Ribozymes E-Book

• Herausgeber: Wiley-VCH GmbH
• Kategorie: Wissenschaft und neue Technologien
• Sprache: Englisch

Seitenzahl: 1815

Veröffentlichungsjahr: 2021

Beschreibung

Ribozymes

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

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.

Ribozymes 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.

• The first reference to tie together all aspects of the multi-faceted field of ribozymes
• Features more than 30 comprehensive chapters in two volumes
• 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
• Includes first-hand accounts of concepts, techniques, and applications by a team of top international experts from leading academic institutions
• Dedicates half of its content to methods and practical applications, ranging from bioanalytical tools to medical diagnostics to therapeutics

Ribozymes is an unmatched resource for all biochemists, biotechnologists, molecular biologists, and bioengineers interested in the topic.

Leseprobe

Table of Contents

Cover

Title Page

Title Page

Copyright

Preface

Foreword

References

Volume 1

Part I: Nucleic Acid Catalysis: Principles, Strategies and Biological Function

1 The Chemical Principles of RNA Catalysis

1.1 RNA Catalysis

1.2 Rates of Chemical Reactions and Transition State Theory

1.3 Phosphoryl Transfer Reactions in the Ribozymes

1.4 Catalysis of Phosphoryl Transfer

1.5 General Acid–Base Catalysis in Nucleolytic Ribozymes

1.6 pKa Shifting of General Acids and Bases in Nucleolytic Ribozymes

1.7 Catalytic Roles of Metal Ions in Ribozymes

1.8 The Choice Between General Acid–Base Catalysis and the Use of Metal Ions

1.9 The Limitations to RNA Catalysis

Acknowledgment

References

2 Biological Roles of Self‐Cleaving Ribozymes

2.1 Introduction

2.2 Use of Self‐cleaving Ribozymes for Replication

2.3 Self‐cleaving Ribozymes as Part of Transposable Elements

2.4 Hammerhead Ribozymes with Suggested Roles in mRNA Biogenesis

2.5 The

glm

S Ribozyme Regulates Glucosamine‐6‐phosphate Levels in Bacteria

2.6 The Biological Roles of Many Ribozymes Are Unknown

2.7 Conclusion

Acknowledgments

References

Part II: Naturally Occurring Ribozymes

3 Chemical Mechanisms of the Nucleolytic Ribozymes

3.1 The Nucleolytic Ribozymes

3.2 Some Nucleolytic Ribozymes Are Widespread

3.3 Secondary Structures of Nucleolytic Ribozymes – Junctions and Pseudoknots

3.4 Catalytic Players in the Nucleolytic Ribozymes

3.5 The Hairpin and VS Ribozymes: The G Plus A Mechanism

3.6 The Twister Ribozyme: A G Plus A Variant

3.7 The Hammerhead Ribozyme: A 2′‐Hydroxyl as a Catalytic Participant

3.8 The Hepatitis Delta Virus Ribozyme: A Direct Role for a Metal Ion

3.9 The Twister Sister (TS) Ribozyme: Another Metallo‐Ribozyme

3.10 The Pistol Ribozyme: A Metal Ion as the General Acid

3.11 The

glm

S Ribozyme: Participation of a Coenzyme

3.12 A Classification of the Nucleolytic Ribozymes Based on Catalytic Mechanism

Acknowledgments

References

Note

4 The

glmS

Ribozyme and Its Multifunctional Coenzyme Glucosamine‐6‐phosphate

4.1 Introduction

4.2 Ribozymes

4.3 Riboswitches

4.4 The

glmS

Riboswitch/Ribozyme

4.5 Biological Function of the glmS Ribozyme

4.6

glmS

Ribozyme Structure and Function – Initial Biochemical Analyses

4.7

glmS

Ribozyme Structure and Function – Initial Crystallographic Analysis

4.8 Metal Ion Usage by the glmS Ribozyme

4.9 In Vitro Selected

glmS

Catalyst Loses Coenzyme Dependence

4.10 Essential Coenzyme GlcN6P Functional Groups

4.11 Mechanism of glmS Ribozyme Self‐Cleavage

4.12 Potential for Antibiotic Development Affecting glmS Ribozyme/Riboswitch Function

Acknowledgments

References

5 The Lariat Capping Ribozyme

5.1 Introduction

5.2 Reactions Catalyzed by LCrz

5.3 The Structure of the LCrz Core

5.4 Communication Between LCrz and Flanking Elements

5.5 Reflections on the Evolutionary Aspect of LCrz

5.6 LCrz as a Research Tool

5.7 Conclusions and Unsolved Problems

References

6 Self‐Splicing Group II Introns

6.1 Introduction

6.2 Milestones in the Characterization of Group II Introns

6.3 Evolutionary Conservation and Biological Role

6.4 Structural Architecture

6.5 Lessons and Tools from Group II Intron Research

6.6 Perspectives and Open Questions

Acknowledgments

References

7 The Spliceosome: an RNA–Protein Ribozyme Derived From Ancient Mobile Genetic Elements

7.1 Discovery of Introns and Splicing

7.2 snRNPs and the Spliceosome

7.3 The Spliceosomal Cycle

7.4 Chemistry of Splicing

7.5 Spliceosome Structural Analysis

7.6 Spliceosome Structures

7.7 Insights from Spliceosome Disassembly

7.8 Conservation of Spliceosomal and Group II Active Sites

7.9 Summary and Perspectives

References

8 The Ribosome and Protein Synthesis

8.1 Central Dogma of Molecular Biology

8.2 Structure of the

E. coli

Ribosome

8.3 Translation Cycle

References

9 The RNase P Ribozyme

