Details

Ribozymes


Ribozymes

Principles, Methods, Applications
1. Aufl.

von: Sabine Müller, Benoît Masquida, Wade Winkler

318,99 €

Verlag: Wiley-VCH
Format: EPUB
Veröffentl.: 09.07.2021
ISBN/EAN: 9783527814534
Sprache: englisch
Anzahl Seiten: 944

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Beschreibungen

<b>Ribozymes</b> <p><b>Provides comprehensive coverage of a core field in the molecular biosciences, bringing together decades of knowledge from the world’s top professionals in the field</b> <p>Timely and unique in its breadth of content, this all-encompassing and authoritative reference on ribozymes documents the great diversity of nucleic acid-based catalysis. It integrates the knowledge gained over the past 35 years in the field and features contributions from virtually every leading expert on the subject. <p><i>Ribozymes</i> is organized into six major parts. It starts by describing general principles and strategies of nucleic acid catalysis. It then introduces naturally occurring ribozymes and includes the search for new catalytic motifs or novel genomic locations of known motifs. Next, it covers the development and design of engineered ribozymes, before moving on to DNAzymes as a close relative of ribozymes. The next part examines the use of ribozymes for medicinal and environmental diagnostics, as well as for therapeutic tools. It finishes with a look at the tools and methods in ribozyme research, including the techniques and assays for structural and functional characterization of nucleic acid catalysts. <ul><li>The first reference to tie together all aspects of the multi-faceted field of ribozymes</li> <li>Features more than 30 comprehensive chapters in two volumes</li> <li>Covers the chemical principles of RNA catalysis; naturally occurring ribozymes, engineered ribozymes; DNAzymes; ribozymes as tools in diagnostics and therapy, and tools and methods to study ribozymes</li> <li>Includes first-hand accounts of concepts, techniques, and applications by a team of top international experts from leading academic institutions</li> <li>Dedicates half of its content to methods and practical applications, ranging from bioanalytical tools to medical diagnostics to therapeutics</li></ul> <p><i>Ribozymes</i> is an unmatched resource for all biochemists, biotechnologists, molecular biologists, and bioengineers interested in the topic.
<p><b>Volume 1</b></p> <p>Preface xvii</p> <p>Foreword xix</p> <p><b>Part I Nucleic Acid Catalysis: Principles, Strategies and Biological Function </b><b>1<br /><br /></b><b>1 The Chemical Principles of RNA Catalysis </b><b>3<br /></b><i>Timothy J. Wilson and David M. J. Lilley</i></p> <p>1.1 RNA Catalysis 3</p> <p>1.2 Rates of Chemical Reactions and Transition State Theory 4</p> <p>1.3 Phosphoryl Transfer Reactions in the Ribozymes 5</p> <p>1.4 Catalysis of Phosphoryl Transfer 6</p> <p>1.5 General Acid–Base Catalysis in Nucleolytic Ribozymes 8</p> <p>1.5.1 The Fraction of Active Catalyst, and the pH Dependence of Reaction Rates 9</p> <p>1.5.2 The Reactivity of General Acids and Bases 13</p> <p>1.6 p<i>K</i><sub>a</sub> Shifting of General Acids and Bases in Nucleolytic Ribozymes 13</p> <p>1.7 Catalytic Roles of Metal