A Note from the Publisher xi
Preface to DNA Replication, Second Edition xii
Preface to DNA Replication, First Edition xiv
Preface to DNA Synthesis xvi
DNA Structure and Function 1
DNA: Past and Present 1
Primary Structure 4
A Double-Helical Structure 8
Melting and Reannealing 12
Base Composition and Sequence 16
Size 19
Shape 23
Crystal Structures 25
Supertwisting 31
Bending 37
Unusual Structures 41
Intramolecular Secondary Structures: Z-DNA; Cruciforms; Triplexes; Single-Stranded Bubbles 43
Intermolecular Structures: R-Loops; D-Loops; Joints; Holliday Junctions; Knots and Catenanes 48
Functions of DNA 51
Biosynthesis of DNA Precursors 53
The Building Blocks of DNA Synthesis 53
De Novo and Salvage Pathways of Nucleotide Synthesis 54
Purine Nucleotide Synthesis de Novo 55
Pyrimidine Nucleotide Synthesis de Novo 62
Nucleoside Monophosphate Conversion to Triphosphate 66
Significance ofPyrophosphate-Releasing Reactions 68
Ribonucleotide Reduction to a Deoxyribonucleotide 69
Origin of Thymine 75
dUTPase in Thymidylate Biosynthesis 77
Salvage Pathways of Nucleotide Synthesis 79
Thymine and Thymidine Conversion to Thymidylate 85
Labeling of DNA in Cells 87
Uncommon Nucleotides 90
One-Carbon Metabolism 94
Traffic Patterns on the Pathways 97
DNA Synthesis 101
Early Attempts at Enzymatic Synthesis of Nucleic Acids 101
Basic Features of Polymerase Action: The Template-Primer 103
Basic Features of Polymerase Action: Polymerization Step 106
Measurement of Polymerase Action 109
DNA Polymerase I of E. coli 113
Isolation and Physicochemical Properties 113
Preview of Polymerase Functions 114
Multiple Sites in an Active Center 116
Proteolytic Cleavage: Three Enzymes in One Polypeptide 116
Structure of the Large Fragment 118
DNA Binding Site 122
Deoxynucleoside Triphosphate (dNTP) Binding Site 126
Nucleoside Monophosphate Binding Site 128
The 3[prime][rarr]5[prime] Exonuclease: Proofreading 130
Pyrophosphorolysis and Pyrophosphate Exchange 132
Kinetic Mechanisms 133
The 5[prime][rarr]3[prime] Exonuclease: Excision-Repair 140
The 5[prime[rarr]3[prime] Exonuclease: Nick Translation 142
Apparent de Novo Synthesis of Repetitive DNA 144
Ribonucleotides as Substrate, Primer Terminus, and Template 150
Products of Pol I Synthesis 152
The Polymerase Chain Reaction (PCR) 157
Mutants and the Physiologic Role of DNA Polymerase in Replication and Repair 159
Prokaryotic DNA Polymerases Other Than E. coli Pol I 165
Discovery of E. coli DNA Polymerases II and III 165
DNA Polymerase II of E. coli 166
DNA Polymerase III Holoenzyme of E. coli: The Core 169
DNA Polymerase III Holoenzyme of E. coli: Accessory Subunits 174
DNA Polymerase III Holoenzyme of E. coli: ATP Activation 178
DNA Polymerase III Holoenzyme of E. coli: Structure and Dynamics 178
Other Bacterial DNA Polymerases 182
Phage T4 DNA Polymerase 187
Phage T7 DNA Polymerase 190
DNA Polymerases of Other Phages: [phgr]29, M2, PRD1, N4, T5 192
Motifs and Homologies Among the DNA Polymerases 194
Eukaryotic DNA Polymerases 197
Introduction 197
DNA Polymerase [Alpha] 200
DNA Polymerases [Delta] and [epsilon] 204
DNA Polymerase [Beta] 207
DNA Polymerase [Gamma] 209
DNA Polymerases of Fungi, Slime Molds, Protozoa, and Sea Urchins 210
DNA Polymerases in Growth and Development 213
DNA Virus-Induced DNA Polymerases 215
RNA-Directed DNA Polymerases: Reverse Transcriptases (RTs) and Telomerase 217
Terminal Deoxynucleotidyl Transferase (TdT) 223
RNA Polymerases 227
Comparison of RNA and DNA Polymerases 227
Structure of E. coli RNA Polymerase 229
Overview of Functions and Regulation of E. coli RNA Polymerase 233
Template Binding and Site Selection by E. coli RNA Polymerase 234
Chain Initiation by E. coli RNA Polymerase 240
Chain Elongation and Pausing by E. coli RNA Polymerase 244
Termination of Transcription by E. coli RNA Polymerase 247
Regulation of Transcription by E. coli RNA Polymerase 250
Eukaryotic RNA Polymerases 254
Eukaryotic RNA Polymerase II 256
Eukaryotic RNA Polymerase III 262
Eukaryotic RNA Polymerase I and Mitochondrial RNA Polymerase 266
RNA Polymerases in Viral Infections 268
Relationships of RNA Synthesis to DNA Replication 271
Primases, Primosomes, and Priming 275
The Need for Priming in DNA Synthesis 275
Discovery of RNA-Primed DNA Synthesis 276
E. coli Primase (dnaG Gene Product) 279
E. coli Primosomes 283
Phage and Plasmid Primases 292
Eukaryotic Primases 296
Endonucleolytic Priming 298
Terminal Protein Priming 303
Ligases and Polynucleotide Kinases 307
Assays and Discovery of DNA Ligases 307
Properties and Abundance of DNA Ligases 308
Enzymatic Mechanism of DNA Ligases 311
Substrate Specificity of DNA Ligases 314
