Download DNA REPLICATION

D N A REPLICATION
SECOND
EDITION
ARTHUR KORNBERG
STANFORD UNIVERSITY
TANIA A. BAKER
STANFORD UNIVERSITY AND
NATIONAL INSTITUTES OF HEALTH
Tecfintscfie UnJversItat Darmsfaclf
FACHBEREICH 10 — BIOLOGIE
— Bibliothek —
SchnittspahnstraBe 10
D-64287 D a r m s t a d t
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W. H. FREEMAN AND COMPANY
New York
Contents
Preface to DNA Replication, Second Edition
Preface to DNA Replication, First Edition
Preface to DNA Synthesis
1
DNA Structure and Function
DNA: Past and Present
Primary Structure
A Double-Helical
Structure
Melting and Reannealing
Base Composition and
Sequence
2
It
H
K
B
Bf?
H
E
Bfc- •
B'
•i
Eg
m-
1
4
Size
Shape
Crystal Structures
Supertwisting
1-10 Bending
1-11 Unusual Structures
1-12 Intramolecular Secondary
Structures: Z-DNA;
16
53
'
2-6
54
2-7
55
62
• - 2-8
2-9
1
I
1
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K
B,
||2
K
E
3
1
Biosynthesis of DNA Precursors
The Building
Blocks of
DNA
Synthesis
De Novo and Salvage
Pathways of Nucleotide
Synthesis
Purine Nucleotide
Synthesis de Novo
Pyrimidine Nucleotide
Synthesis de Novo
Nucleoside
Monophosphate
xi
xiii
1-6
1-7
1-8
1-9
8
12
'
ix
19
23
25
31
37
41
Conversion to
Triphosphate
Significance of
Pyrophosphate-Releasing
Reactions ^ ^
Ribonucleotide
Reduction to a
Deoxyribonucleotide
Origin of Thymine
dUTPase in Thymidylate
Biosynthesis
;
I
;
• '
'
.
66
68
69
75
77
''.I,'
Basic Features of
Polymerase Action:
Polymerization Step
3-4 Measurement of
Polymerase Action
3-3
101
103
43
48
51
53
DNA Synthesis 101
Early Attempts at
Enzymatic Synthesis of
Nucleic Acids
Basic Features of
Polymerase Action: The
Template-Primer
Cruciforms; Triplexes;
Single-Stranded Bubbles
1-13 Intermolecular
Structures: R-Loops;
D-Loops; Joints; Holliday
Junctions; Knots and
Catenanes
1-14 Functions of DNA
106
109
2-10 Salvage Pathways of ,
Nucleotide Synthesis
2-11 Thymine and Thymidine
Conversion to
Thymidylate
2-12 Labeling of DNA in Cells
2-13 Uncommon Nucleotides
2-14 One-Carbon Metabolism
2-15 Traffic Patterns on the
Pathways
79
85
87
90
94
97
VI
4
4-1
4-2
4-3
4-4
4-5
4-6
Isolation and
Physicochemical
Properties
Preview of Polymerase
Functions
Multiple Sites in an
Active Center
Proteolytic Cleavage:
Three Enzymes in One
Polypeptide
Structure of the Large
Fragment
DNA Binding Site
5
5-1
5-2
5-3
5-4
7-2
7-3
7-4
7-5
113
114
116
-
116
118
122
Deoxynucleoside
Triphosphate (dNTP)
Binding Site
Nucleoside
4-8
Monophosphate Binding
Site
4-9
The 3'—»5' Exonuclease:
Proofreading
4-10 Pyrophosphorolysis and
Pyrophosphate Exchange
4-11 Kinetic Mechanisms
4-12 The 5'—»3' Exonuclease:
Excision-Repair
4-13 The 5'—»3' Exonuclease:
Nick Translation
Apparent de Novo
Synthesis of Repetitive
DNA
4-15 Ribonucleotides as
Substrate, Primer
Terminus, and Template
4-16 Products of Pol I Synthesis
4-17 The Polymerase Chain
Reaction (PCR)
• 4-18 Mutants and the
Physiologic Role of DNA
Polymerase in
Replication and Repair
4-14
126
128
130
132
133
140
144
150
152
157
159
142
Prokaryotic DNA Polymerases Other Than E. coli Pol I 165
5-5
165
166
169
5-6
5-7'
5-8
174
DNA Polymerase III
Holoenzyme of E. co]i:
ATP Activation
DNA Polymerase III
Holoenzyme of E. coli:
Structure and Dynamics
Other Bacterial DNA
Polymerases Phage T4 DNA
Polymerase
5-9
178
178
182
Phage T7 DNA
Polymerase
5.10 DNA Polymerases of
Other Phages: 029, M2,
PRD1, N4, T5
5.11 Motifs and Homologies
Among the DNA
Polymerases
190
i(192
194
187
Eukaryotic DNA Polymerases 197
Introduction
DNA Polymerase a
DNA Polymerases S and e