Ions in Ribozymes 14</p> <p>1.8 The Choice Between General Acid–Base Catalysis and the Use of Metal Ions 17</p> <p>1.9 The Limitations to RNA Catalysis 18</p> <p>Acknowledgment 18</p> <p>References 19</p> <p><b>2 Biological Roles of Self-Cleaving Ribozymes </b><b>23<br /></b><i>Christina E. Weinberg</i></p> <p>2.1 Introduction 23</p> <p>2.2 Use of Self-cleaving Ribozymes for Replication 25</p> <p>2.2.1 Viroids 25</p> <p>2.2.2 Viroid-like Satellite RNAs 28</p> <p>2.2.3 Hepatitis δ Virus RNA 29</p> <p>2.2.4 <i>Neurospora </i>Varkud Satellite RNAs Replicate Using a DNA Intermediate 29</p> <p>2.3 Self-cleaving Ribozymes as Part of Transposable Elements 30</p> <p>2.3.1 R2 Elements: Non-LTR Retrotransposons that Use HDV-like Ribozymes for Retrotransposition 30</p> <p>2.3.2 HDV-like Ribozymes in Other Non-LTR Retrotransposon Lineages 34</p> <p>2.3.3 <i>Penelope</i>-like Elements (PLEs) Contain Hammerhead Ribozymes 35</p> <p>2.3.4 Hammerhead Ribozymes Associated with Repetitive Elements in <i>Schistosoma mansoni </i>39</p> <p>2.3.5 Retrozymes: A New Class of Plant Retrotransposons that Contains Hammerhead Ribozymes 40</p> <p>2.4 Hammerhead Ribozymes with Suggested Roles in mRNA Biogenesis 41</p> <p>2.5 The <i>glmS </i>Ribozyme Regulates Glucosamine-6-phosphate Levels in Bacteria 41</p> <p>2.6 The Biological Roles of Many Ribozymes Are Unknown 42</p> <p>2.7 Conclusion 43</p> <p>Acknowledgments 43</p> <p>References 44</p> <p><b>Part II Naturally Occurring Ribozymes </b><b>55</b></p> <p><b>3 Chemical Mechanisms of the Nucleolytic Ribozymes </b><b>57<br /></b><i>Timothy J. Wilson and David M. J. Lilley</i></p> <p>3.1 The Nucleolytic Ribozymes 57</p> <p>3.2 Some Nucleolytic Ribozymes AreWidespread 58</p> <p>3.3 Secondary Structures of Nucleolytic Ribozymes – Junctions and Pseudoknots 58</p> <p>3.4 Catalytic Players in the Nucleolytic Ribozymes 60</p> <p>3.5 The Hairpin and VS Ribozymes: The G Plus A Mechanism 61</p> <p>3.6 The Twister Ribozyme: A G Plus A Variant 66</p> <p>3.7 The Hammerhead Ribozyme: A 2′-Hydroxyl as a Catalytic Participant 69</p> <p>3.8 The Hepatitis Delta Virus Ribozyme: A Direct Role for a Metal Ion 72</p> <p>3.9 The Twister Sister (TS) Ribozyme: Another Metallo-Ribozyme 74</p> <p>3.10 The Pistol Ribozyme: A Metal Ion as the General Acid 76</p> <p>3.11 The <i>glmS </i>Ribozyme: Participation of a Coenzyme 78</p> <p>3.12 A Classification of the Nucleolytic Ribozymes Based on Catalytic Mechanism 79</p> <p>Acknowledgments 83</p> <p>References 83</p> <p><b>4 The<i>glmS </i>Ribozyme and Its Multifunctional Coenzyme Glucosamine-6-phosphate </b><b>91<br /></b><i>Juliane Soukup</i></p> <p>4.1 Introduction 91</p> <p>4.2 Ribozymes 91</p> <p>4.3 Riboswitches 92</p> <p>4.4 The <i>glmS </i>Riboswitch/Ribozyme 93</p> <p>4.5 Biological Function of the <i>glmS </i>Ribozyme 94</p> <p>4.6 <i>glmS </i>Ribozyme Structure and Function – Initial Biochemical Analyses 95</p> <p>4.7 <i>glmS </i>Ribozyme Structure and Function – Initial Crystallographic Analysis 98</p> <p>4.8 Metal Ion Usage by the <i>glmS </i>Ribozyme 99</p> <p>4.9 In Vitro Selected <i>glmS </i>Catalyst Loses Coenzyme Dependence 101</p> <p>4.10 Essential Coenzyme GlcN6P Functional Groups 102</p> <p>4.11 Mechanism