Catalytic RNA

Contributors

Preface

Chapter One. The Hammerhead Ribozyme: Structure, Catalysis, and Gene Regulation

Abstract

1 Discovery and Context

2 The Minimal Sequence

3 The Full-Length Sequence

4 Hammerhead Ribozymes in Mammalian Gene Regulation

References

Chapter Two. Bridging the Gap Between Theory and Experiment to Derive a Detailed Understanding of Hammerhead Ribozyme Catalysis

Abstract

1 Introduction

2 A Metal Ion Story with a Happy Ending

3 Finding the Catalytic Reaction Path Through Multidimensional Free-Energy Surfaces

4 HHR Uses Specific Cation-Binding Modes to Reach Its Catalytically Active Conformation

5 Computational Mutagenesis of Key Residues of HHR

6 Conclusion

Acknowledgments

References

Chapter Three. A Mechanistic Comparison of the Varkud Satellite and Hairpin Ribozymes

Abstract

1 Introduction

2 The Hairpin and VS Ribozymes

3 General Themes

Acknowledgments

References

Chapter Four. HDV Family of Self-Cleaving Ribozymes

Abstract

1 Introduction

2 Hepatitis Delta Virus

3 HDV Ribozymes

4 HDV Ribozymes’ Reaction Mechanism

5 Ribozymes Outside of the Hepatitis Delta Virus

6 Evolutionary Relationship Among HDV-Like Ribozymes

References

Chapter Five. The Structural and Functional Uniqueness of the glmS Ribozyme

Abstract

1 Introduction

2 The glmS Riboswitch/Ribozyme

3 Biological Function of the glmS Ribozyme

4 glmS Ribozyme Uniqueness

5 glmS Ribozyme Structure and Function—Biochemical Analyses

6 glmS Ribozyme Structure and Function—Crystallographic Analysis

7 Metal Ion Usage by the glmS Ribozyme

8 Essential Coenzyme GlcN6P Functional Groups

9 Mechanism of glmS Ribozyme Self-Cleavage Using Coenzyme GlcN6P

10 pH-Reactivity Profiles Provide Mechanistic Insight

11 Potential for Antibiotic Development Affecting glmS Ribozyme/Riboswitch Function

Acknowledgments

References

Chapter Six. The Role of snRNAs in Spliceosomal Catalysis

Abstract

1 Evolution of Eukaryotic Splicing Machines

2 Structural and Functional Similarities Between snRNAs and the Group II Self-Splicing Introns

3 Role of snRNAs in the Spliceosomal Active Site

4 The Three-Dimensional Positioning of snRNAs in the Catalytic Core

5 An RNA-Centric View of the Active Site

6 Functionally Critical snRNA–Metal Ion Interactions

7 Catalytic Activity of the snRNAs in Isolation

8 The snRNAs in the Context of the Spliceosomal Active Site

9 The Role of Proteins in the Spliceosomal Catalytic Core

10 The Role of Spliceosomal Proteins in Remodeling the Catalytic Core

11 Concluding Remarks

References

Index