DNA Polymerase
fi
DNA Polymerase y
DNA Polymerases of
Fungi, Slime Molds,
Protozoa, and Sea Urchins
7
7-1
4-7
Discovery of E. coli DNA
Polymerases II and III
DNA Polymerase II
of E. coli
DNA Polymerase III
Holoenzyme of E. coJi:
The Core
DNA Polymerase III
Holoenzyme of E. coli:
Accessory Subunits
6
6-1
6-2
6-3
6-4
6-5
6-6
DNA Polymerase I of E. coli 113
197
200
204
207
209
6-7
6-8
6-9
210
DNA Polymerases in
Growth and Development
DNA Virus-Induced
DNA Polymerases
RNA-Directed DNA
Polymerases: Reverse •
Transcriptases_(RTs) and
Telomerase
6-10
213
Terminal
Deoxynucleotidyl
Transferase (TdT)
223
215
217
RNA Polymerases 227
Comparison of RNA and
DNA Polymerases
Structure of E. coli RNA
Polymerase
Overview of Functions
and Regulation of E. coli
RNA Polymerase
Template Binding and
Site Selection by E. coli
RNA Polymerase
Chain Initiation by E. coli
RNA Polymerase
7-6
227
229
7-7
233
7-8
. 234
7-9
240
7-10
Chain Elongation and
Pausing by E. coli RNA
Polymerase
Termination of
Transcription by E. coli
RNA Polymerase
Regulation of
Transcription by E. coli
RNA Polymerase
Eukaryotic RNA
Polymerases
Eukaryotic RNA
Polymerase II
7-11
244
7-12
247
7-13
250
254
256
7-14
Eukaryotic RNA
Polymerase III
Eukaryotic RNA
Polymerase I and
Mitochondrial RNA
Polymerase
RNA Polymerases in
Viral Infections
Relationships of RNA
Synthesis to DNA
Replication
262
266
268
271
VII
8
Primases, Primosomes, and Priming 275
-I The Need for Priming in
* DNA Synthesis
1-2 Discovery of RNA-Primed
DNA Synthesis
9
10
11
12
13
§3-5
Eukaryotic Primases
Endonucleolytic Priming
Terminal Protein Priming
296
298
303
292
9-4
-307
9-5
308
9-6
9-7
311
Substrate Specificity of
DNA Ligases
Functions in Vivo of DNA
v
Ligases
RNA Ligases
Polynucleotide Kinases ,
314
316
319
320
323
"
10-4
325
10-5
10-6
. 10-7
329
Ml 3 Phage Gene 5
Protein; Other Phage
and Plasmid SSBs
E. coli SSB
Eukaryotic SSBs
Histones and Chromatin
Prokaryotic Histone-Like
Proteins
10-9
Regulatory Proteins
10-10 Covalent Protein-DNA
Complexes
10-8
332
334
336
339
345
348
353
<
355
358
Recombination, Conjugal
Transfer, or Transcription
: 11-4 Eukaryotic Helicases
11-5 Homologies and
Mechanisms
367
373
374
Topoisomerases 379
2-1 Topoisomerases: Assays
and Functions
2-2 E. coli Topoisomerases I
and III
§2-3 E. coli DNA Gyrase
(E. coli Topoisomerase II)
2
•3
•4
8-6
8-7
8-8
DNA Helicases 355
1-1 Helicases: Actions and
Polarity
1-2 Replicative Helicases of
E. coli and Phages
1-3 Prokaryotic Helicases
That Function in Repair,
1
279
283
DNA-Binding Proteins 323
Introduction
Single-Strand Binding
Proteins (SSBs)
T4 Phage Gene 32
Protein (Gp32)
3
8-4
8-5
276
E. coli Primase (dnaG
Gene Product)
E. coli Primosomes
Phage and Plasmid
Primases
Ligases and Polynucleotide Kinases 307
f-1 Assays and Discovery of
* DNA Ligases
Properties and Abundance
of DNA Ligases
Enzymatic Mechanism of
DNA Ligases
1
2
8-3
275
379
383
12-4 Eukaryotic Type I
Topoisomerases
12-5 Eukaryotic Type II
Topoisomerases
12-6
392
394
12-7
Functions of the
Eukaryotic
Topoisomerases
Other Topoisomerases
395
398
387
Deoxyribonucleases 403
Deoxyribonucleases
in Vitro and in Vivo
Exonucleases: 3'—»5'
Exonucleases: 5'—*3'
Processivity of the
Exonucleases
Endonucleases
13-6
403
404
410
412
414
13-7
Restriction
Endonucleases: General
Considerations
Restriction
Endonucleases:
Nonspecific Cleavage
(Type I)
Restriction
Endonucleases: Specific
Cleavage (Type II)
Nucleases in Repair and
13-9
Recombination
13-10 Ribonuclease H
(RNaseH)
13-8
416
418
420
425
436
VIII
14
Inhibitors of Replication
14-1 Inhibitors as Drugs and