of <i>glmS </i>Ribozyme Self-Cleavage 104</p> <p>4.11.1 Importance of Coenzyme GlcN6P 104</p> <p>4.11.2 pH-Reactivity Profiles 106</p> <p>4.11.3 Role of an Active Site Guanine 108</p> <p>4.12 Potential for Antibiotic Development Affecting <i>glmS </i>Ribozyme/Riboswitch Function 109</p> <p>Acknowledgments 110</p> <p>References 110</p> <p><b>5 The Lariat Capping Ribozyme </b><b>117<br /></b><i>Henrik Nielsen, Nicolai Krogh, Benoît Masquida, and Steinar Daae Johansen</i></p> <p>5.1 Introduction 117</p> <p>5.1.1 The Basics 117</p> <p>5.1.2 A Brief Account of the Discovery of the Lariat Capping Ribozyme 119</p> <p>5.1.3 Readers Guide to Nomenclature 120</p> <p>5.1.4 The Species Involved 120</p> <p>5.2 Reactions Catalyzed by LCrz 121</p> <p>5.2.1 The Branching Reaction 122</p> <p>5.2.2 Ligation and Hydrolysis 122</p> <p>5.2.3 Reaction Conditions 124</p> <p>5.3 The Structure of the LCrz Core 125</p> <p>5.3.1 The Detailed Structure of <i>Dir</i>LCrz 125</p> <p>5.3.2 Structure of the <i>Naegleria</i>-type LCrz 126</p> <p>5.4 Communication Between LCrz and Flanking Elements 128</p> <p>5.4.1 Group I Ribozyme Switching 128</p> <p>5.4.2 LC Ribozyme Switching 130</p> <p>5.4.3 A Role of Spliceosomal Intron I51 in <i>Dir</i>LCrz Regulation? 131</p> <p>5.5 Reflections on the Evolutionary Aspect of LCrz 131</p> <p>5.5.1 A Model for the Emergence of LCrz 132</p> <p>5.5.2 An Evolutionary Path to Spliceosomal Splicing? 132</p> <p>5.6 LCrz as a Research Tool 134</p> <p>5.7 Conclusions and Unsolved Problems 136</p> <p>References 138</p> <p><b>6 Self-Splicing Group II Introns </b><b>143<br /></b><i>Isabel Chillón and Marco Marcia</i></p> <p>6.1 Introduction 143</p> <p>6.2 Milestones in the Characterization of Group II Introns 143</p> <p>6.3 Evolutionary Conservation and Biological Role 145</p> <p>6.3.1 Phylogenetic Classifications 145</p> <p>6.3.2 Differentiation and Evolutionarily Acquired Properties 148</p> <p>6.3.3 Spreading and Survival in the Host Genome 149</p> <p>6.4 Structural Architecture 152</p> <p>6.4.1 Secondary Structure and Long-Range Tertiary Interactions 152</p> <p>6.4.2 Folding 153</p> <p>6.4.3 Stabilization by Solvent and IEP 154</p> <p>6.4.4 Active Site and Reaction Mechanism 154</p> <p>6.5 Lessons and Tools from Group II Intron Research 156</p> <p>6.5.1 Analogies to Other Splicing Machineries 156</p> <p>6.5.2 Lessons to Study Other Large Non-coding RNAs 157</p> <p>6.5.3 Biotechnological Applications of GIIi 157</p> <p>6.6 Perspectives and Open Questions 158</p> <p>Acknowledgments 158</p> <p>References 158</p> <p><b>7 The Spliceosome: an RNA–Protein Ribozyme Derived From Ancient Mobile Genetic Elements </b><b>169<br /></b><i>Erin L. Garside, Oliver A. Kent, and Andrew M. MacMillan</i></p> <p>7.1 Discovery of Introns and Splicing 169</p> <p>7.2 snRNPs and the Spliceosome 170</p> <p>7.3 The Spliceosomal Cycle 171</p> <p>7.4 Chemistry of Splicing 173</p> <p>7.5 Spliceosome Structural Analysis 177</p> <p>7.6 Spliceosome Structures 177</p> <p>7.6.1 Pre-spliceosome: Tri-snRNP 177</p> <p>7.6.2 Pre-spliceosome: A Complex 179</p> <p>7.6.3 B Complex 179</p> <p>7.6.4 Activated B Complex 182</p> <p>7.6.5 C and C* Complexes 183</p> <p>7.6.6 P Complex 185</p> <p>7.6.7 Intron Lariat