
14.4.3.2;12.4.3.2 Pseudoknot;329
14.5;12.5 Conclusion;330
14.6;12.6 Acknowledgments;330
14.6.1;References;330
15;13 Crystallization of RNA for structure determination by X-ray crystallography;341
15.1;13.1 Introduction;341
15.2;13.2 General strategy for crystallization;341
15.2.1;13.2.1 Oligonucleotides and duplex termini;342
15.2.2;13.2.2 Loop engineering and RNP formation and topological permutation;344
15.2.3;13.2.3 An example of success through construct engineering;345
15.3;13.3 Purity and monodispersity;347
15.4;13.4 Postcrystallization treatments;348
15.5;13.5 Construct design and structure determination;350
15.6;13.6 Conclusion;351
15.7;13.7 Acknowledgments;352
15.7.1;References;352
16;14 RNA structure prediction;357
16.1;14.1 The thermodynamic model of RNA folding;358
16.1.1;14.1.1 Free energy and partition function;358
16.1.2;14.1.2 Abstract shapes;359
16.1.3;14.1.3 Free-energy computation of an RNA structure;360
16.1.4;14.1.4 Influence of solvent;362
16.2;14.2 MFE structure;362
16.3;14.3 Partition folding;363
16.3.1;14.3.1 Suboptimal structures;365
16.3.2;14.3.2 Mean and sampled structures;366
16.3.3;14.3.3 Shape representative structures and shape probabilities;367
16.4;14.4 Structure prediction and multiple alignment;367
16.5;14.5 Beyond secondary structure prediction;371
16.5.1;14.5.1 Pseudoknots;371
16.5.2;14.5.2 RNA-RNA hybridization;375
16.6;14.6 Acknowledgments;379
16.6.1;References;379
17;15 Analyzing, searching, and annotating recurrent RNA three-dimensional motifs;385
17.1;15.1 Characteristics of structured RNAs;385
17.1.1;15.1.1 RNA molecules are structurally diverse;385
17.1.2;15.1.2 “Loops” in RNA secondary structures and RNA 3D motifs;386
17.1.3;15.1.3 The 3D motifs and hierarchical organization of RNA;388
17.1.4;15.1.4 Linker regions and 3D motifs;388
17.2;15.2 Structural diversity of RNA 3D motifs;390
17.2.1;15.2.1 Contribution of RNA chain flexibility to motif diversity;390
17.2.2;15.2.2 Contribution of internucleotide interactions to motif diversity;391
17.3;15.3 Pairwise nucleotide interactions that stabilize RNA 3D motifs;392
17.3.1;15.3.1 Base-pairing interactions and 3D motifs;392
17.3.1.1;15.3.1.1 Occurrence frequencies of base pairs is context dependent;392
17.3.1.2;15.3.1.2 Base-pair isostericity and structure conservation during evolution;393
17.3.2;15.3.2 Base-stacking interactions and 3D motifs;394
17.3.3;15.3.3 Base-phosphate interactions and 3D motifs;394
17.4;15.4 Defining RNA 3D motifs;395
17.4.1;15.4.1 Role of induced fit in RNA motif structure;395
17.4.2;15.4.2 Definition of “classic” RNA 3D motifs;396
17.4.2.1;15.4.2.1 Definition of modular motifs;396
17.4.2.2;15.4.2.2 Conservation of motif sequence and structure;397
17.4.3;15.4.3 Recurrent RNA 3D motifs;397
17.5;15.5 Tools for searching for RNA 3D motifs in atomic-resolution RNA structures;397
17.5.1;15.5.1 MC-Search;398
17.5.2;15.5.2 NASSAM;398
17.5.3;15.5.3 PRIMOS;398
17.5.4;15.5.4 FR3D and WebFR3D;400
17.5.5;15.5.5 Apostolico et al., 2009;400
17.5.6;15.5.6 RNAMotifScan;400
17.5.7;15.5.7 FRMF;401
17.5.8;15.5.8 RNA FRABASE 2.0;401
17.5.9;15.5.9 FASTR3D;401
17.5.10;15.5.10 FRASS;402
17.5.11;15.5.11 R3D-BLAST;402
17.5.12;15.5.12 Comparison of 3D search methods;402
17.6;15.6 Classifying RNA 3D motifs;403
17.6.1;15.6.1 Why classify RNA 3D motifs?;403
17.6.2;15.6.2 How to classify RNA 3D motifs?;403
17.6.3;15.6.3 Criteria for grouping motif instances in the same recurrent family;404
17.6.4;15.6.4 Evaluating 3D motif similarity;405
17.6.5;15.6.5 Application of motif classification criteria;405
17.6.6;15.6.6 Automatic classification of RNA 3D motifs;406
17.7;15.7 RNA 3D motif collections;406
17.7.1;15.7.1 Motif-oriented collections;406
17.7.1.1;15.7.1.1 SCOR;406
17.7.1.2;15.7.1.2 Comparative RNA Web Site;408
17.7.1.3;15.7.1.3 K-turn database;408
17.7.1.4;15.7.1.4 RNAMotifScan;408
17.7.1.5;15.7.1.5 FRMF;408
17.7.1.6;15.7.1.6 RNA 3D Motif Atlas;409
17.7.2;15.7.2 Loop-oriented collections;409
17.7.2.1;15.7.2.1 RNAJunction;409
17.7.2.2;15.7.2.2 RNA STRAND;409
17.7.2.3;15.7.2.3 RLooM;410
17.7.2.4;15.7.2.4 RNA CoSSMos;410
17.7.3;15.7.3 Comparing RNA 3D motif collections;410
17.8;15.8 RNA 3D motifs that “break the rules”;412
17.8.1;15.8.1 The 3D motifs that contain isolated cWW base pairs;412
17.8.2;15.8.2 Composite 3D motifs: 3D motifs composed of more than one loop;414
17.8.3;15.8.3 Motifs comprising linker strands;415
17.8.4;15.8.4 Motifs interacting with adjacent helices;416
17.9;15.9 Conclusions;417
17.10;15.10 Acknowledgments;417
17.10.1;References;418
18;Index;421
