DNA polymerases: discovery, characterization and functions in cellular DNA transactions
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| Format: | Book |
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| Language: | English |
| Published: |
New Jersey [u.a.]
World Scientific
2010
|
| Subjects: | |
| Online Access: | Inhaltsverzeichnis |
| Physical Description: | XV, 321 S. graph. Darst. |
| ISBN: | 9789814299169 9814299162 |
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MARC
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| 020 | |a 9814299162 |9 981-4299-16-2 | ||
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| 245 | 1 | 0 | |a DNA polymerases |b discovery, characterization and functions in cellular DNA transactions |c Ulrich Hübscher ... |
| 264 | 1 | |a New Jersey [u.a.] |b World Scientific |c 2010 | |
| 300 | |a XV, 321 S. |b graph. Darst. | ||
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| _version_ | 1804143114966794240 |
|---|---|
| adam_text | Contents
1.
History and Discovery of
DNA Polymerases 1
1.1
Discovering
DNA:
A First Step Towards Understanding
the Basis of Life
.......................... 1
1.1.1
Nuclein
......................... 3
1.1.2
Nucleic Acid
....................... 5
1.1.3
Nucleic Acids Are Composed of Nucleotides
...... 6
1.1.4 DNA
Is the Genetic Material
.............. 7
1.1.5
Structure of
DNA:
The Watson-Crick
DNA
Double
Helix and Mechanism of
DNA
Replication
....... 10
1.2
Imaging an Enzyme that Assembles the Nucleotides
into
DNA............................. 12
1.2.1 DNA Polymerase
Activity in Extracts
of Escherichia
coli
.................... 15
1.2.2
Escherichia
coli
DNA
Polymerase Can Synthesize
DNA
with Genetic Activity: Creating Life
in the Test Tube
..................... 18
1.2.3
Bacteria Contain Many
DNA
Polymerases
....... 19
1.2.4
How Is a New
DNA
Chain Started? Discontinuous
DNA
Synthesis and the Need for an
RNA
Primer
. ... 21
1.2.5
RNA
Priming as a Mechanism for Initiation:
DNA Primase......................
22
1.3
Late
1960s
to Early
1970s: DNA
Replication Shows
Its Complexity
.......................... 23
1.3.1 DNA
Structure Is Much More Complex, Rich
of Conformational Flexibility and thus Full
of Functional Potentialities than the One
Proposed by Watson and Crick
............. 23
1.3.2 DNA
Binding Proteins,
DNA
Helicases,
DNA Topoisomerases............ 24
χ
DNA Polymerases
1.4
Concluding Remarks,
Parts 1.1-1.3 ............... 25
1.5
Multiple
DNA
Polymerases in Eukaryotic Cells:
DNA
Polymerases
α, β
and
γ
as the First Ones
......... 26
1.5.1 DNA
Polymerase
α
................... 27
1.5.2 DNA
Polymerase
β...................
29
1.5.3
Lack of Relationship Between High-
and Low-Molecular Weight
DNA
Polymerases
..... 29
1.5.4 1975:
First Nomenclature System for Eukaryotic
DNA
Polymerases
.................... 30
1.5.5 DNA
Polymerase
γ
................... 31
1.6
Early Attempts to Ascribe an in vivo Function
to
DNA
Polymerases
α, β
and
γ
................. 32
1.6.1
Positive Correlation of
DNA
Polymerase
α
with Cellular
DNA
Replication and Development
... 33
1.6.2 DNA
Polymerase
y
Is the Mitochondrial
DNA
Polymerase and Replicates Mitochondrial
DNA .... 35
1.6.3
Further Evidence for a Major Involvement of
DNA
Polymerase a in
DNA
Replication and of
DNA
Polymerase
β
in
DNA
Repair
.............. 38
1.7 DNA
Polymerases
б
and
ε
.................... 40
1.8 1985 :
Polymerase Chain Reaction (PCR), a Concept with
Tremendous Practical Applications
................ 41
1.9
Yeast
DNA
Polymerases
..................... 44
1.9.1
Revised Nomenclature for Eukaryotic
DNA
Polymerases
....................... 45
1.10
Plant Cell
DNA
Polymerases
................... 46
1.11
Virus-Induced
DNA
Polymerases
................. 48
1.11.1
Herpes Virus
DNA
Polymerase
............. 48
1.11.2
Vaccinia Virus
DNA
Polymerase
............ 49
1.11.3 DNA