Spliceosome Complex 185</p> <p>7.7 Insights from Spliceosome Disassembly 187</p> <p>7.8 Conservation of Spliceosomal and Group II Active Sites 187</p> <p>7.9 Summary and Perspectives 188</p> <p>References 189</p> <p><b>8 The Ribosome and Protein Synthesis </b><b>193<br /></b><i>Paul Huter, Michael Graf, and Daniel N. Wilson</i></p> <p>8.1 Central Dogma of Molecular Biology 193</p> <p>8.2 Structure of the <i>E. coli </i>Ribosome 194</p> <p>8.3 Translation Cycle 194</p> <p>8.3.1 Initiation 196</p> <p>8.3.2 Elongation 199</p> <p>8.3.3 Termination 208</p> <p>8.3.4 Recycling 211</p> <p>References 213</p> <p><b>9 The RNase P Ribozyme </b><b>227<br /></b><i>Markus Gößringer, Isabell Schencking, and Roland Karl Hartmann</i></p> <p>9.1 Introduction 227</p> <p>9.2 Bacterial RNase P 229</p> <p>9.2.1 P RNA Structure and Evolution 229</p> <p>9.2.2 The Single Protein Subunit 233</p> <p>9.2.3 P RNAs – Architectural Principles, Variations, Idiosyncrasies 233</p> <p>9.3 Substrate Interaction 235</p> <p>9.4 RNA-based Metal Ion Catalysis 247</p> <p>9.4.1 The Two-metal Ion Mechanism 247</p> <p>9.4.2 Architecture of the Active Site 250</p> <p>9.4.3 The “A248/nt −1” Interaction 251</p> <p>9.4.4 Specific RNase P Cleavage by the P15 Module 253</p> <p>9.5 RNase P as an Antibiotic Target 254</p> <p>9.5.1 P RNA as a Target 254</p> <p>9.5.2 The Bacterial RNase P Holoenzyme as Target 257</p> <p>9.5.3 P Protein as a Target 258</p> <p>9.6 Application of RNase P as a Tool in Gene Inactivation 258</p> <p>9.6.1 The Guide Sequence (GS) Concept 258</p> <p>9.6.2 EGS Technology in Eukaryotic Cells 259</p> <p>9.6.3 EGS Oligonucleotides and Recruitment of Human Nuclear-Cytoplasmic RNase P 261</p> <p>9.6.4 The M1–GS Approach 265</p> <p>9.6.5 Outlook 266</p> <p>References 267</p> <p><b>10 Ribozyme Discovery in Bacteria </b><b>281<br /></b><i>Adam Roth and Ronald Breaker</i></p> <p>10.1 Introduction 281</p> <p>10.2 Protein Takeover 282</p> <p>10.3 Ribozymes as Evolutionary Holdouts 282</p> <p>10.4 The Role of Serendipity in Early Ribozyme Discoveries 283</p> <p>10.5 Ribozymes Emerge from Structured Noncoding RNA Searches 285</p> <p>10.6 Ribozymes Beget Ribozymes 289</p> <p>10.7 Ribozyme Dispersal Driven by Association with Selfish Elements 291</p> <p>10.8 Domesticated Ribozymes 292</p> <p>10.9 New Ribozymes from Old 294</p> <p>10.10 Will New ncRNAs Broaden the Scope of RNA Catalysis? 295</p> <p>Acknowledgments 296</p> <p>References 296</p> <p><b>11 Small Self-Cleaving Ribozymes in the Genomes of Vertebrates </b><b>303<br /></b><i>Marcos de la Peña</i></p> <p>11.1 The Family of Small Self-Cleaving Ribozymes in Eukaryotic Genomes: From Retrotransposition to Domestication 303</p> <p>11.2 The Widespread Case of the Hammerhead Ribozyme: From Bacteria to Vertebrate Genomes 304</p> <p>11.2.1 The Discontinuous HHR in Mammals 307</p> <p>11.2.2 Intronic HHRs in Amniotes 310</p> <p>11.3 Other Intronic HHRs in Amniotes: Small Catalytic RNAs in Search of a Function 315</p> <p>11.4 The Family of the Hepatitis D Virus Ribozymes 318</p> <p>11.4.1 An Intronic HDV-Like Ribozyme Conserved in the Genome of Mammals 320</p> <p>11.5 Other Small Self-Cleaving Ribozymes Hidden in the Genomes of Vertebrates? 