DNA topology:
"A key aspect of DNA is its ability to form a variety of structures, this book explains the origins and importance of such structures"--Provided by publisher.
Saved in:
| Main Authors: | , |
|---|---|
| Format: | Book |
| Language: | English |
| Published: |
Oxford
Oxford Univ. Press
2005
|
| Edition: | 2. ed. |
| Series: | Oxford bioscience
|
| Subjects: | |
| Online Access: | Inhaltsverzeichnis |
| Summary: | "A key aspect of DNA is its ability to form a variety of structures, this book explains the origins and importance of such structures"--Provided by publisher. |
| Physical Description: | XVIII, 198 S. Ill., graph. Darst. |
| ISBN: | 019856709X 0198506554 |
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| adam_text | Titel: DNA topology
Autor: Bates, Andrew D
Jahr: 2005
CONTENTS
ABBREVIATIONS AND SYMBOLS xvii
1 DNA structure i
1.1 Introduction 1
1.2 DNA structures 1
1.2.1 The Watson-Crick model 1
1.2.2 B-formDNA 6
1.2.3 A-formDNA 7
1.2A Z-formDNA 7
1.3 Alternative DNA structures 8
1.3.1 Cruciforms and Holliday junctions 8
1.3.2 DNA triplexes and H-DNA 12
1.3.3 Telomeres and DNA quadruplexes 13
1.4 Intrinsic curvature and DNA flexibility 15
1.4.1 Intrinsic curvature 16
1.4.2 DNA flexibility 18
1.4.3 Protein-induced DNA bending 18
1.5 Conclusions 19
1.6 Further Reading 20
1.7 References 20
2 DNA supercoiling 25
2.1 Introduction 25
2.2 Historical perspective 25
2.2.1 The problem of the double helix 25
2.2.2 Closed-circular DNA and supercoiling 27
2.3 A quantitative measure of DNA supercoiling 31
2.3.1 Linking number 31
2.3.2 Supercoiling, linking difference, and specific
linking difference 34
2.4 Geometrical properties of closed-circular DNA 36
2.4.1 Twist and writhe 36
2.4.2 The interconversion of twist and writhe 37
xiw CONTENTS
2.4.3 Pkctonemic and toroidal conformations 41
2.4.4 Nomenclature 42
2.5 Topology and geometry of real DNA 43
2.5.1 Agarose gel electrophoresis of plasmids 43
2.5.2 Relaxation with topoisomerases 44
2.5.3 The effect of solution conditions on supercoiling 45
2.5.4 The effect of intercalators 48
2.5.5 Two-dimensional gels 50
2.5.6 Relaxationin the presence of intercalators 53
2.5.7 The effect of protein binding 55
2.6 Thermodynamics of DNA supercoiling 55
2.6.1 Ethidium bromide titration 56
2.6.2 The Gaussian distribution of topoisomers 57
2.6.3 The effect of DNA circle size 60
2.6.4 Supercoiling free energy and solution conditions 61
2.6.5 Supercoiling in small DNA circles 63
2.7 Theoretical approaches to DNA supercoiling 65
2.7.1 Bending and twisting rigidity and persistence length 66
2.7.2 Excluded volume and effective diameter 68
2.7.3 Simulations of DNA conformation and energetics 70
2.7.4 Applications of circular DNA simulations 72
2.8 Biological effects of supercoiling free energy 75
2.8.1 Stabilization of alternative structures by DNA supercoiling 75
2.9 Conclusions 77
2.10 Further Reading 77
2.11 References 78
3 DNA on surfaces 83
3.1 Introduction 83
3.2 The helical repeat of DNA 84
3.3 The surface linking treatment 87
3.3.1 DNA winding number ( P) 87
3.3.2 Surface linking number (SLk) 88
3.4 Interwound supercoiled DNA 90
3.5 The nucleosome 93
3.5.1 Linking difference and the linking number paradox 93
CONTENTS XV
3.5.2 Early resolution of the linking number paradox 95
3.5.3 The helical repeat at the nudeosome surface 96
3.5.4 Measurements ofhs for the nudeosome 96
3.5.5 Topology and geometry of DMA in the nudeosome 97