Polymerase Activity in Hepatitis
В
Particle
.... 49
1.11.4
Retrovirases Reverse Transcriptase
........... 50
1.12 1999-2000:
Nucleotide Sequence Analysis of Eukaryotic
Organisms Allowed the Identification of Many Novel
Specialized
DNA
Polymerases
.................. 50
1.12.1 DNA
Polymerase
ζ,
the Lesion Extender
........ 50
1.12.2 DNA
Polymerases
λ
and
μ,
Two Family X
DNA
Polymerases
.................... 51
1.12.3
The Complex
Y
Family of
DNA
Polymerases
..... 51
Contents xi
1.12.4
Present
Nomenclature for Eukaryotic
DNA
Polymerases
....................... 52
1.13
Concluding Remarks, Parts
1.5-1.12............... 52
References
................................ 55
2. DNA
Polymerases in the Three Kingdoms of Life:
Bacteria, Archaea and Eukaryotes
59
2.1
Synthesis and Maintenance of
DNA in
Nature Need
DNA
Polymerases
........................ 59
2.2
The
DNA Polymerase
Reaction
.................. 61
2.3
The Universal Structure of
a
DNA
Polymerase Resembles
a Human Right Hand
....................... 63
2.4
The Seven
DNA
Polymerase Families and Their Functions:
An Overview
........................... 64
2.5 DNA
Polymerase Holoenzymes
................. 70
2.6 DNA
Polymerases, Ring-Like Clamps and Clamp Loaders
... 73
2.7 DNA
Polymerases, Alternative Clamps and Clamp Loaders
... 75
2.8
Replicative
DNA
Polymerases Interacting with
Other Proteins
........................... 78
2.9 DNA
Polymerases and the Single-Stranded
DNA
Binding
Protein Replication Protein A
................... 79
2.10
Chapter Summary
......................... 80
References
................................ 82
3.
Structural and Functional Aspects of the Prokaryotic
and Archaea
DNA
Polymerase Families
85
3.1
Escherichia
coli
.......................... 85
3.1.1
Family
A:
DNA
Polymerase I
.............. 85
3.1.2
Family B:
DNA
Polymerase II
............. 88
3.1.3
Family C:
DNA
Polymerase III Holoenzyme
...... 89
3.1.4
Family Y:
DNA
Polymerases IV and V
......... 93
3.2
Bacillus subtilis
.......................... 96
3.2.1
Family A:
DNA
Polymerase I
.............. 96
3.2.2
Family C:
DNA
Polymerase
С
and DnaE
........ 97
3.2.3
Family X:
DNA
Polymerase X
............. 98
3.2.4
Family Y:
DNA
Polymerases
Y
1
and Y2
........ 98
3.3
Other Bacteria
........................... 99
3.3.1
Mycobacteria
...................... 99
3.3.2
Deinococcus radiodurans
................ 100
xii DNA Polymerases
3.4 Archaea.............................. 101
3.4.1 Family B: DNA Polymerase
В
............. 101
3.4.2 Family
D:
DNA Polymerase
D
............. 102
3.4.3 Family
Y:
DNA Polymerases Dbh and Dpo4...... 103
3.5
Chapter Summary.........................
105
References
................................ 106
4.
Structural and Functional Aspects of the Eukaryotic
DNA
Polymerase Families 111
4.1
The High Number of Specialized Pathways in Eukaryotic
Cells Requires a Plethora of Specialized
DNA
Synthesizing Enzymes
......................
Ill
4.2
Eukaryotic
DNA
Polymerase Structure: The Right Hand
of the Cell
............................. 113
4.2.1
Common Features
.................... 113
4.2.2
Specific Features of the Different Families
....... 115
4.3
Eukaryotic
DNA
Polymerases Accessory Subunits
....... 120
4.4
Eukaryotic
DNA
Polymerase Fidelity: Structural
and Functional Aspects
...................... 123
4.5
Biochemical and Functional Properties of the Different
Eukaryotic
DNA
Polymerases
.................. 127
4.5.1
Family
A
DNA
Polymerases
.............. 127
4.5.2
Family
В
DNA
Polymerases
.............. 131
4.5.3
Family X
DNA
Polymerases
.............. 137
4.5.4
Family
Y
DNA
Polymerases
............... 142
4.6
Interaction with Auxiliary Factors
................ 146
4.7
Eukaryotic
DNA
Polymerases Are Tightly Regulated
in the Cell Cycle
......................... 148
4.8
Chapter Summary
......................... 152
References
................................ 152
5.