322</p> <p>References 323</p> <p><b>Part III Engineered Ribozymes </b><b>329</b></p> <p><b>12 Phosphoryl Transfer Ribozymes </b><b>331<br /></b><i>Razvan Cojocaru and Peter J. Unrau</i></p> <p>12.1 Introduction 331</p> <p>12.2 Kinase Ribozymes 332</p> <p>12.3 Glycosidic Bond Forming Ribozymes 336</p> <p>12.4 Capping Ribozymes 340</p> <p>12.5 Ligase Ribozymes 344</p> <p>12.6 Polymerase Ribozymes 351</p> <p>12.7 Summary 353</p> <p>References 353</p> <p><b>13 RNA Replication and the RNA Polymerase Ribozyme </b><b>359<br /></b><i>Falk Wachowius and Philipp Holliger</i></p> <p>13.1 Introduction 359</p> <p>13.2 Nonenzymatic RNA Polymerization 360</p> <p>13.3 Enzymatic RNA Polymerization 361</p> <p>13.4 Essential Requirements for an RNA Replicator 363</p> <p>13.4.1 Likelihood of Replicating Sequences in RNA Sequence Space 364</p> <p>13.4.2 Reaction Conditions for RNA Replication 366</p> <p>13.4.3 The Strand Separation Problem 367</p> <p>13.5 The Class I Ligase and the First RNA Polymerase Ribozymes 367</p> <p>13.6 Structural Insight into the Catalytic Core of the RNA Polymerase Ribozyme 372</p> <p>13.7 Selection for Improved Polymerase Activity I 374</p> <p>13.8 Selection for Improved Polymerase Activity II 377</p> <p>13.9 Conclusion and Outlook 380</p> <p>References 381</p> <p><b>14 Maintenance of Genetic Information in the First Ribocell </b><b>387<br /></b><i>Ádám Kun</i></p> <p>14.1 The Ribocell and the Stages of the RNAWorld 387</p> <p>14.1.1 Replication of the Genetic Information 389</p> <p>14.1.2 On the Metabolic Complexity of Ribocells 389</p> <p>14.2 The Error Thresholds 391</p> <p>14.2.1 Introducing the Error Threshold 391</p> <p>14.2.2 The Fitness Landscape and Neutrality of Mutations 393</p> <p>14.3 Compartmentalization 396</p> <p>14.3.1 Surface Metabolism and Transient Compartmentalization 397</p> <p>14.3.2 The Stochastic Corrector Model 399</p> <p>14.4 Minimal Gene Content of the First Ribocell 401</p> <p>14.4.1 Intermediate Metabolism 402</p> <p>14.4.2 Cell-Level Processes 404</p> <p>Acknowledgments 406</p> <p>References 406</p> <p><b>15 Ribozyme-Catalyzed RNA Recombination </b><b>419<br /></b><i>Benedict A. Smail and Niles Lehman</i></p> <p>15.1 Introduction 419</p> <p>15.2 RNA Recombination Chemistry 420</p> <p>15.3 <i>Azoarcus </i>Group I Intron 421</p> <p>15.4 Crystal Structure 422</p> <p>15.5 Mechanism 422</p> <p>15.6 Model for Prebiotic Chemistry 423</p> <p>15.7 Spontaneous Self-assembly of <i>Azoarcus </i>RNA Fragments 425</p> <p>15.8 Autocatalysis 428</p> <p>15.9 Cooperative Self-assembly 429</p> <p>15.10 Game Theoretic Treatment 430</p> <p>15.11 Significance of Game Theoretic Treatments 432</p> <p>15.12 Other Recombinase Ribozymes 433</p> <p>15.13 Conclusions 435</p> <p>References 436</p> <p><b>16 Engineering of Hairpin Ribozymes for RNA Processing Reactions </b><b>439<br /></b><i>Robert Hieronymus, Jikang Zhu, Bettina Appel, and Sabine Müller</i></p> <p>16.1 Introduction 439</p> <p>16.2 The Naturally Occurring Hairpin Ribozyme 440</p> <p>16.3 Structural Variants of the Hairpin Ribozyme 442</p> <p>16.4 Hairpin Ribozymes that are Regulated by External Effectors 443</p> <p>16.5 Twin Ribozymes for RNA Repair and Recombination 446</p> <p>16.6 Hairpin Ribozymes as RNA Recombinases 