Nucleic Acids and Molecular Biology 13 Series Editor H. J. Gross Springer-Verlag Berlin Heidelberg GmbH Marina A. Zenkova (Ed.) Artificial Nucleases With 81 Figures i Springer Dr. MARINA A. ZENKOVA Novosibirsk Institute of Bioorganic Chemistry 8, Lavrentiev ave. 630090 Novosibirsk Russia ISBN 978-3-642-62139-0 Ubrary of Congress Cataloging-in-Publication Data Artificial nuc1eases 1 Marina A. Zenkova (ed.). p. cm. -- (Nuc1eic acids and molecular biology, ISSN 0933-1891 ; 13) Inc1udes bibliographical references and index. ISBN 978-3-642-62139-0 ISBN 978-3-642-18510-6 (eBook) DOI 10.1007/978-3-642-18510-6 1. Artificial nuc1eases.1. Zenkova, Marina A., 1955- 11. Series. QP609.N78A785 2004 572'78-dc22 2003066404 This work is subject to copyright. All rights are reserved, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilm or in any other way, and storage in data banks. Duplication of this publication or parts thereof is permit- ted only under the provisions of the German Copyright Law of September 9, 1965, in its current version, and per- missions for use must always be obtained from Springer-Verlag. Violations are liable for prosecution under the German Copyright Law. springeronline.com © Springer-Verlag Berlin Heidelberg 2004 Originally published by Springer·Veriag Berlin Heidelberg New York in 2004 Softcover reprint ofthe hardcover Ist edition 2004 The use of general descriptive names, registered names, trademarks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. Production and typesetting: Friedmut Kröner, 69115 Heidelberg, Germany Cover design: design & production GmbH, Heidelberg 31/3150YK - 5 4 3 2 1 0 - Printedonacidfreepaper Contents Introduction 1 DNA Hydrolysis: Mechanism and Reactivity 3 N.H. WILLIAMS 1 Introduction . . . . . . . . . . . . . . . . . . 3 2 The Importance of the Background Reaction 3 3 Mechanism ....... . 4 4 Spontaneous Hydrolysis 7 5 c-o Cleavage 8 6 p-o Cleavage 9 7 Base Catalysis 10 8 Acid Catalysis 12 9 Conclusion 13 References . . . . . . . . 14 Active Site of Ribonuclease A 19 R.T. RAINES 1 Introduction . . . . . . 19 2 Mechanism of Catalysis 20 3 Active-Site Residues . . 21 3.1 Histidine 12 and Histidine 119 21 3.2 Lysine 41 ..... 24 3.3 Phenylalanine 120 24 3.4 Aspartic Acid 121 25 3.5 Glutamine 11 27 4 Catalytic Rate Enhancement 28 5 Envoi 29 References . . . . . . . . . . . . . . . . 29 VI Contents Structural Considerations Concerning Cleavage of RNA 33 R.KIERZEK 1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . 33 2 Facts About the Influence of Oligo ribonucleotide Structure on Cleavage of Phospho diester Bonds 34 2.1 How to Cleave Oligoribonucleotides . . . . . . . 34 2.2 Cleavage Requires a Single-Stranded Character of the Oligoribonucleotide ........... . 34 2.3 Sequence and Position of the Scissile Phospho diester Bond Within the Oligomer is Important for Cleavage 35 2.4 Oiigoribonucleotide Length Affects Cleavage of Diester Bond .................... . 36 2.5 The Functional Groups of the Pyrimidine Nucleobases Flanking the Cleaved Phosphodiester Bond Affect Cleavage 36 2.6 The Functional Groups of the Purine Nucleobases Flanking the Cleaved Phospho diester Bond Influence Cleavage . . . 38 2.7 The C5 Substituents of Uridine Affect the Hydrolysis Rate of the UA Phospho diester Bond ........... . 39 2.8 Chimeric DNA/RNA Oligomers Affect the Cleavage of Phospho diester Bonds . . . . . . . . . . . . . . . . 40 2.9 The Motives of RNA Structure are Affected by Spontaneous Cleavage . . . . . . . . . . 41 2.10 The Effects of Polyamines on the Cleavage of Oligoribonucleotides ......... . 43 3 Mechanism of Phospho diester Bond Cleavage 44 4 Conclusions 46 References . . . . . . . . . . . . . . . . . . . . . . . . . . 