9.1 Introduction

9.2 Bacterial RNase P

9.3 Substrate Interaction

9.4 RNA‐based Metal Ion Catalysis

9.5 RNase P as an Antibiotic Target

9.6 Application of RNase P as a Tool in Gene Inactivation

References

10 Ribozyme Discovery in Bacteria

10.1 Introduction

10.2 Protein Takeover

10.3 Ribozymes as Evolutionary Holdouts

10.4 The Role of Serendipity in Early Ribozyme Discoveries

10.5 Ribozymes Emerge from Structured Noncoding RNA Searches

10.6 Ribozymes Beget Ribozymes

10.7 Ribozyme Dispersal Driven by Association with Selfish Elements

10.8 Domesticated Ribozymes

10.9 New Ribozymes from Old

10.10 Will New ncRNAs Broaden the Scope of RNA Catalysis?

Acknowledgments

References

11 Small Self‐Cleaving Ribozymes in the Genomes of Vertebrates

11.1 The Family of Small Self‐Cleaving Ribozymes in Eukaryotic Genomes: From Retrotransposition to Domestication

11.2 The Widespread Case of the Hammerhead Ribozyme: From Bacteria to Vertebrate Genomes

11.3 Other Intronic HHRs in Amniotes: Small Catalytic RNAs in Search of a Function

11.4 The Family of the Hepatitis D Virus Ribozymes

11.5 Other Small Self‐Cleaving Ribozymes Hidden in the Genomes of Vertebrates?

References

Part III: Engineered Ribozymes

12 Phosphoryl Transfer Ribozymes

12.1 Introduction

12.2 Kinase Ribozymes

12.3 Glycosidic Bond Forming Ribozymes

12.4 Capping Ribozymes

12.5 Ligase Ribozymes

12.6 Polymerase Ribozymes

12.7 Summary

References

13 RNA Replication and the RNA Polymerase Ribozyme

13.1 Introduction

13.2 Nonenzymatic RNA Polymerization

13.3 Enzymatic RNA Polymerization

13.4 Essential Requirements for an RNA Replicator

13.5 The Class I Ligase and the First RNA Polymerase Ribozymes

13.6 Structural Insight into the Catalytic Core of the RNA Polymerase Ribozyme

13.7 Selection for Improved Polymerase Activity I

13.8 Selection for Improved Polymerase Activity II

13.9 Conclusion and Outlook

References

14 Maintenance of Genetic Information in the First Ribocell

14.1 The Ribocell and the Stages of the RNA World

14.2 The Error Thresholds

14.3 Compartmentalization

14.4 Minimal Gene Content of the First Ribocell

Acknowledgments

References

15 Ribozyme‐Catalyzed RNA Recombination

15.1 Introduction

15.2 RNA Recombination Chemistry

15.3 Azoarcus Group I Intron

15.4 Crystal Structure

15.5 Mechanism

15.6 Model for Prebiotic Chemistry

15.7 Spontaneous Self‐assembly of Azoarcus RNA Fragments

15.8 Autocatalysis

15.9 Cooperative Self‐assembly

15.10 Game Theoretic Treatment

15.11 Significance of Game Theoretic Treatments

15.12 Other Recombinase Ribozymes

15.13 Conclusions

References

16 Engineering of Hairpin Ribozymes for RNA Processing Reactions

16.1 Introduction

16.2 The Naturally Occurring Hairpin Ribozyme

16.3 Structural Variants of the Hairpin Ribozyme

16.4 Hairpin Ribozymes that are Regulated by External Effectors

16.5 Twin Ribozymes for RNA Repair and Recombination

16.6 Hairpin Ribozymes as RNA Recombinases

16.7 Self‐Splicing Hairpin Ribozymes

16.8 Closing Remarks

References

17 Engineering of the

Neurospora

Varkud Satellite Ribozyme for Cleavage of Nonnatural Stem‐Loop Substrates

17.1 Introduction

17.2 Simple Primary and Secondary Structure Changes Compatible with Substrate Cleavage by the VS Ribozyme

17.3 The Structural Context

17.4 Structure‐Guided Engineering Studies

17.5 Summary and Future Prospects for VS Ribozyme Engineering

References

18 Chemical Modifications in Natural and Engineered Ribozymes

18.1 Introduction

18.2 Chemical Modifications to Study Natural Ribozymes

18.3 In Vitro Selection with Chemically Modified Nucleotides: Expanding the Scope of DNA and RNA Catalysis

18.4 Outlook

References

19 Ribozymes for Regulation of Gene Expression

19.1 Introduction

19.2 Conditional Gene Expression Control by Riboswitches

19.3 Allosteric Ribozymes as Engineered Riboswitches

19.4 In Vitro Selection Methods

19.5 In Vivo Screening Methods

19.6 Rational Design of Allosteric Ribozymes

19.7 Applications of Aptazymes for Gene Regulation

References

20 Development of Flexizyme Aminoacylation Ribozymes and Their Applications

20.1 Introduction

20.2 The First Ribozymes Catalyzing Acyl Transfer to RNAs

20.3 The ATRib Variant Family: Ribozymes Catalyzing tRNA Aminoacylation via Self‐Acylated Intermediates

20.4 Prototype Flexizymes: Ribozymes Catalyzing Direct tRNA Aminoacylation

20.5 Flexizymes: Versatile Ribozymes for the Preparation of Aminoacyl‐tRNAs

20.6 Application of Flexizymes to Genetic Code Reprogramming

20.7 Development of Orthogonal tRNA/Ribosome Pairs Using Mutant Flexizymes

20.8 In Vitro Selection of Bioactive Peptides Containing nPAAs Through RaPID Display

20.9 tRid: A Method for Selective Removal of tRNAs from an RNA Pool

20.10 Use of a Natural Small RNA Library Lacking tRNA for In Vitro Selection of a Folic Acid Aptamer: Small RNA Transcriptomic SELEX