449</p> <p>16.7 Self-Splicing Hairpin Ribozymes 452</p> <p>16.8 Closing Remarks 454</p> <p>References 456</p> <p><b>17 Engineering of the <i>Neurospora </i>Varkud Satellite Ribozyme for Cleavage of Nonnatural Stem-Loop Substrates </b><b>463<br /></b><i>Pierre Dagenais, Julie Lacroix-Labonté, Nicolas Girard, and Pascale Legault</i></p> <p>17.1 Introduction 463</p> <p>17.2 Simple Primary and Secondary Structure Changes Compatible with Substrate Cleavage by the VS Ribozyme 464</p> <p>17.2.1 Circular Permutations and <i>trans </i>Cleavage 464</p> <p>17.2.2 The I/V Kissing-Loop Interaction and the Associated Conformational Change in SLI 466</p> <p>17.2.3 Summary of SLI Sequences Compatible with Cleavage by the Wild-Type VS Ribozyme 468</p> <p>17.3 The Structural Context 470</p> <p>17.3.1 NMR Investigations of the VS Ribozyme 470</p> <p>17.3.2 Crystal Structures of a Dimeric Form of the VS Ribozyme 473</p> <p>17.3.3 Open and Closed States of the <i>S</i>/<i>R </i>Complex 473</p> <p>17.4 Structure-Guided Engineering Studies 474</p> <p>17.4.1 Helix-Length Compensation 474</p> <p>17.4.2 Kissing-Loop Substitutions 475</p> <p>17.4.3 Role of KLI Dynamics in the Cleavage Reaction 476</p> <p>17.4.4 Improving the Cleavage Activity of a Designer Ribozyme 478</p> <p>17.5 Summary and Future Prospects for VS Ribozyme Engineering 480</p> <p>References 481</p> <p><b>18 Chemical Modifications in Natural and Engineered Ribozymes </b><b>487<br /></b><i>Stephanie Kath-Schorr</i></p> <p>18.1 Introduction 487</p> <p>18.2 Chemical Modifications to Study Natural Ribozymes 488</p> <p>18.2.1 Modified Nucleotides for Mechanistic and Structural Studies on Ribozymes 488</p> <p>18.2.2 Stabilization of Ribozymes by Chemical Modifications for in Cell Applications 489</p> <p>18.3 In Vitro Selection with Chemically Modified Nucleotides: Expanding the Scope of DNA and RNA Catalysis 490</p> <p>18.3.1 General Aspects for In Vitro Selection Using Unnatural Nucleotides 491</p> <p>18.3.2 Selection of Deoxyribozymes with Modified Nucleotides 492</p> <p>18.3.3 Artificial Ribozymes with Nonnatural Nucleobases 494</p> <p>18.3.4 Catalysts With Nonnatural Backbones: XNAzymes 495</p> <p>18.4 Outlook 495</p> <p>References 496</p> <p><b>19 Ribozymes for Regulation of Gene Expression </b><b>505<br /></b><i>Julia Stifel and Jörg S. Hartig</i></p> <p>19.1 Introduction 505</p> <p>19.2 Conditional Gene Expression Control by Riboswitches 505</p> <p>19.3 Allosteric Ribozymes as Engineered Riboswitches 506</p> <p>19.4 In Vitro Selection Methods 507</p> <p>19.5 In Vivo Screening Methods 508</p> <p>19.6 Rational Design of Allosteric Ribozymes 511</p> <p>19.7 Applications of Aptazymes for Gene Regulation 512</p> <p>References 514</p> <p><b>20 Development of Flexizyme Aminoacylation Ribozymes and Their Applications </b><b>519<br /></b><i>Takayuki Katoh, Yuki Goto, Toby Passioura, and Hiroaki Suga</i></p> <p>20.1 Introduction 519</p> <p>20.2 The First Ribozymes Catalyzing Acyl Transfer to RNAs 520</p> <p>20.3 The ATRib Variant Family: Ribozymes Catalyzing tRNA Aminoacylation via Self-Acylated Intermediates 521</p> <p>20.4 Prototype Flexizymes: Ribozymes Catalyzing Direct tRNA Aminoacylation 523</p> <p>20.5 Flexizymes: Versatile