Synthetic Nucleic Acids as Inhibitors of Gene Expression Mechanisms, Applications, and Therapeutic Implications Synthetic Nucleic Acids as Inhibitors of Gene Expression Mechanisms, Applications, and Therapeutic Implications Levon Michael Khachigian Edited by CRC PR ESS Boca Raton London New York Washington, D.C. Library of Congress Cataloging-in-Publication Data Synthesis nucleic acids as inhibitors of gene expression: mechanisms, applications, and therapeutic implications / edited by Levon Khachigian. p. cm. Includes bibliographical references and index. ISBN 0-8493-3025-4 (alk. paper) 1. Catalytic RNA. 2. Repressors, Genetic. 3. Genetic regulation. I. Khachigian, Levon. QP623.5.C36S966 2004 572.8—dc22 2004054474 This book contains information obtained from authentic and highly regarded sources. Reprinted material is quoted with permission, and sources are indicated. A wide variety of references are listed. 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Visit the CRC Press Web site at www.crcpress.com © 2005 by CRC Press No claim to original U.S. Government works International Standard Book Number 0-8493-3025-4 Library of Congress Card Number 2004054474 Printed in the United States of America 1 2 3 4 5 6 7 8 9 0 Printed on acid-free paper Preface In the postgenomic era, we have at our fingertips complete genome sequences and huge numbers of predicted gene sequences from a multitude of complex organisms. There remains, however, the critical need to understand the functions of these gene products to delineate the precise roles of these genes in complex biological milieu. Synthetic nucleic acids are at the cutting-edge of molecular strategies that target genes of interest in a specific and cost-effective manner. These agents are now being used as new and exciting gene-silencing agents in vitro, in animal models of disease, and in humans. This book brings together timely authoritative, in-depth reviews by renowned international leaders in the fields of ribozymes, RNA interference, DNAzymes and oligonucleotide decoys, with emphasis on biochemistry and translational research. No other book draws together these topics. Sections by Nobura Fukuda (Chapter 1) and Mehdi Nosrati et al. (Chapter 2) on ribozymes include an in-depth discussion of ribozyme subtypes (hammerhead, chimeric, minizymes, maxizymes, zinzymes, group I introns), structure-functional aspects including modifications, cellular delivery and therapeutic applications in diseases such as cancer and cardiovascular disease. McManus and Harfe’s (Chapter 3) section on RNA interference provides a historical and mechanistic account of small interfering RNAs and microRNAs as suppressors of gene expression. Contributions by Steve Santoro (Chapter 4), Gail Mitchell Emilsson and Ron Breaker (Chapter 5), Masaki Warashina et al. (Chapter 6), Akhil Banerjea et al. (Chapter 7), Michael Eisbacher and Lun-Quan Sun (Chapter 8), and Levon Khachi- gian (Chapter 9) provide a comprehensive discussion on DNAzymes, their various subtypes, modifications, selection strategies, kinetics and biochemistry, cellular delivery, applications in target validation, and diagnostic and therapeutic applications in a diverse array of pathologies. Finally, Ryuichi Morishita et al. (Chapter 10) discuss the mechanisms and multiple therapeutic applications of double-stranded oligonucleotide decoys as non- catalytic nucleic acid strategies specifically targeting transcription factors. I am confident this book will serve as a valuable practical and informative resource to basic and applied academic and industrial scientists alike. Levon Khachigian Sydney, Australia About the Editor Professor Levon Michael Khachigian (BSc[Hons], PhD, DSc) is a Principal Research Fellow of the National Health and Medical Research Council of Australia and Head of the Transcription and Gene Targeting Laboratory at The Centre for Vascular Research, University of New South Wales and Prince of Wales Hospital, Sydney. His research, encompassed in over 100 journal articles and book chapters, has greatly increased our understanding of the fundamental transcriptional mechanisms that lead to the inap- propriate expression of harmful genes in cells of the artery wall. It has also led to his generation of novel DNA-based drugs that block arterial renarrowing after balloon angioplasty in a variety of experimental models. More recently, he has been unravelling the mechanisms behind tumor growth control and other neovascular pathologies by inhibiting angiogenesis. Professor Khachigian has been a major contributor to the broader workings of science on matters of policy, advocacy, consultancy, peer-review, mentorship, and societal service. For example, he is National Executive Director and President-Elect of the Australian Society for Medical Research and former President of the Australian Vascular Biology Society. He has served on numerous grant review, fellowship, and policy formulation panels for the National Health and Medical Research Council of Australia and the National Heart Foundation of Australia. He sits on the Editorial Boards of five international journals. Professor Khachigian has won many highly competitive awards for innovative research including recently the Commonwealth Health Minister’s Award for Excel- lence in Health and Medical Research, the Gottschalk Award from the Australian Academy of Science, Eureka Prize for Scientific Research from the Australian Museum, RT Hall Prize from the Cardiac Society of Australian and New Zealand, AMGEN Medical Researcher Award, Eppendorf Award for the Young Australian Researcher, Quantum Scientific Research Award, Young Tall Poppy Award, and numerous named research awards for research excellence from the Heart Foundation of Australia. Professor Khachigian received his BSc with first class honors in biochemistry and a PhD in cell and molecular biology from the University of New South Wales, then studied transcriptional control in the Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School. In 2004, he was awarded a DSc in vascular pathobiology and translational research from the University of New South Wales. Contributors Akhil C. Banerjea, Ph.D. Ritu Goila, Ph.D. Laboratory of Virology, National Laboratory of Virology, National Institute of Immunology Institute of Immunology New Delhi, India New Delhi, India Ronald R. Breaker, Ph.D. Brian D. Harfe, Ph.D. Department of Molecular, Cellular and Department of Molecular Genetics and Developmental Biology, Yale Microbiology, University of Florida University College of Medicine New Haven, Connecticut Gainesville, Florida Samitabh Chakraborti, Ph.D. Takeshi Imanishi, M.D. Laboratory of Virology, National Graduate School of Pharmaceutical Institute of Immunology Sciences, Osaka University New Delhi, India Osaka, Japan Bipin C. Dash, Ph.D. Mohammed Kashani-Sabet, M.D. Laboratory of Virology, National Cancer Center and Department of Institute of Immunology Dermatology, University of New Delhi, India California–San Francisco San Francisco, California Michael Eisbacher, Ph.D. Levon M. Khachigian, Ph.D., D.Sc. Johnson & Johnson Research Pty. Ltd. Centre for Vascular Research, Sydney, Australia University of New South Wales Department of Haematology, Prince of Gail Mitchell Emilsson, Ph.D. Wales Hospital Department of Molecular, Cellular and Sydney, Australia Developmental Biology, Yale University Tomoko Kuwabara, M.D. New Haven, Connecticut Gene Discovery Research Center, National Institute of Advanced Noboru Fukuda, M.D., Ph.D. Industrial Science and Technology Second Department of Internal (AIST) Medicine, and Division of Cell Higashi, Japan Regeneration and Transplantation Advanced Medical Research Centre Michael T. McManus, Ph.D. Nihon University School of Medicine Massachusetts Institute of Technology Tokyo, Japan Cambridge, Massachusetts