46 Cleavage of RNA by Imidazole 49 v.v. VLASSOV and A.V. VLASSOV 1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . .. 49 2 Imidazole as the Simplest Mimic of the Ribonuclease Catalytic Structure . . . . . . . . 50 3 Mechanism of RNA Cleavage by Imidazole . . . . . . 51 4 Imidazole as a Reagent for Probing RNA Structure 54 5 Conclusions 59 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59 Contents VII Principles of Nucleic Acid Cleavage by Metal Ions 61 A. DALLAS,A.V. VLASSOV, and S.A. KAZAKOV 1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . 61 2 General Mechanisms for the Cleavage of Nucleic Acids 62 3 Basic Properties of Metal Ions in Solution 65 4 Metal Ion Binding to Nucleic Acids ..... 69 5 Transesterification and Hydrolytic Cleavage of Nucleic Acids Catalyzed by Metal Ions . . 72 5.1 Efficacy of Cleavage of Nucleic Acids by Metal Ions 72 5.2 Possible Mechanism of Metal Ion Catalysis . . . . . 72 5.3 Nucleic Acid Structure and Specificity of Metal-Catalyzed Cleavage Reactions ........... 75 6 Oxidative Cleavage of Nucleic Acids Induced by Metal Ions 77 6.1 Cleavage Reactions Promoted by Metal Ions in High Oxidation States .................... 77 6.2 Cleavage Reactions Involving Metal-Induced Oxygen Radicals . . . . . . . . . . . . . . . . . . . . . . . .. 78 7 Probing Metal Binding Sites in RNA by Metal-Induced Cleavage 81 References . . . . . . . . . . . . . . . . . . . . 83 Allosterically Controlled Ribozymes as Artificial Ribonucleases 89 M. Iyo, H. KAWASAKI, M. MIYAGISHI, and K. TAIRA 1 Introduction . . . . . . . . . . . . . . . . 89 2 Maxizymes are Allosterically Controllable Ribozymes 90 2.1 Expression of Ribozymes in Cells ........... 90 2.2 The Design of Allosterically Controllable Maxizymes . 91 2.3 Allosteric Control of Ribozyme Activity ........ 94 2.4 Selection of Allosterically Controllable Ribozymes in Vitro 95 3 Maxizymes . . . . . . . . . . . . . . . . . . . . . . . 96 3.1 Truncated Hammerhead Ribozymes that Function as Dimers ............................ 96 3.2 General Design of an Allosterically Controllable Maxizyme 97 3.3 The Antitumor Effects of an Allosterically Controllable Maxizyme . . . . . . . . . . . . . . 101 3.4 General Applications of Maxizyme Technology 101 4 Conclusion 104 References . . . . . . . . . . . . . . . . . . . . . . . . . . . 104 VIII Contents Small Ribonuclease Mimics 111 1.1. KUZNETSOVA and V.N. SU,'NIKOV 1 Introduction . . . . . . . . . . . . . . . 111 2 RNA-Cleaving Compounds . . . . . . . 112 2.1 RNA-Cleaving Compounds Mimicking Ribonucleases A and T1 ....... . 112 2.2 Mimics of the Active Center of Nuclease S 113 3 Design of Active Centers of Natural Enzymes 113 3.1 Spatial Organization of RNA-Cleaving Groups in Active Centers of RNases and Nucleases Sand Sm 114 3.2 RNA-Binding Groups ................. . 115 4 Design of Artificial Ribonucleases Mimicking RNase A 115 4.1 Artificial Ribonucleases with Polycyclic RNA-Binding Domains ...... . 116 4.2 Polycationic RNA-Binding Groups. 117 5 Specificity of RNA Cleavage .. 121 6 Effects of Buffer on the Cleavage . . 122 7 Mechanism of RNA Cleavage with the Artificial Ribonucleases ABLkCm and nLm 123 8 Potential Applications of Small Ribonuclease Mimics 125 9 Conclusions 125 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 126 Copper-Containing Nuclease Mimics: Synthetic Models and Biochemical Applications . . . . . . . . . . . . . . . 129 S. VERMA, S.G. SRIVATSAN, and C. MADHAVAIAH 1 Introduction . . . . . 129 2 Model Systems . . . . 130 3 Mechanistic Pathways 130 4 Copper Complexes with Synthetic Ligands 131 4.1 Hydrolysis of Phosphate Diesters .... 131 4.2 Cleavage of Nucleic Acids . . . . . . . . . 