Functions in Vivo of DNA Ligases 316
RNA Ligases 319
Polynucleotide Kinases 320
DNA-Binding Proteins 323
Introduction 323
Single-Strand Binding Proteins (SSBs) 325
T4 Phage Gene 32 Protein (Gp32) 329
M13 Phage Gene 5 Protein; Other Phage and Plasmid SSBs 332
E. coli SSB 334
Eukaryotic SSBs 336
Histones and Chromatin 339
Prokaryotic Histone-Like Proteins 345
Regulatory Proteins 348
Covalent Protein-DNA Complexes 353
DNA Helicases 355
Helicases: Actions and Polarity 355
Replicative Helicases of E. coli and Phages 358
Prokaryotic Helicases That Function in Repair, Recombination, Conjugal Transfer, or Transcription 367
Eukaryotic Helicases 373
Homologies and Mechanisms 374
Topoisomerases 379
Topoisomerases: Assays and Functions 379
E. coli Topoisomerases I and III 383
E. coli DNA Gyrase (E. coli Topoisomerase II) 387
Eukaryotic Type I Topoisomerases 392
Eukaryotic Type II Topoisomerases 394
Functions of the Eukaryotic Topoisomerases 395
Other Topoisomerases 398
Deoxyribonucleases 403
Deoxyribonucleases in Vitro and in Vivo 403
Exonucleases: 3[prime][rarr]5[prime] 404
Exonucleases: 5[prime][rarr]3[prime] 410
Processivity of the Exonucleases 412
Endonucleases 414
Restriction Endonucleases: General Considerations 416
Restriction Endonucleases: Nonspecific Cleavage (Type I) 418
Restriction Endonucleases: Specific Cleavage (Type II) 420
Nucleases in Repair and Recombination 425
Ribonuclease H (RNase H) 436
Inhibitors of Replication 439
Inhibitors as Drugs and Reagents 439
Inhibitors of Nucleotide Biosynthesis 441
Nucleotide Analogs Incorporated into DNA or RNA 446
Inhibitors That Modify DNA 451
Inhibitors of Topoisomerases 461
Inhibitors of Polymerases and Replication Proteins 463
Radiation Damage of DNA 470
Replication Mechanisms and Operations 471
Basic Rules of Replication 471
Replication Fork: Origin, Direction, Structure 473
Semidiscontinuous Replication 475
Replication Genes and Crude Systems 478
Replication Proteins and Reconstituted Systems 483
Enzymology of the Replication Fork 487
Start of DNA Chains 490
Processivity of Replication 494
Fidelity of Replication 496
Uracil Incorporation in Replication 500
Rolling-Circle Replication 502
Termination of Replication 503
Genome Origins 511
Identification of Origins 511
The E. coli Chromosomal Origin (oriC) 521
Initiation from the E. coli Chromosomal Origin (oriC) 524
Other Prokaryotic Origins 533
Eukaryotic Virus and Organelle Origins 542
Eukaryotic Chromosome Origins 547
Bacterial DNA Viruses 553
Viral Windows on Cellular Replication 553
Stages in the Viral Life Cycle 555
Small Filamentous (Ff) Phages: M13, fd, f1 557
Small Polyhedral Phages: [phgr]X174, S13, G4 571
Medium-Sized Phages: T7 and Other T-Odd Phages (T1, T3, T5) 576
Large Phages: T4 and Other T-Even Phages (T2, T6) 597
Temperate Phages: [Lambda], P22, P2, P4, P1, Mu 610
Other Phages: N4, PM2, PR4, and the Bacillus Phages (SPO1, PBS1, PBS2, [phgr]29, SPP1) 632
Plasmids and Organelles 637
Bacterial Plasmids 637
ColE1 641
pSC101 648
R Plasmids: R1 and R100 650
R6K 655
F Plasmid 658
Bacterial Conjugation 664
Broad-Host-Range Plasmids 671
Plasmids of Gram-Positive Bacteria 672
Yeast Plasmids: The 2[mgr] Circle and Others 675
Mitochondria, Kinetoplasts, and Chloroplasts 680
Animal DNA Viruses and Retroviruses 689
Utility of Animal Viruses 689
Papovaviruses: Simian Virus 40 (SV40), Polyoma Virus, and Bovine Papilloma Virus (BPV) 690
Parvoviruses: Autonomous and Helper-Dependent Viruses 700
Adenoviruses 703
Herpesviruses 709
Poxviruses: Vaccinia 713
Retroviruses 717
Hepadna Viruses: Hepatitis B Virus (HBV) 724
Plant and Insect Viruses 727
Regulation of Chromosomal Replication and Cell Division 731
Regulation of Replication: Multiple Types of Control 731
The Bacterial Cell Cycle 732
Control of Initiation of Bacterial Chromosomes 734
Bacterial Envelopes and Chromosome-Membrane Association 747
Bacterial Cell Division 753
The Eukaryotic Cell Cycle 759
Control of Replication in Eukaryotes 762
Repair, Recombination, Transformation, Restriction, and Modification 771
DNA Damage and Mutations 771
Repair by Photolysis, Dealkylation, and Nucleotide Excision 775
Repair Responses and Regulation 784
Repair in Disease and Aging 788
Homologous Recombination 791
Site-Specific Recombination 806
Transposition 817
Bacterial Transformation and Competence 822
Restriction and Modification 827
Synthesis of Genes and Chromosomes 833
Origin of DNA on Earth 833
Determination of DNA Sequence 837
Chemical Synthesis of Oligodeoxyribonucleotides and Genes 840
Assembling Genes into Chromosomes: Recombinant DNA 844
Homage to Enzymes; An epilogue 849
Author Index 851
Subject Index 871