20.11 Summary and Perspective

Acknowledgments

References

21 In Vitro Selected (Deoxy)ribozymes that Catalyze Carbon–Carbon Bond Formation

21.1 Introduction

21.2 Diels–Alderase Ribozymes

21.3 Aldolase Ribozyme

21.4 A DNAzyme that Catalyzes a Friedel–Crafts Reaction

21.5 Alkylating Ribozymes

21.6 Conclusion

References

22 Nucleic Acid‐Catalyzed RNA Ligation and Labeling

22.1 Introduction

22.2 Ribozymes for RNA Labeling at Internal Positions

22.3 RNA‐Catalyzed Labeling of RNA at the 3′‐end

22.4 Potential Ribozymes for RNA Labeling at the 5′‐end

22.5 Conclusions

Acknowledgments

References

Volume 2

Part IV: DNAzymes

23 The Chemical Repertoire of DNA Enzymes

23.1 Introduction

23.2 Catalytic Repertoire of DNAzymes

23.3 Chemical Modifications as Rescue and Expansion of Catalytic Activity

23.4 Conclusions

Acknowledgment

References

24 Light‐Utilizing DNAzymes

24.1 Introduction

24.2 PhotoDNAzymes (PDZs)

24.3 Pseudo‐photo DNAzymes

24.4 Photoactive DNA Components for Future PDZ Design

24.5 Conclusions

References

Chapter 25: Diverse Applications of DNAzymes in Computing and Nanotechnology

25.1 Introduction

25.2 Loop‐Based Control of DNAzyme Logic Gates

25.3 Strand Displacement Control of DNAzyme Cascades

25.4 Trainable and Adaptive DNAzyme Networks

25.5 DNAzyme Nanorobots

25.6 Conclusions

Acknowledgments

References

Part V: Ribozymes/DNAzymes in Diagnostics and Therapy

26 Optimization of Antiviral Ribozymes

26.1 Introduction

26.2 Antiviral Catalytic Antisense RNAs

26.3 A General Experimental Strategy for Designing Catalytic Antisense RNAs

26.4 Concluding Remarks

Acknowledgments

References

27 DNAzymes as Biosensors

27.1 Introduction

27.2 Advantages of DNAzyme‐Based Sensors

27.3 General Mechanism of RNA Cleavage

27.4 Representative DNAzymes

27.5 DNAzyme‐Based Fluorescent Sensors

27.6 Colorimetric Sensors Based on DNAzymes

27.7 Electrochemical Sensors and Other Sensors

27.8 DNAzyme Sensors Coupled with Signal Amplification Mechanisms

27.9 Conclusions

Acknowledgment

References

28 Compartmentalization‐Based Technologies for In Vitro Selection and Evolution of Ribozymes and Light‐Up RNA Aptamers

28.1 Introduction

28.2 Selection of Self‐Modifying Ribozymes

28.3 Conclusions

Acknowledgments

References

Part VI: Tools and Methods to Study Ribozymes

29 Elucidation of Ribozyme Mechanisms at the Example of the Pistol Ribozyme

29.1 Introduction

29.2 Structural Aspects – Overall Fold and Cleavage Site Architecture

29.3 Cleavage Mechanism and Catalysis

29.4 Mechanistic Proposal for the Pistol Ribozyme

29.5 Outlook

References

Note

30 Strategies for Crystallization of Natural Ribozymes

30.1 Introduction

30.2 Strategies to Inactivate the Nucleophile

30.3 When the Cleavage Site is at the Edge of the Ribozyme

30.4 Removal or Neutralization of the Catalytic 2′‐Hydroxyl Group

30.5 Removal of the Scissile Phosphodiester Bond Using Circular Permutation

30.6 Mutation of Residues Involved in the Acido‐Basic Aspects of Transesterification

30.7 Recently Discovered Ribozymes

30.8 Conclusions and Perspectives

Acknowledgments

References

31 NMR Spectroscopic Investigation of Ribozymes

31.1 Introduction

31.2 Methods and Preparation

31.3 Resonance Assignment

31.4 NMR‐Based Characterization of Particular Ribozymes

31.5 Closing Remarks

References

32 Studying Ribozymes with Electron Paramagnetic Resonance Spectroscopy

32.1 Introduction

32.2 EPR Methods

32.3 Site‐Directed Spin Labeling

32.4 Examples for Applications of EPR to Ribozymes

32.5 Conclusion

References

33 Computational Modeling Methods for 3D Structure Prediction of Ribozymes

33.1 Introduction

33.2 Computational Modeling Approaches

33.3 Case Studies

33.4 Future Perspectives

Acknowledgments

References

Index

End User License Agreement

List of Tables

Chapter 2

Table 2.1 Summary of known self‐cleaving ribozyme classes and their abundance...

Chapter 3

Table 3.1 Catalytic participants in the cleavage reactions of the nucleolytic...

Chapter 5

Table 5.1 Comparison of currently known LCrz.

Chapter 6

Table 6.1 Characteristics of retrohoming and retrotransposition pathways in G...

Chapter 9

Table 9.1 Correlation of potential hydrogen bonding contacts at the P RNA:tRN...

Chapter 14

Table 14.1 RNA‐dependent RNA polymerase ribozymes.

Chapter 15

Table 15.1 Possible routes from

Azoarcus

RNA fragments to a full‐length covale...

Chapter 26

Table 26.1 Processing of TAR‐containing artificial target molecules.

Chapter 33

Table 33.1 List of experimentally solved and computationally modeled structur...

List of Illustrations

Chapter 1

Figure 1.1 Three ribozyme‐catalyzed transesterification reactions. In the nu...

Figure 1.2 The geometry of a phosphorane. (a) A representation of phosphorus...

Figure 1.3 The chemical mechanism of the nucleolytic ribozymes and possible ...

Figure 1.4 Simulations of the pH dependence of general acid–base catalyzed r...

Figure 1.5 Hexaquo‐magnesium ions. The Mg

2+

ion has an inner hydration s...

Figure 1.6 The positions of Mg

2+

ions bound in the transition state of t...

Chapter 2

Figure 2.1 Rolling circle replication mechanisms in viroids and viroid‐like ...

Figure 2.2 The R2 element in

Bombyx mori

and its transposition mechanism. (a...

Figure 2.3 Self‐cleaving ribozymes as parts of transposable elements. (a) Sc...

Chapter 3

Figure 3.1 The chemical mechanism of the nucleolytic ribozymes catalyzed by ...

Figure 3.2 Secondary structure depictions of the nucleolytic ribozymes with ...

Figure 3.3 Experimental rate‐pH profiles for the VS and hairpin ribozymes. (...

Figure 3.4 Proposed mechanisms for three ribozymes using guanine and adenine...

Figure 3.5 The structure of the VS ribozyme in dimeric form. In this and sub...

Figure 3.6 The structure and active center of the hairpin ribozyme in its na...

Figure 3.7 Schematic of the structures of the hairpin and VS ribozyme drawn ...

Figure 3.8 The structure of the twister ribozyme. This representation was ge...

Figure 3.9 The structure of the hammerhead ribozyme. This representation was...

Figure 3.10 Proposed mechanisms for the hammerhead and pistol ribozymes. Bot...

Figure 3.11 The structure of the HDV ribozyme. (a) The overall structure of ...

Figure 3.12 Proposed mechanisms for the HDV and TS ribozymes. These ribozyme...

Figure 3.13 The structure of the TS ribozyme. This representation was genera...

Figure 3.14 The structure of the pistol ribozyme. This representation was ge...

Figure 3.15 The structure of the

glmS

ribozyme bound to glucose‐6‐phosphate....

