Artificial nucleases:
Saved in:
| Format: | Book |
|---|---|
| Language: | English |
| Published: |
Berlin [u.a.]
Springer
2004
|
| Series: | Nucleic acids and molecular biology
13 |
| Subjects: | |
| Online Access: | Inhaltsverzeichnis |
| Physical Description: | XVI, 287 S. Ill., graph. Darst. |
| ISBN: | 3540201122 |
Staff View
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Record in the Search Index
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| adam_text | 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 0 Cleavage 8
6 P 0 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 Lysine41 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. KlERZEK
1 Introduction 33
2 Facts About the Influence of Oligoribonucleotide
Structure on Cleavage of Phosphodiester 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 Phosphodiester
Bond Within the Oligomer is Important for Cleavage .... 35
2.4 Oligoribonucleotide 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 Phosphodiester Bond Influence Cleavage .... 38
2.7 The C5 Substituents of Uridine Affect the Hydrolysis Rate
of the UA Phosphodiester Bond 39
2.8 Chimeric DNA/RNA Oligomers Affect the Cleavage
of Phosphodiester 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 Phosphodiester 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 Ill
I.L. Kuznetsova and V.N. Sil nikov
1 Introduction Ill
2 RNA Cleaving Compounds 112
2.1 RNA Cleaving Compounds Mimicking
Ribonucleases A and Tl 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 S and 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 Oligonudeotide 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 Peptides 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 Complex]/DNA Hybrids 178
3.1.2 [Dinuclear Metal Complex]/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 Ribonudeases: Conjugates
of Oligonucleotides with Catalytic Groups 189
M.A. Zenkova and N.G. Beloglazova
1 Introduction 189
2 Oligonucleotide Conjugate Based Artificial Ribonudeases . 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 Ribonudeases 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
References 216
Contents XI
DNA and RNA Cleavage Mediated by Phenanthroline Cuprous
Oligonucleotides: From Properties to Applications 223
J.C. Francis, M. Faria, D. Perrin, and C. Giovannangeli
1 Introduction 223
2 The 1,10 Phenanthroline Cuprous Complex 224
2.1 Background 224
2.2 Structural Probes for Nucleic Acid Containing Complexes . 226
3 Phenanthroline Conjugates 228
3.1 Conjugation of Biomolecules to Phenanthroline 228
3.2 Neighborhood Sensors 230
3.3 Oligonucleotide Phenanthroline
as Site Specific Ribonuclease 232
3.4 Oligonucleotide Phenanthroline Targeted
to Double Stranded DNA 233
3.4.1 Artificial Endonucleases for in Vitro Applications 233
3.4.2 Biological Activities of Oligonucleotide Phenanthroline . . 235
3.4.2.1 Phenanthroline Cleavage Activity Inside Cells 236
3.4.2.2 Modulation of DNA Metabolism Induced by
Oligonucleotide Phenanthroline 236
4 Conclusion 237
References 238
Sequence Specific Cleavage of Double Stranded DNA 243
A.S. Boutorine and P.B. Arimondo
1 Introduction 243
2 DNA Cleavage by Natural Enzymes and Their Conjugates . 246
2.1 Restriction Endonucleases 246
2.2 Conjugates of Nucleases with Oligonucleotides 246
2.3 The Achilles Heel Cleavage Method 247
3 Sequence Specific Cleavage Using Conjugated
Chemical Reagents 247
3.1 Direct Cleavage by Sequence Specific Conjugates
of Metal Complexes 247
3.2 Alkylating Reagents Conjugated
to Sequence Specific Molecules 250
4 DNA Photocleavage 251
4.1 Photocleavage by Blue Light Absorbing Reagents 251
4.2 Long Distance Electron Transfer in Photocleavage Reactions 253
4.3 Photocleavage by Red Light Absorbing Reagents 254
5 Recruitment of Intracellular Enzymes
for Sequence Specific DNA Cleavage 255
XII Contents
5.1 RecA Protein 255
5.2 Recruitment of Topoisomerases
by Conjugated Topoisomerase Inhibitors 255
6 Application of the Non Specific Single Stranded
DNA Cleaving Agents for Site Specific Scission
of Double Stranded DNA 259
7 Conclusions 260
References 261
Bleomycin Oligonucleotide Conjugates as Site Specific Nucleases . . 269
RE. Vorobjev and V.F. Zarytova
1 Introduction 269
2 Structure and Properties of Bleomycins 270
3 Conjugates of Bleomycin with Oligonucleotides:
Synthesis and Structure 273
4 Cleavage of Nucleic Acids
by Bleomycin Oligonucleotide Conjugates 275
4.1 Site Specific Cleavage of Single Stranded DNA Fragments
by Bleomycin Oligonucleotide Conjugates 275
4.2 Cleavage of RNA by Bleomycin Oligonucleotide Conjugates 276
4.3 Cleavage of Double Stranded DNA by Triplex Forming
Bleomycin oligonucleotide Conjugates 278
4.4 Catalytic Degradation of DNA Target by
Oligonucleotide Bleomycin Conjugate 279
5 Bleomycin Oligonucleotide Conjugates
in Tandem Sets with Effectors as Efficient Nucleases .... 282
6 Conclusion 284
References 284
Subject Index 289
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| id | DE-604.BV017491962 |
| illustrated | Illustrated |
| indexdate | 2024-07-09T19:18:41Z |
| institution | BVB |
| isbn | 3540201122 |
| language | English |
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| physical | XVI, 287 S. Ill., graph. Darst. |
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| series | Nucleic acids and molecular biology |
| series2 | Nucleic acids and molecular biology |
| spelling | Artificial nucleases Marina A. Zenkova (Ed.) Berlin [u.a.] Springer 2004 XVI, 287 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Nucleic acids and molecular biology 13 Artificial nucleases Aktives Zentrum (DE-588)4337771-3 gnd rswk-swf Biomimetikum (DE-588)4589414-0 gnd rswk-swf Nucleasen (DE-588)4172116-0 gnd rswk-swf (DE-588)4143413-4 Aufsatzsammlung gnd-content Nucleasen (DE-588)4172116-0 s DE-604 Aktives Zentrum (DE-588)4337771-3 s Biomimetikum (DE-588)4589414-0 s Zenkova, Marina A. Sonstige oth Nucleic acids and molecular biology 13 (DE-604)BV000695008 13 HBZ Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=010537719&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Artificial nucleases Nucleic acids and molecular biology Artificial nucleases Aktives Zentrum (DE-588)4337771-3 gnd Biomimetikum (DE-588)4589414-0 gnd Nucleasen (DE-588)4172116-0 gnd |
| subject_GND | (DE-588)4337771-3 (DE-588)4589414-0 (DE-588)4172116-0 (DE-588)4143413-4 |
| title | Artificial nucleases |
| title_auth | Artificial nucleases |
| title_exact_search | Artificial nucleases |
| title_full | Artificial nucleases Marina A. Zenkova (Ed.) |
| title_fullStr | Artificial nucleases Marina A. Zenkova (Ed.) |
| title_full_unstemmed | Artificial nucleases Marina A. Zenkova (Ed.) |
| title_short | Artificial nucleases |
| title_sort | artificial nucleases |
| topic | Artificial nucleases Aktives Zentrum (DE-588)4337771-3 gnd Biomimetikum (DE-588)4589414-0 gnd Nucleasen (DE-588)4172116-0 gnd |
| topic_facet | Artificial nucleases Aktives Zentrum Biomimetikum Nucleasen Aufsatzsammlung |
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| volume_link | (DE-604)BV000695008 |
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