Ribozymes for the Preparation of Aminoacyl-tRNAs 526</p> <p>20.6 Application of Flexizymes to Genetic Code Reprogramming 527</p> <p>20.7 Development of Orthogonal tRNA/Ribosome Pairs Using Mutant Flexizymes 530</p> <p>20.8 In Vitro Selection of Bioactive Peptides Containing nPAAs Through RaPID Display 532</p> <p>20.9 tRid: A Method for Selective Removal of tRNAs from an RNA Pool 535</p> <p>20.10 Use of a Natural Small RNA Library Lacking tRNA for In Vitro Selection of a Folic Acid Aptamer: Small RNA Transcriptomic SELEX 535</p> <p>20.11 Summary and Perspective 537</p> <p>Acknowledgments 539</p> <p>References 539</p> <p><b>21 In Vitro Selected (Deoxy)ribozymes that Catalyze Carbon–Carbon Bond Formation </b><b>545<br /></b><i>Michael Famulok</i></p> <p>21.1 Introduction 545</p> <p>21.2 Diels–Alderase Ribozymes 546</p> <p>21.3 Aldolase Ribozyme 547</p> <p>21.4 A DNAzyme that Catalyzes a Friedel–Crafts Reaction 548</p> <p>21.5 Alkylating Ribozymes 550</p> <p>21.6 Conclusion 554</p> <p>References 555</p> <p><b>22 Nucleic Acid-Catalyzed RNA Ligation and Labeling </b><b>557<br /></b><i>Mohammad Ghaem Maghami and Claudia Höbartner</i></p> <p>22.1 Introduction 557</p> <p>22.2 Ribozymes for RNA Labeling at Internal Positions 558</p> <p>22.2.1 Fluorescein Iodoacetamide Reactive Ribozyme 558</p> <p>22.2.2 Genomically Derived Epoxide Reactive Ribozyme 559</p> <p>22.2.3 Twin Ribozyme 561</p> <p>22.2.4 DNA as a Catalyst for Ligation of Modified RNA 562</p> <p>22.2.5 Site-Specific Internal Labeling of RNA with DNA Enzymes 563</p> <p>22.3 RNA-Catalyzed Labeling of RNA at the 3′-end 564</p> <p>22.4 Potential Ribozymes for RNA Labeling at the 5′-end 565</p> <p>22.5 Conclusions 566</p> <p>Acknowledgments 566</p> <p>References 568</p> <p><b>Volume 2</b></p> <p>Preface xiii</p> <p>Foreword xv</p> <p><b>Part IV DNAzymes 571</b></p> <p>23 The Chemical Repertoire of DNA Enzymes 573<br /><i>Marcel Hollenstein</i></p> <p>24 Light-Utilizing DNAzymes 621<br /><i>Adam Barlev and Dipankar Sen</i></p> <p>25 Diverse Applications of DNAzymes in Computing and Nanotechnology 633<br /><i>Matthew R. Lakin, Darko Stefanovic, and Milan N. Stojanovic</i></p> <p><b>Part V Ribozymes/DNAzymes in Diagnostics and Therapy </b><b>661</b></p> <p>26 Optimization of Antiviral Ribozymes 663<br /><i>Alfredo Berzal-Herranz and Cristina Romero-López</i></p> <p>27 DNAzymes as Biosensors 685<br /><i>Lingzi Ma and Juewen Liu</i></p> <p>28 Compartmentalization-Based Technologies for In Vitro Selection and Evolution of Ribozymes and Light-Up RNA Aptamers 721<br /><i>Farah Bouhedda and Michael Ryckelynck</i></p> <p><b>Part VI Tools and Methods to Study Ribozymes </b><b>739</b></p> <p>29 Elucidation of Ribozyme Mechanisms at the Example of the Pistol Ribozyme 741<br /><i>Christoph Falschlunger, Josef Leiter, and Ronald Micura</i></p> <p>30 Strategies for Crystallization of Natural Ribozymes 753<br /><i>Benoît Masquida, Diana Sibrikova, and Maria Costa</i></p> <p>31 NMR Spectroscopic Investigation of Ribozymes 785<br /><i>Bozana Knezic, Oliver Binas, Albrecht Eduard Völklein, and Harald Schwalbe</i></p> <p>32 Studying Ribozymes with Electron Paramagnetic Resonance Spectroscopy 817<br /><i>Olav Schiemann</i></p> <p>33 Computational Modeling Methods for 3D Structure Prediction of Ribozymes 861<br /><i>Pritha Ghosh, Chandran Nithin, Astha Joshi, Filip Stefaniak, Tomasz K. Wirecki, and Janusz M. Bujnicki</i></p> <p>Index 883</p>