Figure 3.16 The sequence and proposed secondary structure of the hatchet rib...

Chapter 4

Figure 4.1 Structure of the

glmS

ribozyme. (a) Secondary structure. The core...

Figure 4.2 GlcN6P coenzyme and recognition by the

glmS

ribozyme. (a) Structu...

Figure 4.3 Interpretation of

glmS

ribozyme pH‐reactivity profile. (a) By ana...

Chapter 5

Figure 5.1 (a) Branching reaction catalyzed by LCrz. The 2′ OH of the intern...

Figure 5.2 Secondary structure diagrams of the three known LCrz.

Dir

LCrz is ...

Figure 5.3 (a) Three different views of the structure of

Dir

LCrz. In the lef...

Figure 5.4 (a) The three processing pathways that have been characterized fo...

Figure 5.5 (a) Model for the evolution of a GrIrz into LCrz. The evolution i...

Figure 5.6 Lariat capping as a tool. Lariat capping constructs are made as f...

Chapter 6

Figure 6.1 Milestones in the research of GIIi. Schematic representation of s...

Figure 6.2 Secondary and tertiary structures of GIIi. Schematic secondary RN...

Figure 6.3 Evolutionary classification. The indicated classes are a compilat...

Figure 6.4 GIIi retrohoming pathways. (a) Schematic showing retrohoming in i...

Figure 6.5 Active site representations of three group II introns of know 3D ...

Chapter 7

Figure 7.1 Chemical mechanisms of splicing. Splicing of nuclear pre‐mRNA (le...

Figure 7.2 Recognition of pre‐mRNA introns. (a) Conserved intron sequences a...

Figure 7.3 Spliceosome assembly pathway.

Figure 7.4 Comparison of group II and spliceosomal snRNA structures. (Top le...

Figure 7.5 Two metal ion hypothesis. (a) Two metals at the active site of

E.

...

Figure 7.6 Model for the spliceosome active site. Inhibition of splicing by ...

Figure 7.7 The pre‐spliceosome: tri‐snRNP structure. (a) Cryo‐EM structure o...

Figure 7.8 The pre‐spliceosome: A complex structure.

(

a) The A complex is co...

Figure 7.9 B complex structure. (a) Cryo‐EM structure of the

S. cerevisiae

...

Figure 7.10 Activation of the spliceosome: B

act

complex structure. (a) Cryo‐...

Figure 7.11 C complex structure. (a) Cryo‐EM structure of the

S. cerevisiae

...

Figure 7.12 C* complex structure. (a) Cryo‐EM structure of the

S. cerevisiae

...

Figure 7.13 Post‐catalytic spliceosome: P complex structure. (a) Cryo‐EM str...

Figure 7.14 Comparison of group II and spliceosomal RNP. (a) Detail of struc...

Chapter 8

Figure 8.1 Structural overview of the bacterial ribosome. (a) View on the SS...

Figure 8.2 The translation cycle. During initiation (green), the SSU incorpo...

Figure 8.3 Main events during formation of the 70S initiation complex. (a) S...

Figure 8.4 Decoding and accommodation of the A‐site tRNA. (a) View on the SS...

Figure 8.5 Conformation of residues involved in the proton wire of the PTC. ...

Figure 8.6 Structural rearrangements of the ribosome and EF‐G during translo...

Figure 8.7 Termination of translation in the presence of a stop codon. (a) V...

Figure 8.8 Post‐termination 70S ribosome in complex with RRF and P/E‐tRNA. (...

Chapter 9

Figure 9.1 Family tree of RNA‐based RNase P enzymes (top) and sketches of pr...

Figure 9.2 Secondary structures of (a)

E. coli

(type A), (b)

T. maritima

(ty...

Figure 9.3 (a) Secondary structure of

T. maritima

tRNA

Phe

, including te...

Figure 9.4 Tertiary structure of the

T. maritima

RNase P holoenzyme in ...

Figure 9.5 Arrangement of core structural elements in the crystal structures...

Figure 9.6 Correlation of

T. maritima

P RNA secondary (a) and tertiary ...

Figure 9.7 Top: tertiary structures of the S‐domains from bacterial A‐type (

Figure 9.8 (a) Interface between RNA and protein subunit in the post‐cleavag...

Figure 9.9 Interactions between the

T. maritima

RNase P holoenzyme and ...

Figure 9.10 (a) Interactions between the

T. maritima

RNase P holoenzyme...

Figure 9.11 (a), Left: Transition state model for site‐specific phosphodiest...

Scheme 9.1 Rate constants for individual steps of pre‐tRNA processing by bac...

Figure 9.12 Structures of reported bacterial RNase P inhibitors. (a) In NeoR...

Figure 9.13 Degradation of target mRNAs by external guide sequence (EGS) app...

Figure 9.14 EGS variants to induce target RNA cleavage by human nuclear‐cyto...

Figure 9.15 EGS:target RNA complexes for cleavage by human nuclear‐cytoplasm...

Chapter 10

Figure 10.1 Consensus structures for

glmS

, twister and twister sister ribozy...

Figure 10.2 Consensus structures for pistol and hatchet ribozymes. Annotatio...

Figure 10.3 Sizes and structural complexities of ribozymes and other structu...

Chapter 11

Figure 11.1 Diagrams of the hammerhead ribozyme drawn in (a) the classical s...

Figure 11.2 (a) Representative example of a minimal type I hammerhead presen...

Figure 11.3 (a) Schematic representation of the discontinuous hammerhead rib...

Figure 11.4 DNA sequence alignment of the discontinuous hammerhead motifs fr...

Figure 11.5 (a) Schematic representation of the intronic HH9 hammerhead ribo...

Figure 11.6 DNA sequence alignment of representative HH9 hammerhead motifs c...

Figure 11.7 (a) Schematic representation of the intronic HH10 hammerhead rib...

Figure 11.8 (a) Schematic representation of the intronic hammerhead ribozyme...

Figure 11.9 Splicing graphs of the human RECK (a) and CCDC186 (b) genes obta...

Figure 11.10 Schematic representations of (a) the human and (b) the microbat...

Figure 11.11 DNA sequence alignment of the intronic HDV‐like motifs conserve...

Chapter 12

Figure 12.1 Kinase ribozymes have been characterized that catalyze phosphory...

Figure 12.2 Glycosidic bond‐forming ribozymes catalyze the synthesis of (a) ...