3.5.6 Nudeosome structure at atomic resolution 99
3.5.7 Summary 102
3.6 Conclusions 102
3.7 Further Reading 103
3.8 References 103
4 Knots and catenanes 107
4.1 Introduction 107
4.2 Knots 107
4.2.1 Occurrence of knots 107
4.2.2 Description of knots 110
4.3 Catenanes 114
4.3.1 Occurrence of catenanes 114
4.3.2 Description of catenanes 115
4.4 Analysis of knots and catenanes 117
4.5 Knots and catenanes as probes of DNA—protein interactions 118
4.6 Conclusions 121
4.7 Further Reading 121
4.8 References 121
S DNA topoisomerases 125
5.1 Introduction 125
5.2 Reactions of topoisomerases 127
5.3 Structures and mechanisms of topoisomerases 129
5.3.1 Type I topoisomerases 131
5.3.2 Type II topoisomerases 135
5.4 Topoisomerases as drug targets 138
5.5 Biological role of topoisomerases 139
5.6 Conclusions 140
5.7 Further Reading 141
5.8 References 141
xvi CONTENTS
6 Biological consequences of DNA topology 145
6.1 Introduction: the ubiquity of topology 145
6.1.1 General biological consequences of negative supercoiling 146
6.2 Genome organization 148
6.2.1 Prokaryotes 148
6.2.2 Eukaryotes 151
6.3 Replication 152
6.3.1 Replication initiation 154
6.3.2 Replication elongation 155
6.3.3 Termination of replication 156
6.4 Control of gene expression 158
6.4.1 RNA polymerase binding 159
6.4.2 Transcriptional regulatory proteins I62
6.5 Transcription: the twin supercoiled domain model 165
6.5.1 The role of topoisomerases in transcription 168
6.6 Recombination 169
6.6.1 General recombination 169
6.6.2 Site-specific recombination 170
6.6.2.1 Integrase-type recombination 171
6.6.2.2 Resolvase-type recombination 175
6.7 Conclusions 178
6.8 Further Reading 179
6.9 References 180
Glossary 187
Index 193
|
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| dewey-hundreds | 500 - Natural sciences and mathematics |
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| dewey-tens | 570 - Biology |
| discipline | Biologie Chemie |
| edition | 2. ed. |
| format | Book |
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| language | English |
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| spelling | Bates, Andrew D. Verfasser aut DNA topology Andrew D. Bates ; Anthony Maxwell 2. ed. Oxford Oxford Univ. Press 2005 XVIII, 198 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Oxford bioscience "A key aspect of DNA is its ability to form a variety of structures, this book explains the origins and importance of such structures"--Provided by publisher. ADN - Structure DNA Structure DNA physiology DNA ultrastructure Konformation (DE-588)4164965-5 gnd rswk-swf DNS (DE-588)4070512-2 gnd rswk-swf DNS (DE-588)4070512-2 s DE-604 Konformation (DE-588)4164965-5 s Maxwell, Anthony Verfasser aut HBZ Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=013054945&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Bates, Andrew D. Maxwell, Anthony DNA topology ADN - Structure DNA Structure DNA physiology DNA ultrastructure Konformation (DE-588)4164965-5 gnd DNS (DE-588)4070512-2 gnd |
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| title | DNA topology |
| title_auth | DNA topology |
| title_exact_search | DNA topology |
| title_full | DNA topology Andrew D. Bates ; Anthony Maxwell |
| title_fullStr | DNA topology Andrew D. Bates ; Anthony Maxwell |
| title_full_unstemmed | DNA topology Andrew D. Bates ; Anthony Maxwell |
| title_short | DNA topology |
| title_sort | dna topology |
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