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Sabine Müller - Ribozymes: Principles, Methods, Applications

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This all-encompassing reference on ribozymes integrates the knowledge that has gained in the field over the past 35 years, with contributions by virtually all leading experts in the field. Organized six major parts, it describes general principles and strategies of nucleic acid catalysis, introduces naturally occurring ribozymes including the search for new catalytic motifs or novel genomic locations of known motifs, followed by an extensive section on ribozyme engineering and artificial ribozymes. The fourth part covers DNAzymes, their development and potential application. The design of ribozymes and DNAzymes for medical diagnostics and as therapeutic tools is covered in part 5. The final part looks at tools and methods in ribozyme research, including the techniques and assays for structural and functional characterization of nucleic acid catalysts.

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Table of Contents List of Tables Chapter 2 Chapter 3 Chapter 5 Chapter - photo 1
Table of Contents
List of Tables
  1. Chapter 2
  2. Chapter 3
  3. Chapter 5
  4. Chapter 6
  5. Chapter 9
  6. Chapter 14
  7. Chapter 15
  8. Chapter 26
  9. Chapter 33
List of Illustrations
  1. Chapter 1
  2. Chapter 2
  3. Chapter 3
  4. Chapter 4
  5. Chapter 5
  6. Chapter 6
  7. Chapter 7
  8. Chapter 8
  9. Chapter 9
  10. Chapter 10
  11. Chapter 11
  12. Chapter 12
  13. Chapter 13
  14. Chapter 14
  15. Chapter 15
  16. Chapter 16
  17. Chapter 17
  18. Chapter 18
  19. Chapter 19
  20. Chapter 20
  21. Chapter 21
  22. Chapter 22
  23. Chapter 23
  24. Chapter 24
  25. Chapter 25
  26. Chapter 26
  27. Chapter 27
  28. Chapter 28
  29. Chapter 29
  30. Chapter 30
  31. Chapter 31
  32. Chapter 32
  33. Chapter 33
Guide
Pages
Ribozymes

Volume 1

Edited by

Sabine Mller
Benot Masquida
Wade Winkler

Ribozymes Volume 2 Edited by Sabine Mller Benot Masquida Wade Winkler - photo 2
Ribozymes

Volume 2

Edited by

Sabine Mller
Benot Masquida
Wade Winkler

Editors Sabine Mller University Greifswald Institut fr Biochemie - photo 3

Editors

Sabine Mller

University Greifswald

Institut fr Biochemie

FelixHausdorffStr. 4

17489 Greifswald

Germany

Benot Masquida

CNRS Universit de Strasbourg

UMR 7156

Gntique Mol\xE9culaire Gnomique Microbiologie

4 alle 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. Benot Masquida

All books published by WILEYVCH are carefully produced. Nevertheless, authors, editors, and publisher do not warrant the information contained in these books, including this book, to be free of errors. Readers are advised to keep in mind that statements, data, illustrations, procedural details or other items may inadvertently be inaccurate.

Library of Congress Card No.:

applied for

British Library CataloguinginPublication Data

A catalogue record for this book is available from the British Library.

Bibliographic information published by

the Deutsche Nationalbibliothek

The Deutsche Nationalbibliothek lists this publication in the Deutsche Nationalbibliografie; detailed bibliographic data are available on the Internet at .

2021 WILEYVCH GmbH, Boschstr. 12, 69469 Weinheim, Germany

All rights reserved (including those of translation into other languages). No part of this book may be reproduced in any form by photoprinting, microfilm, or any other means nor transmitted or translated into a machine language without written permission from the publishers. Registered names, trademarks, etc. used in this book, even when not specifically marked as such, are not to be considered unprotected by law.

Print ISBN: 9783527344543

ePDF ISBN: 9783527814558

ePub ISBN: 9783527814534

oBook ISBN: 9783527814527

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 predefined function. Yet, there is still much to be learned. Improvements in highthroughput 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 highquality 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 Mller

Benot Masquida

Wade Winkler

Foreword

The study of ribozymes, RNAbased catalysts, and subsequently nucleic acidbased 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 () 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.

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