Figure 12.3 Ribozyme mediated self‐capping. (A) RNA capping ribozymes cataly...

Figure 12.4 Protein mediated RNA ligation proceeds via a three‐step mechanis...

Figure 12.5 Ligase ribozymes catalyze the ligation of an RNA molecule throug...

Figure 12.6 Self‐replication schematic (A). The ribozyme, R

1

, ligates substr...

Figure 12.7 Template dependent RNA and DNA polymerization is catalyzed by RN...

Chapter 13

Figure 13.1 Nonenzymatic polymerization of 5′‐methylimidazole activated RNA....

Figure 13.2 Different ideal requirements for RNA template (−) and replicase ...

Figure 13.3 Cross‐replicating RNA ligases. Ligase E1 catalyzes the ligation ...

Figure 13.4 Selection of the class I ligase and the R18 RNA polymerase riboz...

Figure 13.5 Structure of the class I RNA ligase. (a) Secondary structure of ...

Figure 13.6 Secondary structure representation of the R18 polymerase ribozym...

Figure 13.7 Overview of ribozyme RNA polymerase ribozymes. Residues in red i...

Figure 13.8 Principle of templated RNA polymerization catalyzed by the RNA p...

Chapter 14

Figure 14.1 Stages of the RNA world. Between the two well‐defined endpoints ...

Figure 14.2 The error threshold for the original Eigen's formulation (Eq. (1...

Figure 14.3 Error rate of the replicase ribozymes as function of their lengt...

Figure 14.4 The stochastic corrector model. Three essential independently re...

Figure 14.5 A hypothetical minimal metabolism for a ribocell. The replicatio...

Chapter 15

Figure 15.1 Two mechanisms of trans‐esterification as catalyzed by the

Azoar

...

Figure 15.2 Spontaneous self‐assembly of the

Azoarcus

ribozyme from four fra...

Figure 15.3 Base pairing between two fragments (e.g.

X

and

Y

) that is requir...

Figure 15.4 Demonstration of autocatalysis during

Azoarcus

ribozyme self‐ass...

Figure 15.5 Self‐assembly of the

Azoarcus

ribozyme from

WXY

and

Z

fragments....

Figure 15.6 Arrangement of three short RNA oligomers in a spontaneous RNA–RN...

Chapter 16

Figure 16.1 (a) Secondary structure of the hairpin ribozyme. The arrow denot...

Figure 16.2 Structural variants of the hairpin ribozyme (schematically). (a)...

Figure 16.3 Hairpin ribozyme variants that can be activated by external olig...

Figure 16.4 Repressible (a) and inducible (b) hairpin ribozyme variants. Red...

Figure 16.5 FMN‐responsive hairpin ribozyme. (a) Secondary structure of the ...

Figure 16.6 Twin ribozyme‐mediated RNA recombination. The fragments to be re...

Figure 16.7 Scheme of hairpin ribozyme‐mediated recombination as described i...

Figure 16.8 Scheme of hairpin ribozyme‐mediated RNA circularization as descr...

Figure 16.9 Scheme of hairpin ribozyme‐mediated self‐splicing. A linear in v...

Chapter 17

Figure 17.1 Sequence and proposed secondary structure of a minimal VS ribozy...

Figure 17.2 Diverse sequence and structural contexts for the SLI substrate t...

Figure 17.3 Formation of the KLI and associated conformational change. (a) M...

Figure 17.4 SLI substrate variants that can be cleaved by the wild‐type VS r...

Figure 17.5 Bipartite binding and conformational changes associated with sub...

Figure 17.6 Sequence and activity of rationally engineered VS ribozyme varia...

Figure 17.7 Sequence and activity of rationally engineered VS ribozyme varia...

Figure 17.8 Improving the activity of a kissing‐loop substitution variant of...

Chapter 18

Figure 18.1 Ribose modifications to stabilize ribozymes for in cell applicat...

Figure 18.2 Examples for nucleosides with functional groups mimicking amino ...

Figure 18.3 In vitro selection strategy for an amide‐hydrolyzing deoxyribozy...

Figure 18.4 XNA and XNA‐based catalysts developed by Holliger and coworkers....

Chapter 19

Figure 19.1

General structure of an aptazyme

. The tripartite construct can b...

Figure 19.2

Helix slippage mechanism

. The signal of ligand binding is transm...

Figure 19.3 Mechanism of ON‐ and OFF‐switches in hammerhead‐based aptazymes ...

Figure 19.4 Mechanism of ON‐ and OFF‐switches in hammerhead‐based aptazymes ...

Figure 19.5

Aptazyme‐based regulation of different RNA classes

. a) The...

Chapter 20

Figure 20.1 Evolution of ATRib family ribozymes. (a) Self‐aminoacylation of ...

Figure 20.2 Evolution of flexizymes. (a) The N70–tRNA library containing a 5...

Figure 20.3 Combinations of flexizymes and activating groups compatible with...

Figure 20.4 Genetic code reprogramming in a reconstituted in vitro translati...

Figure 20.5 Translation of a model peptide consisting of 23 different amino ...

Figure 20.6 Development of an orthogonal tRNA/ribosome pair. (a) Recognition...

Figure 20.7 Scheme of RaPID selection using a macrocyclic peptide library. A...

Figure 20.8 tRid, a method for selectively depleting tRNAs from an RNA pool,...

Chapter 21

Figure 21.1 Reaction between a biotin maleimide substrate and a 5'‐polyethyl...

Figure 21.2 Crystal structure of selenium‐modified Diels‐Alder ribozyme comp...

Figure 21.3 Aldol reaction between a biotinylated benzaldehyde moiety and a ...

Figure 21.4 DNAzyme‐catalyzed Friedel‐Crafts reaction between an acyl imidaz...

Figure 21.5 Self‐alkylation reaction between a biotinylated iodoacetamide su...

Figure 21.6 Michael reaction between a biotinylated cysteine Michael‐donor s...

Figure 21.7 Self‐alkylation reaction between a biotinylated epoxide substrat...

Chapter 22

Figure 22.1 (a) Schematic representation of the iodoacetamide‐reactive riboz...

Figure 22.2 Schematic representation of RNA labeling using a twin ribozyme. ...

Figure 22.3 (a) DNA‐catalyzed RNA ligation by the 9DB1 deoxyribozyme and str...

Figure 22.4 Schematic presentation of the RNA polymerase ribozyme that catal...

