Table Of Content

DNA REPLICATION SECOND EDITION DNA REPLICATION DNA REPLICATION SECOND EDITION ARTHUR KORNBERG STANFORD UNIVERSITY TANIA A. BAKER STANFORD UNIVERSITY AND NATIONAL INSTITUTES OF HEALTH W. H. FREEMAN AND COMPANY New York COVER: A looped rolling circle of the duplex replicative form of phage 0X174, based on an electron micrograph provided by Dr Jack Griffith. See Fig. 8-13 for more detail. (Design by Robert Ishi) Library of Congress Cataloging-in-Publication Data Kornberg, Arthur, 1918- DNA replication. — 2d ed./by Arthur Kornberg and Tania A. Baker, p. cm. Includes bibliographical references and indexes. ISBN 0-7167-2003-5 1. DNA—Synthesis. I. Baker, Tania A. II. Title. QP624.K668 1991 574.87'3282 — dc20 90-26456 Copyright © 1992 by W. H. Freeman and Company No part of this book may be reproduced by any mechanical, photographic, or electronic process, or in the form of a phonographic recording, nor may it be stored in a retrieval system, transmitted, or otherwise copied for public or private use, without written permission from the publisher. Printed in the United States of America 23456789 RRD 98765432 -V> — Contents Preface to DNA Replication, Second Edition x Preface to DNA Replication, First Edition xii Preface to DNA Synthesis xiv 1 DNA Structure and Function 1 1-1 DNA: Past and Present 1 1-6 Size 19 Cruciforms; Triplexes; 1-2 Primary Structure 4 1-7 Shape 23 Single-Stranded Bubbles 43 1-3 A Double-Helical 1-8 Crystal Structures 25 1-13 Intermolecular Structure 8 1-9 Supertwisting 31 Structures: R-Loops; 1-4 Melting and Reannealing 12 1-10 Bending 37 D-Loops; Joints; Holliday Junctions; Knots and 1-5 Base Composition and 1-11 Unusual Structures 41 Catenanes 48 Sequence 16 1-12 Intramolecular Secondary 1-14 Functions of DNA 51 Structures: Z-DNA; 2 Biosynthesis of DNA Precursors 53 2-1 The Building Blocks of Conversion to 2-10 Salvage Pathways of DNA Synthesis 53 Triphosphate 66 Nucleotide Synthesis 79 2-2 De Novo and Salvage 2-6 Significance of 2-11 Thymine and Thymidine Pathways of Nucleotide Pyrophosphate-Releasing Conversion to Synthesis 54 Reactions 68 Thymidylate 85 2-3 Purine Nucleotide 2-7 Ribonucleotide 2-12 Labeling of DNA in Cells 87 Synthesis de Novo 55 Reduction to a 2-13 Uncommon Nucleotides 90 2-4 Pyrimidine Nucleotide Deoxyribonucleotide 69 2-14 One-Carbon Metabolism 94 Synthesis de Novo 62 2-8 Origin of Thymine 75 2-15 Traffic Patterns on the 2-5 Nucleoside 2-9 dUTPase in Thymidylate Pathways 97 Monophosphate Biosynthesis 77 3 DNA Synthesis 101 3-1 Early Attempts at 3-3 Basic Features of Enzymatic Synthesis of Polymerase Action: Nucleic Acicls 101 Polymerization Step 106 3-2 Basic Features of 3-4 Measurement of Polymerase Action: The Polymerase Action 109 Template-Primer 103 v Vi 4 DNA Polymerase I of E. coli 113 4-1 Isolation and 4-7 Deoxynucleoside 4-14 Apparent de Novo Physicochemical Triphosphate (dNTP) Synthesis of Repetitive Properties 113 Binding Site 126 DNA 144 4-2 Preview of Polymerase 4-8 Nucleoside 4-15 Ribonucleotides as Functions 114 Monophosphate Binding Substrate, Primer 4-3 Multiple Sites in an Site 128 Terminus, and Template 150 Active Center 116 4-9 The 3'—>5' Exonuclease: 4-16 Products of Pol I Synthesis 152 4-4 Proteolytic Cleavage: Proofreading 130 4-17 The Polymerase Chain Three Enzymes in One 4-10 Pyrophosphorolysis and Reaction (PCR) 157 Polypeptide 116 Pyrophosphate Exchange 132 4-18 Mutants and the 4-5 Structure of the Large 4-11 Kinetic Mechanisms 133 Physiologic Role of DNA Fragment 118 4-12 The 5'-* 3' Exonuclease: Polymerase in 4-6 DNA Binding Site 122 Excision-Repair 140 Replication and Repair 159 4-13 The 5'—*3' Exonuclease: Nick Translation 142 5 Prokaryotic DNA Polymerases Other Than E. coli Pol I 165 5-1 Discovery of E. coli DNA 5-5 DNA Polymerase III 5-9 Phage T7 DNA Polymerases II and III 165 Holoenzyme of E. coli: Polymerase 190 5-2 DNA Polymerase II ATP Activation 178 5-10 DNA Polymerases of of E. coli 166 5-6 DNA Polymerase III Other Phages: 029, M2, 5-3 DNA Polymerase III Holoenzyme of E. coli: PRDl, N4, T5 192 Holoenzyme of E. coli: Structure and Dynamics 178 5-11 Motifs and Homologies The Core 169 5-7 Other Bacterial DNA Among the DNA 5-4 DNA Polymerase III Polymerases 182 Polymerases 194 Holoenzyme of E. coli: 5-8 Phage T4 DNA Accessory Subunits 174 Polymerase 187 6 Eukaryotic DNA Polymerases 197 6-1 Introduction 197 6-7 DNA Polymerases in 6-10 Terminal 6-2 DNA Polymerase a 200 Growth and Development 213 Deoxynucleotidyl 6-3 DNA Polymerases 6 and e 204 6-8 DNA Virus-Induced Transferase (TdT) 223 6-4 DNA Polymerase /? 207 DNA Polymerases 215 6-5 DNA Polymerase y 209 6-9 RNA-Directed DNA Polymerases: Reverse 6-6 DNA Polymerases of Transcriptases (RTs) and Fungi, Slime Molds, Telomerase 217 Protozoa, and Sea Urchins 210 7 RNA Polymerases 227 7-1 Comparison of RNA and 7-6 Chain Elongation and 7-11 Eukaryotic RNA DNA Polymerases 227 Pausing by E. coli RNA Polymerase III 262 7-2 Structure of E. coli RNA Polymerase 244 7-12 Eukaryotic RNA Polymerase 229 7-7 Termination of Polymerase I and 7-3 Overview of Functions Transcription by E. coli Mitochondrial RNA and Regulation of E. coli RNA Polymerase 247 Polymerase 266 RNA Polymerase 233 7-8 Regulation of 7-13 RNA Polymerases in 7-4 Template Binding and Transcription by E. coli Viral Infections 268 Site Selection by E. coli RNA Polymerase 250 7-14 Relationships of RNA RNA Polymerase 234 7-9 Eukaryotic RNA Synthesis to DNA 7-5 Chain Initiation by E. coli Polymerases 254 Replication 271 RNA Polymerase 240 7-10 Eukaryotic RNA Polymerase II 256