Principles of Nucleic Acid Structure

Front Cover......Page 1
Principles of Nucleic Acid Structure......Page 4
Copyright Page......Page 5
Dedication Page......Page 6
Preface......Page 8
Contents......Page 10
1.1 Introduction......Page 14
1.2.1 Overview......Page 15
1.2.2 Fiber Diffraction Methods......Page 18
1.2.3 Single-Crystal Methods......Page 20
1.3 NMR Methods for Studying Nucleic Acid Structure and Dynamics......Page 23
1.4 Molecular Modelling and Simulation of Nucleic Acids......Page 24
1.5 Chemical, Enzymatic, and Biophysical Probes of Structure and Dynamics......Page 27
1.7 Visualization of Nucleic Acid Molecular Structures......Page 28
References......Page 29
Further Reading......Page 30
2.1 Introduction......Page 33
2.2 Base Pairing......Page 36
2.3 Base and Base Pair Flexibility......Page 37
2.4 Sugar Puckers......Page 41
2.5 Conformations About the Glycosidic Bond......Page 45
2.6 The Backbone Torsion Angles and Correlated Flexibility......Page 46
References......Page 49
Further Reading......Page 50
3.1.2 Base-Pair Morphological Features......Page 51
3.2.1 Classic DNA Structures......Page 52
3.2.2 DNA Polymorphism in Fibers......Page 56
3.3.1 The Dickerson–Drew Dodecamer......Page 60
3.3.2 Other Studies of the Dickerson–Drew Dodecamer......Page 62
3.3.3 Other B-DNA Oligonucleotide Structures......Page 64
3.3.4 Sequence-Dependent Features of B-DNA: Their Occurrence and Their Prediction......Page 69
3.4.1 A-Form Octanucleotides......Page 73
3.4.2 Do A-Form Oligonucleotides Occur in Solution? Crystal-Packing Effects......Page 74
3.4.3 The A harr B Transition in Crystals......Page 76
3.5.1 The Z-DNA Hexanucleotide Crystal Structure......Page 77
3.5.2 Overall Structural Features......Page 78
3.5.3 The Z-DNA Helix......Page 79
3.5.5 Biological Aspects of Z-DNA......Page 80
3.6.1 DNA Periodicity in Solution......Page 82
3.6.2 A-Tracts and Bending......Page 83
3.6.3 Structures Showing Bending......Page 84
3.6.4 The Structure of Poly dAmiddotdT......Page 86
References......Page 87
Further Reading......Page 93
4.1.1 General Features......Page 94
4.1.2 Purine:Purine Mismatches......Page 95
4.1.3 Alkylation Mismatches......Page 98
4.2.1 Introduction......Page 101
4.2.2 Structural Studies......Page 103
4.2.3 Antiparallel Triplexes and Nonstandard Base-pairings......Page 108
4.2.4 Triplex Applications......Page 113
4.3.1 Introduction......Page 114
4.3.2 Overall Structural Features of Quadruplex DNA......Page 116
4.3.3 Examples of Simple Quadruplex Structures......Page 120
4.3.4 Some Complex Quadruplex Structures......Page 121
4.3.5 The i-Motif......Page 126
4.4.1 Holliday Junction Structures......Page 127
4.4.2 DNA Enzyme Structures......Page 131
4.5 Unnatural DNA Structures......Page 133
References......Page 137
Further Reading......Page 144
5.1 Introduction......Page 145
5.2 DNA-Water Interactions......Page 149
5.2.1 Hydration in the Grooves in Detail......Page 153
5.3 General Features of DNA-Drug and Small-Molecule Recognition......Page 156
5.4 Intercalative Binding......Page 157
5.4.1 Simple Intercalators......Page 159
5.4.2 Complex Intercalators......Page 160
5.4.3 Major-Groove Intercalation......Page 164
5.4.4 Bis-Intercalators......Page 171
5.5.1 Triplex DNA–Ligand Interactions......Page 176
5.5.2 Ligand Binding to Quadruplex DNAs......Page 177
5.5.3 Ligand Binding to Junction DNAs......Page 179
5.6.1 Simple Groove Binding Molecules......Page 182
5.6.2 Netropsin and Distamycin......Page 191
5.6.3 Sequence-Specific Polyamides......Page 195
5.7 Small Molecule Covalent Bonding to DNA......Page 200
5.7.1 The Platinum Drugs......Page 201
5.7.2 Covalent-Binding Combined with Sequence-Specific Recognition......Page 204
References......Page 208
Further Reading......Page 215
6.1 Introduction......Page 217
6.2.1 Helical RNA Conformations......Page 219
6.2.2 Mismatched and Bulged RNA Structures......Page 223
6.3 Transfer RNA Structures......Page 230
6.4 Ribozymes......Page 234
6.4.1 The Hammerhead Ribozyme......Page 236
6.4.2 Complex Ribozymes......Page 237
6.5 Riboswitches......Page 240
6.6 The Ribosome, a Ribozyme Machine......Page 242
6.6.1 The Structure of the 30S Subunit......Page 245
6.6.3 Complete Ribosome Structures......Page 247
6.7 RNA-Drug Complexes......Page 248
6.8 RNA Motifs......Page 254
6.9 Web Sites of Interest......Page 256
References......Page 257
Further Reading......Page 261
7.1 Introduction......Page 262
7.2 Direct Protein-DNA Contacts......Page 265
7.3 Major-Groove Interactions – the alpha-Helix as the Recognition Element......Page 270
7.4 Zinc-Finger Recognition Modes......Page 272
7.5 Other Major Groove Recognition Motifs......Page 276
7.6.1 Recognition of B-DNA......Page 277
7.6.2 The Opening-up of the Minor Groove by TBP......Page 280
7.6.3 Other Proteins that Induce Bending of DNA......Page 281
7.7 DNA-Bending and Protein Recognition......Page 285
7.8 Protein-DNA-Small Molecule Recognition......Page 288
References......Page 291
Further Reading......Page 295
Index......Page 296