Figure 22.5 (a) Iso6 capping ribozyme exemplarily shown with m7GDP as labeli...

Chapter 23

Figure 23.1 Schematic representation of the putative secondary structures of...

Figure 23.2 Selection scheme for the isolation of DNAzymes with phosphatase ...

Figure 23.3 (a) Close‐up view on the structure of the catalytic core of the ...

Figure 23.4 Schematic representations of the putative chemical mechanisms

of...

Figure 23.5 (a) Chemical structures of base modified nucleosides introduced ...

Figure 23.6 Chemical structures of photocaging groups that have been used fo...

Figure 23.7 Chemical structures of dN*TPs that have been used for the isolat...

Figure 23.8 Sequences and hypothetical 2D structures of M

2+

‐independent ...

Chapter 24

Figure 24.1 (a) A photoenzyme binds its substrates in the ground state but o...

Figure 24.2 (a) Thymine dimer repair photoDNAzymes plotted by wavelength. Al...

Figure 24.3 (a) Pseudo‐photoDNAzymes are photocatalysts for a single turnove...

Figure 24.4 (a) The 2‐Aminopurine design of photochemical DNAzymes may begin...

Chapter 25

Figure 25.1 DNAzyme loop‐based logic gates. (a) DNAzyme structure (here the ...

Figure 25.2 Distribution of logic gates in wells for

MAYA‐I

, a DNAzyme...

Figure 25.3 Design and application of structured chimeric substrates for mul...

Figure 25.4 The

MAYA‐III

trainable game‐playing automaton [37]. (a) An...

Figure 25.5 Theoretical studies of molecular learning circuits using DNAzyme...

Figure 25.6 Nanoscale locomotion on patterned surfaces by molecular spiders....

Chapter 26

Figure 26.1 Secondary structure model and sequence requirements of the trans...

Figure 26.2 Mechanism of action of a natural antisense RNA system, illustrat...

Figure 26.3 Hypothesized mode of action of catalytic antisense RNAs. The dia...

Figure 26.4 Sequence and secondary structure of the HVI‐1 5′NTR. The functio...

Figure 26.5 Artificial long RNA target series used to validate the usefulnes...

Figure 26.6 Anti‐HIV‐1 effect of TAR‐based catalytic antisense RNAs. (a) The...

Figure 26.7 In vitro anti‐HIV‐1 activity of catalytic antisense RNAs. (a) An...

Figure 26.8 The hepatitis C virus genome is shown in the upper panel. The pr...

Figure 26.9 In vitro selection strategy for the identification of anti‐HCV I...

Figure 26.10 Anti‐HCV IRES activity of different catalytic antisense RNAs. I...

Chapter 27

Figure 27.1 Possible catalytic functions of metal ions in the RNA cleavage r...

Figure 27.2 Secondary structures of two Pb

2+

‐dependent DNAzymes: (a) GR5...

Figure 27.3 (a) The Zn

2+

‐dependent RNA‐cleaving DNAzyme, where the red U...

Figure 27.4 Secondary structures of two Na

+

‐dependent RNA‐cleaving DNAzy...

Figure 27.5 (a) G‐quadruplex DNAzyme (or peroxidase‐mimicking DNAzyme) that ...

Figure 27.6 (a) The structure change of an ATP aptazyme. The ATP aptamer reg...

Figure 27.7 (a) A rational design of the DNAzyme‐based catalytic beacon sens...

Figure 27.8 (a) The NaA43 DNAzyme‐based intracellular sensing of Na

+

bas...

Figure 27.9 (a) Sensing design of an internally labeled RNA‐cleaving DNAzyme...

Figure 27.10 (a) The folding‐based sensing of Na

+

using 2AP‐labeled Ce13...

Figure 27.11 A colorimetric Pb

2+

sensor by using the 17E DNAzyme to dire...

Figure 27.12 (a) The working principle of the target‐responsive DNAzyme hydr...

Figure 27.13 (a) Colorimetric sensing of Cu

2+

using the dual‐DNAzyme sys...

Figure 27.14 (a) Methylene‐blue‐modified DNAzyme generates electrochemical s...

Figure 27.15 (a) Amplified sensing platform combining molecular beacons with...

Figure 27.16 A sensing strategy using Mg

2+

‐dependent DNAzymes in HCR for...

Chapter 28

Figure 28.1 Establishment of genotype/phenotype link. (a) Strategy based on ...

Figure 28.2 Isolation of an RNA ligase ribozyme by a self‐modification strat...

Figure 28.3 Isolation of ribozymes using in vitro compartmentalization (IVC)...

Figure 28.4 Droplet‐based microfluidic screening strategy. (a) A gene librar...

Chapter 29

Figure 29.1 Pistol ribozymes. (a) Consensus RNA sequence and secondary struc...

Figure 29.2 Three‐dimensional fold of the

env25

pistol ribozyme [8] in carto...

Figure 29.3 RNA phosphodiester cleavage by phosphodiester transfer involving...

Figure 29.4 Active site of the

env25

pistol ribozyme (PDB code 5K7C) [8]. (a...

Figure 29.5 Overlay of cleavage site G53–U54 (yellow) and G40 of the X‐ray s...

Figure 29.6 Current understanding of the chemical mechanism for phosphodiest...

Chapter 30

Figure 30.1 The folded core of the HdV ribozyme corresponds to the 3′‐cleava...

Figure 30.2 The GlmS riboswitch is also a ribozyme. (a) The GlmS riboswitch ...

Figure 30.3 This figure displays the structures of the minimal (PDB: 1mme) (...

Figure 30.4 (a) Splicing pathway mediated by the group I introns in general ...

Figure 30.5 Structure of a group II intron lariat primed for reverse splicin...

Figure 30.6 The hairpin ribozyme can be active as a short or an extended ver...

Figure 30.7 Organization of the LC ribozyme constructs. (a) Representation o...

Figure 30.8 The secondary structure of the crystallized construct of the VS ...

Figure 30.9 The twister (a, b) and twister sister (TS) (c, d) ribozymes. In ...

Figure 30.10 Structural aspects of the pistol ribozyme (PDB: 5k7e). (a) The ...

Chapter 31

Figure 31.1 Different classes of ribozymes are shown. Ribozymes can be class...

Figure 31.2 Outline of three different RNA labeling methods. Labeled nucleot...

Figure 31.3 Illustration of the effect caused by the incorporation of a phot...