Reagents
14-2 Inhibitors of Nucleotide
Biosynthesis
14-3 Nucleotide Analogs
Incorporated into DNA
or RNA
15
15-1
15-2
15-3
15-4
441
446
15-5
471
15-6
473
478
511
16-1 Identification of Origins
16-2 The E. coli Chromosomal
Origin (oriC)
16-3 Initiation from the E. coli
Chromosomal Origin
511
17
„
18
18-1
18-2
18-3
18-4
18-5
521
524
Bacterial DNA Viruses
17-1 Viral Windows on
Cellular Replication
17-2 Stages in the Viral Life
Cycle
17-3 Small Filamentous (Ff)
Phages: M13, fd, fl
553
555
557
Plasmids and Organelles
Bacterial Plasmids
ColEl
pSClOl
R Plasmids: Rl and R100
R6K
15-7
15-8
475
Genome Origins
foriCJ
14-4 Inhibitors That Modify
DNA
14-5 Inhibitors of
Topoisomerases
14-6 Inhibitors of Polymerases
and Replication Proteins
14-7 Radiation Damage of DNA
Replication Mechanisms and Operations
Basic Rules of
Replication
Replication Fork:
Origin, Direction,
Structure
Semidiscontinuous
Replication
Replication Genes and
Crude Systems
16
439
439
637
641
648
650
655
15-9
451
461
463
470
471
Replication Proteins and
Reconstituted Systems
Enzymology of the
Replication Fork
Start of DNA Chains
Processivity of
Replication
Fidelity of Replication
16-4 Other Prokaryotic Origins
16-5 Eukaryotic Virus and
Organelle Origins
16-6 Eukaryotic Chromosome
Origins
483
487
490
15-10 Uracil Incorporation in
Replication
15-11 Rolling-Circle
Replication
15-12 Termination of
Replication
500
502
503
494
496
533
542
547
553
17-4 Small Polyhedral Phages:
0X174, S13, G4.
17-5 Medium-Sized Phages: T7
and Other T-Odd Phages
(Tl, T3, T5)
17-6 Large Phages: T4 and
Other T-Even Phages
(T2, T6)
571
576
17-7 Temperate Phages: A,
P22, P2, P4, PI, Mu
17-8 Other Phages: N4, PM2,
PR4, and the Bacillus
Phages (SPOl, PBS1,
PBS2, 029, SPP1)
610
632
597
637
18-6
18-7
18-8
18-9
F Plasmid
Bacterial Conjugation
Broad-Host-Range
Plasmids
Plasmids of GramPositive Bacteria
658
664
671
672
18-10 Yeast Plasmids: The 2/i
Circle and Others
18-11 Mitochondria,
Kinetoplasts, and
Chloroplasts
675
680
IX
19
Animal DNA Viruses and Retroviruses
fcl Utility of Animal Viruses
I-2 Papovaviruses: Simian
Virus 40 (SV40), Polyoma
Virus, and Bovine
Papilloma Virus (BPV)
20
21
-1
-2
-3
731
732
734
Chromosome - Membrane
Association
20-5 Bacterial Cell Division
20-6 The Eukaryotic Cell Cycle
-20-7 Control of Replication in
Eukaryotes
19-6 Poxviruses: Vaccinia
19-7 Retroviruses
19-8 Hepadna Viruses:
Hepatitis B Virus (HBV)
19-9 Plant and Insect Viruses
700
703
709
21-4
771
21-5
775
21-6
Repair in Disease and
Aging
Homologous
Recombination
Site-Specific
Recombination
Origin of DNA on Earth
§2-2 Determination of DNA
Sequence
22-3 Chemical Synthesis of
Oligodeoxyribonucleotides and Genes
762
788
21-7
21-8
791
21-9
806
837
840
Author Index
Subject Index
833
22-4 Assembling Genes into
Chromosomes:
Recombinant DNA
22-5 Homage to Enzymes; An
epilogue
833
851
871
724
727
747
753
759
784c
Synthesis of Genes and Chromosomes
713
717
731
Repair, Recombination, Transformation, Restriction, and Modification
DNA Damage and
Mutations
Repair by Photolysis,
Dealkylation, and
Nucleotide Excision
Repair Responses and
Regulation
22
690
19r3 Parvoviruses:
Autonomous and
Helper-Dependent '
Viruses
19-4 Adenoviruses 19-5 Herpesviruses
Regulation of Chromosomal Replication and Cell Division
20-1 Regulation of Replication:
Multiple Types of Control
|0-2 The Bacterial Cell Cycle
[20-3 Control of Initiation of *
Bacterial Chromosomes
1-4 Bacterial Envelopes and
y
689
689
844
849
771
Transposition
Bacterial
Transformation and
Competence
Restriction and
Modification
817
'822
827