138 5 Copper Complexes of Natural Ligands 143 6 Outlook 145 References . . . . . . . . . . . . . . . . . . . . . . 145 Contents IX RNA-Cleaving Oligonucleotide-Peptide Conjugates 151 N.L. MIRONOVA, D.V. PYSHNYI, and E.M. IVANOVA 1 Introduction . . . . . . . . . . . . . . . . . . . . . . . 151 2 Proteins Displaying Ribonuclease Activity 151 2.1 Natural Ribonuclease . . . . . . . . . . . . . . . . . . 151 2.2 Small Natural Pep tides ................ . 154 2.3 Synthetic Polypeptides ............. . 155 3 Conjugates of RNA-Cleaving Peptides with Constructs Capable of Binding to RNA .. 156 3.1 Conjugates of Enzymes and Oligonucleotides ... 156 3.2 Conjugates of Short Peptides and Intercalators . . . 157 3.3 Oligonucleotide-Peptide Conjugates Displaying Ribonuclease Activity . . . . . . . . . . . . . . . . 158 3.3.1 Influence of Peptide Structure on the Efficacy of RNA Cleavage . . . . . . . . . . . . . . . . . . . 159 3.3.2 Site-Directed RNA Hydrolysis by Peptidyloligonucleotides . 161 3.3.3 Hydrolysis of RNA by the Conjugates of Random Oligonucleotides . . . . . . . 163 3.3.4 Influence of Oligonucleotide Sequence on the Specificity of RNA Cleavage . 164 3.3.5 Cleavage of Short RNA 167 4 Discussion 168 References . . . . . . . . . . . . . 170 Sequence Selective Artificial Ribonucleases Employing Metal Ions as Scissors . . . . . . 173 A. KUZUYA, R. MIZOGUCHI, and M. KOMIYAMA 1 Introduction . . . . . . . . . . . . . . . . . . . . . 173 1.1 Significance of Artificial Ribonucleases . . . . . . 173 1.2 Molecular Design of Artificial Ribonucleases . . . 174 2 Metal Ion Catalysts for RNA Cleavage . . . . . . . . . . . 175 2.1 Divalent Metal Ions and Their Complexes 175 2.2 Trivalent Lanthanide Ions and Their Complexes . . . . . 177 3 Sequence-Selective Artificial Ribonucleases with Covalently Attached Catalysts ......... . 178 3.1 Attaching the Catalysts to the End of DNA Oligomers 178 3.1.1 [Lanthanide ComplexJIDNA Hybrids ... 178 3.1.2 [Dinuclear Metal ComplexJ/DNA Hybrids ..... . 179 x Contents 3.2 Attaching the Catalysts at an Internal Position Within DNA Oligomers . . . . . . . . . . . . . . . . . . . . 180 4 Noncovalent Systems for Sequence-Selective RNA Scission 180 4.1 Molecular Design ...................... . 181 4.2 Site-Selective RNA Scission by Lanthanide Ions ..... . 182 4.3 Requirements for the Sequence-Selective RNA Activation 184 4.4 Site-Selective RNA Scission by Non-Lanthanide Ions 185 4.5 Mechanism of the Site-Selective Scission 185 5 Prospect 186 References . . . . . . . . . . . . . . . . . . . . . . . 186 Site-Specific Artificial Ribonucleases: Conjugates of Oligonucleotides with Catalytic Groups . . . . . 189 M.A. Zenkova and N.G. Beloglazova 1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . .. 189 2 Oligonucleotide Conjugate-Based Artificial Ribonucleases 190 2.1 Conjugates of Oligonucleotides and Metal Complexes 190 2.2 Conjugates of Oligonucleotides and RNA-Cleaving Molecules ........... 197 2.3 Design of Artificial Ribonucleases for Site-Specific RNA Cleavage ............... 202 2.3.1 Synthetic Approaches . . . . . . . . . . . . . 202 2.3.2 Effect of the Catalytic Structure Location in the Conjugate Structure .......... 203 2.3.3 RNA Sequences Optimal for Site-Specific Cleavage 206 2.4 Site-Specific Cleavage of Cellular RNA ....... 206 3 Site-Specific RNA Cleavage by Conjugates of Oligonucleotides with Imidazole-Based Catalytic Groups 207 3.1 Mono- and Bis-Imidazole-Containing Conjugates 207 3.2 Binary Systems of Oligonucleotide Conjugates 209 3.3 Conjugates with Anthracene-Based Linkers 210 3.4 Conjugates with Multiple Imidazole Residues in the Catalytic Domain 212 4 Conclusions 216 ~furenres ............. . 216