Figure 31.4 Graphical representation of further assignment of an RNA, utiliz...

Figure 31.5 Graphical representation of the assignment of an RNA, utilizing

Figure 31.6

1

H‐1D NMR spectra of the HDV ribozyme measured and published by ...

Figure 31.7 The imino proton regions of 1H‐1D NMR spectra of different riboz...

Chapter 32

Figure 32.1 The energy levels and corresponding EPR spectra of an unpaired e...

Figure 32.2 EPR spectra for (a) an isotropic

g

‐tensor with

g

iso

, (b) an axia...

Figure 32.3 EPR spectra of a nitroxide in the frozen state at (a)

X

‐band (9 ...

Figure 32.4 Dependence of cw X‐band EPR nitroxide spectra on the rotational ...

Figure 32.5 Pulse sequences for commonly used pulsed hyperfine experiments. ...

Figure 32.6 Scheme of (a) the electron A–electron B arrangement within

B

0

an...

Figure 32.7 Pulse sequences of the most often used PDS methods: (a) 4‐pulse ...

Figure 37.8 Conversion of the PELDOR time trace into a distance distribution...

Figure 32.9 Scheme showing (a) the rotatable bonds for the nitroxide MTSSL u...

Figure 32.10 Spin labels for RNA labeling during synthesis.

Figure 32.11 Spin labeling of RNA postsynthetically.

Figure 32.12 Obtaining long, labeled RNAs via ligation using (a) a T4‐ligase...

Figure 32.13 Obtaining long, labeled RNAs via (a) sequence recognition, alky...

Figure 32.14 Non‐covalent labeling with

ç

and

Ġ

.

Figure 32.15 A trityl‐

9

and Gd(III)‐based

10

spin label for oligonucleotide...

Figure 32.16 Secondary and tertiary arrangements of the m‐ (a, b) and tsHHRz...

Figure 32.17 (a) 3‐Pulse ESEEM spectra of Mn

2+

bound to different constr...

Figure 32.18 (a) HYSCORE spectrum of the high‐affinity Mn

2+

binding site...

Figure 32.19 Structure of the tsHHRz and the PELDOR‐derived distance distrib...

Figure 32.20 (a) Structure of the Diels–Alder ribozyme. (b) cw X‐band EPR sp...

Figure 32.21 Spin labeling of the

Tetrahymena

group I intron and sketches of...

Figure 32.22 (a) Structure of HP92 with Mn

2+

indicated as red sphere and...

Figure 32.23 Top: The derived distance distributions (red lines) for the dou...

Figure 32.24 PELDOR measurements on (a) PcrA with labels at different sites ...

Chapter 33

Figure 33.1 An overview of applications of modeling approaches depending on ...

Guide

Cover Page

Title Page

Title Page

Copyright

Preface

Foreword

Table of Contents

Begin Reading

Index

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Ribozymes

Volume 1

Edited by

Sabine MüllerBenoît MasquidaWade Winkler

Ribozymes

Volume 2

Edited by

Sabine MüllerBenoît MasquidaWade Winkler

Editors

Sabine Müller

University Greifswald

Institut für Biochemie

Felix‐Hausdorff‐Str. 4

17489 Greifswald

Germany

Benoît Masquida

CNRS – Université de Strasbourg

UMR 7156

Génétique Mol\xE9culaire Génomique Microbiologie

4 allée Konrad Roentgen

67084 Strasbourg

France

Wade Winkler

The University of Maryland

Cell Biology & Molecular Genetics

3112 Biosciences Bldg.

MD

United States

Cover

Courtesy of Dr. Benoît Masquida

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Preface

Ribozymes, a neologism that appeared in 1982 in a paper of Tom Cech, triggered the blossom of a field of research on which the RNA community gathered its countless efforts over years. Thus, after the discovery of the first naturally occurring catalytic RNAs, more than 30 years ago, research in the field of ribozymes and RNA catalysis has made tremendous progress. In the 1990s, many of the catalytic RNAs known today were first identified in nature. In parallel to these discoveries, the powerful SELEX method for discovery of novel nucleic acids was invented, which allowed the development of artificial ribozymes with rather diverse functionalities. Over the years, investigation into the structure and mechanism of ribozymes led to a deep understanding of their catalytic strategies. Today, ribozymes are understood to an extent that it is possible to utilize rational design and molecular engineering to construct catalytic RNAs with pre‐defined function. Yet, there is still much to be learned. Improvements in high‐throughput bioinformatics approaches are still fostering the discovery of new ribozymes and novel genomic locations of known motifs in highly diverse genetic contexts for all branches of life. In spite of an apparent loss of attraction due to the discovery of the RNAi and CRISPR/cas mechanisms, which at times seemed more appealing, ribozymes still inspire activity of many research groups. Even after three decades of research following discovery of the first catalytic RNA, ribozyme research has not lost the intriguing and highly motivating flair of the first days. There are still many questions to be addressed and much is waiting to be discovered.

This book aims to survey what we have learned over the past 35 years about ribozymes and nucleic acid catalysis and to present the today state of the art. It musters over 30 chapters demonstrating this activity. From the study of artificial ribozymes developed by Darwinian selection to natural ribozymes including the large translation and splicing machineries, via ribozyme engineering, and their biochemical and biophysical studies, this book takes the reader through a thrilling journey. An enormous knowledge has been accumulated on ribozyme structure, function and mechanism. However, the wealth of data also makes apparent the missing parts, which encompass what are the cellular processes regulated by ribozymes and how this is done. For instance, only little is known about the role of ribozymes identified in the human genome, and the biological roles of the new ribozymes discovered in bacteria have just started to be studied. Ribozymes deserve a continuous look from researchers, and state of the art investigation methods need to be coupled with classical ones to unravel the still unknown.

We wish to thank all participating authors for the tremendous work. Their efforts and high‐quality contributions have made this book come true. We hope we have succeeded in providing a source of information on mechanistic and structural aspects of nucleic acid catalysis, on tools and methods for characterization, engineering and application of ribozymes, as well as on the key questions, strategies and challenges in ribozyme research today.