Global Functions of
DNA
Polymerases
161
5.1
Fifteen
DNA
Polymerases: Share of Workload and
Redundancies
........................... 161
5.2 DNA
Replication in Living Organisms Requires Three
DNA
Polymerase Molecules at the Replication Fork
....... 165
5.2.1
Prokaryotes
....................... 166
5.2.2
Eukaryotes
........................ 171
5.2.3
Proofreader versus Non-proofreader
DNA
Polymerases
....................... 172
Contents xiii
5.3
Different
DNA
Repair Pathways Have Their Own
DNA
Polymerases, But Can also Borrow Them from
the Replication Machinery
.................... 173
5.4 Translesion DNA
Synthesis in Eukaryotes Generally
Requires Two
DNA
Polymerases: An Inserter
and an Extender
.......................... 177
5.5
Expression of
DNA
Polymerases
................. 182
5.6 DNA
Polymerases Switch between Different
DNA
Transactions
............................ 183
5.6.1
Prokaryotes
....................... 183
5.6.2
Eukaryotes
........................ 185
5.7
Functions of
DNA
Polymerases in Checkpoint Control
..... 192
5.8
Chapter Summary
......................... 193
References
................................ 194
6.
Viral
DNA
Polymerases
199
6.1
Bacteriophage T4
DNA
Polymerase
............... 199
6.2
Bacteriophage T7
DNA
Polymerase
............... 203
6.3
HSV-1
DNA
Polymerase
..................... 207
6.4
Protein Primed
DNA
Replication: Adenoviruses
and Bacteriophage
ф29
...................... 211
6.4.1
Adenovirus
DNA
Polymerase
.............. 211
6.4.2
Bacteriophage
ф29
DNA
Polymerase
.......... 214
6.5
African Swine Virus
DNA
Polymerase
.............. 217
6.6 RNA-Dependent DNA
Synthesis: Reverse Transcriptases
.... 219
6.6.1 HIV-1
Reverse Transcriptase
.............. 220
6.6.2
Other Retroviral Reverse Transcriptases
........ 228
6.6.3
Reverse Transcriptase Activity of Mobile
Genetic Elements: The Retrotransposons
........ 230
6.6.4
Hepadnaviras Reverse Transcriptase
.......... 231
6.7
Chapter Summary
......................... 234
References
................................ 234
7.
Synthetic Evolution of
DNA
Polymerases with
Novel Properties
241
7.1
Why Design Enzymes with Novel Properties?
.......... 241
7.2 DNA
Polymerases Have a Tight Active Site to Which
the Substrates Fit
......................... 242
xiv DNA Polymerases
7.3
Methods to Evolve
DNA
Polymerases with Novel
Properties
............................. 245
7.3.1
Detection and Characterization of
DNA
Polymerases and Mutants Thereof by Functional
Complementation in Escherichia
coli
.......... 245
7.3.2 DNA Polymerase
Evolution by Random Point
Mutagenesis
....................... 246
7.3.3 DNA
Polymerase Evolution by Compartmentalized
Self-Replication (CSR)
................. 247
7.3.4 DNA
Polymerase Evolution by Phage Display
..... 248
7.3.5 DNA
Polymerase Evolution by Oligonucleotide
Addressed Enzyme Assay (OAEA)
........... 248
7.4
Applications of
DNA
Polymerases with Novel Properties
.... 250
7.5 DNA
Polymerases with Novel Properties
............ 253
7.5.1
Increased Fidelity
.................... 253
7.5.2
Decreased Fidelity
.................... 255
7.5.3
Amplification of Damaged and Ancient
DNA...... 255
7.5.4
A
DNA
Polymerase Becomes an
RNA
Polymerase
. . . 256
7.5.5
Evolving the dNTP Substrates and Expansion
of the Genetic Code
................... 256
7.6
Chapter Summary
......................... 258
References
................................ 259
8. DNA
Polymerases and Diseases
261
8.1
Introduction
............................ 261
8.2 DNA
Polymerases and Genetic Stability
............. 261
8.3 DNA
Polymerases and Resistance to Chemotherapy
....... 271
8.4 DNA
Polymerase
γ
and Human Diseases
............ 273
8.5
Chapter Summary
......................... 275
References
................................ 276
9. DNA
Polymerases and Chemotherapy
281
9.1 DNA
Polymerases Are Important Chemotherapeutic Targets
. . 281
9.2
Strategies and Problems for the Design of Inhibitors