<p><i><b>Sabine Müller</b> is Full Professor for Biochemistry/Bioorganic Chemistry at University Greifswald (Germany), and is a member of the Leibniz-Sozietät der Wissenschaften zu Berlin and of AcademiaNet. She has been working in the field of RNA engineering and has made important contributions to ribozyme research.</i></p> <p><i><b>Benoît Masquida</b> is a Research Director at Centre National de la Recherche Scientifique, and carries on research and teaching activities at the University of Strasbourg (France). He made important contributions in the field of RNA structural biology, notably through identification of new RNA folds and their evolutionary relationships. </i> <p><i><b>Wade Winkler</b> is Professor of Cell Biology and Molecular Genetics at the University of Maryland (USA), and has authored multiple influential publications on the different types of regulatory RNAs in bacteria.</i>
<p><b>Provides comprehensive coverage of a core field in the molecular biosciences, bringing together decades of knowledge from the world’s top professionals in the field</b></p> <p>Timely and unique in its breadth of content, this all-encompassing and authoritative reference on ribozymes documents the great diversity of nucleic acid-based catalysis. It integrates the knowledge gained over the past 35 years in the field and features contributions from virtually every leading expert on the subject. <p><i>Ribozymes</i> is organized into six major parts. It starts by describing general principles and strategies of nucleic acid catalysis. It then introduces naturally occurring ribozymes and includes the search for new catalytic motifs or novel genomic locations of known motifs. Next, it covers the development and design of engineered ribozymes, before moving on to DNAzymes as a close relative of ribozymes. The next part examines the use of ribozymes for medicinal and environmental diagnostics, as well as for therapeutic tools. It finishes with a look at the tools and methods in ribozyme research, including the techniques and assays for structural and functional characterization of nucleic acid catalysts. <ul><li>The first reference to tie together all aspects of the multi-faceted field of ribozymes</li> <li>Features more than 30 comprehensive chapters in two volumes</li> <li>Covers the chemical principles of RNA catalysis; naturally occurring ribozymes, engineered ribozymes; DNAzymes; ribozymes as tools in diagnostics and therapy, and tools and methods to study ribozymes</li> <li>Includes first-hand accounts of concepts, techniques, and applications by a team of top international experts from leading academic institutions</li> <li>Dedicates half of its content to methods and practical applications, ranging from bioanalytical tools to medical diagnostics to therapeutics</li></ul> <p><i>Ribozymes</i> is an unmatched resource for all biochemists, biotechnologists, molecular biologists, and bioengineers interested in the topic.

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