December 2019

Sabine Müller

Benoît Masquida

Wade Winkler

Foreword

The study of ribozymes, RNA‐based catalysts, and subsequently nucleic acid‐based catalysis has been immensely instrumental in the push of efforts toward a deeper understanding of RNA structure and function. The field attracted many scientists trained in chemistry, biology, or computer science. In 1993, a few years after the Noble Prize in Chemistry (https://www.nobelprize.org/prizes/lists/all-nobel-prizes-in-chemistry) was awarded to Tom Cech [1] and Sidney Altman [2] for the discovery of ribozymes, the RNA Society (www.rnasociety.org) was founded and two years later the RNA Journal (https://rnajournal.cshlp.org) started. Ever since, the annual RNA meetings have gathered more than 1000 scientists from all over the world. Many new techniques and approaches were developed accelerating the pace of discoveries on RNA. For many years, the meetings started with a session on “RNA Catalysis.” However, with the avalanche of new data, new RNAs, and new biology, the session on catalysis session has dwindled. Billions of years ago, RNA did start the chemistry of the game of life, but was overwhelmed by the initiated evolutionary processes.

The central group of the chemical and biological feats achieved by RNA is the ribose hydroxyl O2′, at the same time key actor and Achilles's heel. And a DNA phosphodiester bond is 104–105 less prone to cleavage than a RNA phosphodiester bond [3]. As Paracelsus wrote several centuries ago: “All things are poison and nothing is without poison; only the dose makes a thing not a poison”.

The catalytic power of the 2′‐hydroxyl group must be strongly controlled and amplified only at specific location in the RNA sequence. Catalysis generally is initiated by the formation of an anionic O2′ oxygen. In any biological system, catalysis requires accessibility, local molecular dynamics and solvent molecules (water, ions, or small ligands). A water molecule (or a hydroxide ion), or a solvated divalent ion, or an amine group from a ligand can thus capture the proton from the 2′‐hydroxyl group. Afterwards, depending on the available mobility of the nucleotide, the anionic O2′ oxygen can attack its own 3′‐phosphate group or another phosphodiester bond. Other types of chemical reactions have also been achieved using ribozymes as described in several chapters of this book.

Accessibility and local dynamics depend on the RNA sequence and the ensuing RNA architecture. The distinctive mark of nucleic acids is the formation of pairs between the bases of the nucleotides with the complementary Watson–Crick pairs the most frequent ones. However, such pairs form only regular helices and any complex fold or assemblies of helices require linking segments that engage in some type of non‐Watson–Crick base pairs. Depending on the complexity and compactness of the RNA fold, not many bases will remain unpaired with a large number of degrees of freedom. Such regions are particularly prone to phosphodiester cleavages through hydrolysis or metal ion attack. Further, it was noticed a long time ago that, in single‐stranded regions, dinucleotide steps with sequence pyrimidine‐adenosine (UpA and CpA) were particularly sensitive to cleavage [4, 5]. These early observations were later thoroughly studied [6, 7]. Such cleavages are regularly observed in control lanes during gel electrophoresis. The precise molecular mechanism for these spontaneous cleavages in YpA sequences, however, has remained elusive. Recently, a surprising interpretation, based on mass spectrometry data and implying the syn conformation of the A and its protonation at N3 position, has been put forward [8].

In each ribozyme, cleavage occurs at a very precise dinucleotide location and generally with weak sequence dependence. The more extensively studied are the endonucleolytic, ribozymes (see Chapters 1 and 2). New data and results confirm the involvement of unexpected chemistry with anionic guanosine residues acting as a general base for capturing the O2′‐hydroxyl proton [9, 10]. Interestingly, a proposal has been forwarded in which the tautomeric enol form of guanosine in which N1(G) carries an in‐plane electron doublet would capture the proton from the O2′‐hydroxyl group [11, 12]. Interestingly, such tautomers have been observed in functional ribosome crystals and related to the occurrence of miscoding at the first and second codon positions following the formation of tautomeric GoU pairs [13, 14]. The tautomeric ratio of G is around 1 in 104, a value close to the average miscoding error in bacteria [15]. The tautomeric forms trapped in a constrained environment (stacking, H‐bond between the amino group of G and an anionic phosphate oxygen, minor groove contacts, etc.) are stabilized as observed in several crystal structures [12, 16]. The frequent occurrence of stacked Gs forming H‐bonds through their Watson–Crick edge to phosphate anionic oxygens has been analyzed and described thoroughly [17]. It has also been shown that the tautomeric form coexists with the anionic form [18].

Overall, this book is timely and unique in its breadth of content. The book describes the great diversity of nucleic acid base catalysis beautifully. The reader is conveyed to a chemical journey extending from biologically functional ribozymes (like RNaseP or group I and II introns) to engineered and designed ribozymes as well as DNAzymes. For example, we now have three distinct structural environments with a natural 2′–5′ phosphodiester linkage: the group II ribozyme [19, 20], the spliceosome [21], and the lariat‐capping ribozyme [22]. Despite the clear structural similarities between the active sites of group II ribozyme and of the spliceosome, the striking observation is how the 2′–5′ linkage promotes a highly constrained environment with nested non‐Watson–Crick pairs and sugar‐phosphate contacts. Given those three‐dimensional visions, one can only wonder at the structural and molecular fitness of nucleic acids, especially RNA. Here I have selected some topics that I enjoy particularly, and I apologize for not discussing many other aspects that are covered in this book. Indeed, some chapters extend to biotechnology and to ribozymes used in diagnostics and therapeutics. Finally, the major tools and techniques used for the analysis of nucleic acid structures are presented up to date. In this regard, I cannot resist citing Sydney Brenner [23, 24], Nobel Prize 2002 in Physiology or Medicine: “Progress in science depends on new techniques, new discoveries and new ideas, probably in that order.”

Eric Westhof

Architecture et Réactivité de l′ARN

Université de Strasbourg

Institut de biologie moléculaire et cellulaire du CNRS

2 allée Konrad Roentgen, 67084 Strasbourg, France

August 2019

References

1

Cech, T.R., Zaug, A.J., and Grabowski, P.J. (1981). In vitro splicing of the ribosomal RNA precursor of

Tetrahymena

: involvement of a guanosine nucleotide in the excision of the intervening sequence.

Cell

27 (3 Pt 2): 487–496.

2

Guerrier‐Takada, C., Gardiner, K., Marsh, T. et al. (1983). The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme.

Cell

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Part INucleic Acid Catalysis: Principles, Strategies and Biological Function

1The Chemical Principles of RNA Catalysis

Timothy J. Wilson and David M. J. Lilley

The University of Dundee, Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, Dow Street, Dundee, DD1 5EH, UK

1.1 RNA Catalysis