Looking at Ribozymes

Benoît Masquida is director of research at the French National Center for Scientific Research (CNRS) and carries out his research and teaching activities at the University of Strasbourg, France. He is the author of over 60 publications and is one of France’s leading specialists in ribozymes.Fabrice Leclerc is a research fellow at the CNRS and conducts his research at the Paris-Saclay University, France. He has published numerous articles on RNA catalysis in ribozymes and their role in viroids and in the RNA world.

• Foreword viiPreface xiChapter 1 Fundamentals of RNA and Ribozyme Structure 11.1 Sequences and secondary structures 21.2 RNA folding, tertiary structures and 3D 81.2.1 Secondary structures and RNA folding 81.2.2 The pseudoknot 121.2.3 The loop E 141.2.4 The k-turn 161.2.5 Tetra-loop receptors 181.2.6 The A-minor pattern 201.2.7 Comparative analysis of sequences 24Chapter 2 Ribozymes and the "Central Dogma" of Molecular Biology 292.1 The discovery of RNA catalysis and the central dogma of molecular biology 292.2 In search of the primordial polymerase 34Chapter 3 The Discovery of Ribozymes 373.1 The discovery of catalysis by autocatalytic introns 383.2 The discovery of RNA catalysis of RNase P 423.3 The first consequences of these discoveries 463.3.1 The ribosome, a long-ignored ribozyme 473.3.2 The modified bases 523.4 The spliceosome, another ribozyme 553.4.1 Nucleolytic ribozymes 56Chapter 4 Ribozyme Engineering and the RNA World 734.1 Classification of ribozymes 754.2 Classification of ribozymes according to catalytic mechanism 76Chapter 5 Structures of Ribozymes 815.1 Structures and catalytic mechanisms of ribozymes 815.1.1 Hammerhead ribozymes 815.1.2 The example of the hairpin ribozyme 875.1.3 The example of the glmS ribozyme 895.2 An example of catalysis control: lariat-capping ribozyme 91Chapter 6 Evolution of the Vision of the Catalytic Mechanisms of Ribozymes, the Hammerhead Ribozyme 996.1 Chemistry and catalysis: between general acid/base and metal cations 996.2 Difficulties in interpreting catalysis data 103Chapter 7 The Distribution of Ribozymes in Living Organisms and Molecular Adaptations during Evolution 1117.1 Ubiquitous ribozymes 1117.2 Selection pressures at work in ribozyme shaping 1137.3 Ribozymes in cellular processes: from viroids to eukaryotes 1177.4 Very human ribozymes 123Conclusion 133References 135Index 165