of
DNA
Polymerases
....................... 282
9.2.1
Substrate Analogs
.................... 282
9.2.2
Non-substrate Analogs
.................. 284
Contents xv
9.2.3
Novel in silico
Technologies
for Designing
Inhibitors
of
DNA Polymerases.............284
9.3 Inhibitors
of Herpesvirus
DNA
Replication
...........287
9.3.1 Anti-Herpetic Nucleoside
Analogs Require
Activation by the Viral Thymidine Kinase (TK)
.... 287
9.3.2
Nucleoside Analogs Modified in the Base Ring
..... 289
9.3.3
Nucleoside Analogs Modified in the Sugar Moiety
... 291
9.3.4
Active-Site Directed Non-nucleoside Inhibitors
of Herpesvirus
DNA
Polymerases
............297
9.4
The Lack of Enantioselectivity of Viral and Human Enzymes
and the L-Enantiomers of Nucleosides: The Dawn of a New
Generation of Antiviral Drugs
..................297
9.4.1
Herpesvirus Thymidine Kinase Has Low
Enantioselectivity
....................298
9.4.2
The Discovery of a Relaxed Enantioselectivity
of Human and Viral
DNA
Polymerases
.........299
9.4.3
Lack of Enantiospecificity of Human 2 -Deoxycytidine
Kinase: Relevance for the Activation
of L-Deoxycytidine Analogs
..............300
9.5
Inhibitors of HIV-
1
Reverse Transcriptase
............301
9.5.1
Nucleoside Reverse Transcriptase Inhibitors
......301
9.5.2
Non-nucleoside Reverse Transcriptase Inhibitors
.... 307
9.5.3
Combined Toxicities of Reverse Transcriptase
Inhibitors
.........................310
9.5.4
Molecular Interactions of HIV-1 Reverse Transcriptase
with Nucleoside- and Non-nucleoside Inhibitors:
The Problem of Drug Resistance
............312
9.6
Inhibitors of Hepatitis
В
DNA Polymerase............316
9.7
Chapter Summary
.........................318
References
................................319
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| id | DE-604.BV036545365 |
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| physical | XV, 321 S. graph. Darst. |
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| spelling | DNA polymerases discovery, characterization and functions in cellular DNA transactions Ulrich Hübscher ... New Jersey [u.a.] World Scientific 2010 XV, 321 S. graph. Darst. txt rdacontent n rdamedia nc rdacarrier DNS-abhängige-DNS-Polymerasen (DE-588)4150345-4 gnd rswk-swf DNS-abhängige-DNS-Polymerasen (DE-588)4150345-4 s b DE-604 Hübscher, Ulrich Sonstige oth Digitalisierung UB Regensburg application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=020467062&sequence=000004&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | DNA polymerases discovery, characterization and functions in cellular DNA transactions DNS-abhängige-DNS-Polymerasen (DE-588)4150345-4 gnd |
| subject_GND | (DE-588)4150345-4 |
| title | DNA polymerases discovery, characterization and functions in cellular DNA transactions |
| title_auth | DNA polymerases discovery, characterization and functions in cellular DNA transactions |
| title_exact_search | DNA polymerases discovery, characterization and functions in cellular DNA transactions |
| title_full | DNA polymerases discovery, characterization and functions in cellular DNA transactions Ulrich Hübscher ... |
| title_fullStr | DNA polymerases discovery, characterization and functions in cellular DNA transactions Ulrich Hübscher ... |
| title_full_unstemmed | DNA polymerases discovery, characterization and functions in cellular DNA transactions Ulrich Hübscher ... |
| title_short | DNA polymerases |
| title_sort | dna polymerases discovery characterization and functions in cellular dna transactions |
| title_sub | discovery, characterization and functions in cellular DNA transactions |
| topic | DNS-abhängige-DNS-Polymerasen (DE-588)4150345-4 gnd |
| topic_facet | DNS-abhängige-DNS-Polymerasen |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=020467062&sequence=000004&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
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