Eukaryotic DNA Replication: A Practical Approach (Practical Approach Series) PDF
Preview Eukaryotic DNA Replication: A Practical Approach (Practical Approach Series)
Eukaryotic DNA Replication The Practical Approach Series SERIES EDITOR B. D. HAMES Department of Biochemistry and Molecular Biology University of Leeds, Leeds LS2 9JT, UK See also the Practical Approach web site at http://www.oup.co.uk/PAS * indicates new and forthcoming titles Affinity Chromatography Cellular Calcium Affinity Separations Cellular Interactions in Development Anaerobic Microbiology Cellular Neurobiology Animal Cell Culture (2nd edition) if Chromatin Animal Virus Pathogenesis if Chromosome Structural Analysis Antibodies I and II Clinical Immunology Antibody Engineering Complement Antisense Technology * Crystallization of Nucleic Applied Microbial Physiology Acids and Proteins Basic Cell Culture (2nd edition) Behavioural Neuroscience Cytokines (2nd edition) Bioenergetics The Cytoskeleton Biological Data Analysis Diagnostic Molecular Pathology I and II Biomechanics - Materials DNA and Protein Sequence Biomechanics—Structures and Analysis Systems DNA Cloning 1: Core Biosensors Techniques (2nd edition) Carbohydrate Analysis DNA Cloning 2: Expression (2nd edition) Systems (2nd edition) Cell-Cell Interactions DNA Cloning 3: Complex The Cell Cycle Genomes (2nd edition) Cell Growth and Apoptosis DNA Cloning 4: Mammalian Cell Separation Systems (2nd edition) * Drosophila (2nd edition) Immunochemistry 1 Electron Microscopy in Immunochemistry 2 Biology Immunocytochemistry Electron Microscopy in * In Situ Hybridization (2nd Molecular Biology edition) Electrophysiology lodinated Density Gradient Enzyme Assays Media Epithelial Cell Culture Ion Channels Essential Developmental if Light Microscopy (2nd edition) Biology Essential Molecular Biology I Lipid Modification of and I Lipoprotein Analysis if Eukaryotic DNA Replication Liposomes Experimental Neuroanatomy Mammalian Cell Biotechnology Extracellular Matrix Medical Parasitology Flow Cytometry (2nd edition) Medical Virology Free Radicals MHC Volumes 1 and 2 Gas Chromatography * Molecular Genetic Analysis of Gel Electrophoresis of Nucleic Populations (2nd edition) Acids (2nd edition) 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(2nd *PCR3:PCRInSitu edition) Hybridization Tumour Immunobiology Peptide Antigens Last 10 published Photosynthesis: Energy Chromatin 1.4.98 Trans duction Drosophila 2/e 19.3.98 Plant Cell Biology Molecular Genetic Analysis of Plant Cell Culture (2nd edition) Populations 2/e 19.3.98 Plant Molecular Biology Mutation Detection 15.2.98 Plasmids (2nd edition) Antisense Technology 18.12.97 Platelets PCR3:ISH.12.98 Postimplantation Mammalian Genome Mapping 21.8.98 Embryos MHC Volume 2 21.8.97 Preparative Centrifugation MHC Volume 121.8.97 Protein Blotting Signalling by Inositides * Protein Expression Vol 1 In prod * Protein Expression Vol 2 HPLCofMac2/e Protein Engineering RNA-Protein Interactions Protein Function (2nd edition) Growth Factors and Protein Phosphorylation Receptors Protein Purification Cell Sepn Applications Light Mic Protein Purification Methods ISH2/e Protein Sequencing GEP3/e Protein Structure (2nd edition) Immobilized Biomolecules Protein Structure Prediction Eukaryotic DNA Replication Protein Targeting Chromosone Structural Proteolytic Enzymes Analysis Pulsed Field Gel Electrophoresis Protein Expression Vol 1 Eukaryotic DNA Replication A Practical Approach Edited by SUE COTTERILL Marie Curie Research Institute, Oxted, Surrey OXPORD UNIVERSITY PRESS 1999 OXPORD UNIVERSITY PRESS Great Clarendon Street, Oxford OX2 6DP Oxford University Press is a department of the University of Oxford and furthers the University's aim of excellence in research, scholarship, and education by publishing worldwide in Oxford New York Athens Auckland Bangkok Bogota Buenos Aires Calcutta Cape Town Chennai Dar es Salaam Delhi Florence Hong Kong Istanbul Karachi Kuala Lumpur Madrid Melbourne Mexico City Mumbai Nairobi Paris Sao Paulo Singapore Taipei Tokyo Toronto Warsaw and associated companies in Berlin Ibadan Oxford is a registered trade mark of Oxford University Press Published in the United States by Oxford University Press Inc., New York © Oxford University Press, 1999 All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted, in any form or by any means, without the prior permission in writing of Oxford University Press. Within the UK, exceptions are allowed in respect of any fair dealing for the purpose of research or private study, or criticism or review, as permitted under the Copyright, Designs and Patents Act, 1988, or in the case of reprographic reproduction in accordance with the terms of licenses issued by the Copyright Licensing Agency. Enquiries concerning reproduction outside those terms and in other countries should be sent to the Rights Department, Oxford University Press, at the address above. This book is sold subject to the condition that it shall not, by way of trade or otherwise, be lent, re-sold, hired out, or otherwise circulated without the publisher's prior consent in any form of binding or cover other than that in which it is published and without a similar condition including this condition being imposed on the subsequent purchaser Users of books in the Practical Approach Series are advised that prudent laboratory safety procedures should be followed at all times. Oxford University Press makes no representation, express or implied, in respect of the accuracy of the material set forth in books in this series and cannot accept any legal responsibility or liability for any errors or omissions that may be made. A catalogue record for this book is available from the British Library Library of Congress Cataloging in Publication Data (Data available) ISBN 0 19 963681 8 (Hbk) 0 19 963680 X (Pbk) Typeset by Footnote Graphics, Warminster, Wilts Printed in Great Britain by Information Press, Ltd, Eynsham, Oxon. Preface The aim of this book is to allow easy access to the techniques that are currently in use to study eukaryotic DNA replication. The subject area that falls under this heading is quite diverse, and its boundaries with related fields (e.g. the cell cycle) are also rather blurred. This span is reflected in the scope of the chapters chosen for this book which cover not only ways of working with specific repli- cation proteins and examples of the various model systems used to study eukaryotic DNA replication but also more general techniques. By necessity many of the examples that are used in the text are quite specific but attempts have been made to put these into their relevant context, and also to include more general advice that should make the methods usable at several levels. The field of eukaryotic DNA replication has moved fast in the last ten years and the pace of progress shows no signs of decreasing at this point. However the techniques that are covered here are all fundamental to the study of the subject area. They should therefore remain useful for some time to come and provide a good starting point for the study of any aspect of eukaryotic DNA replication. Oxted S.C. May 1998 This page intentionally left blank Contents List of con trib u tors Abbreviations 1. Methods to map origins of replication in eukaryotes i Susan A. Gerbi, Anja K. Bielinsky, Chun Liang, Victoria V. Lunyak, and Fyodor D. Urnov 1. Introduction 1 Overview 1 Methods to map origins as regions of initiation of DNA synthesis 2 Methods to map origins based on the asymmetry of bidirectional replication 3 2. Two-dimensional (2D) and three-dimensional (3D) gels 4 Background 4 Preparation of replicating DNA 7 Neutral/Neutral (N/N) 2D gels and Southern hybridization 13 Neutral/Alkaline (N/A) 2D gels 17 3D gels 18 3. PCR analysis of nascent DNA strands 19 Background 19 DNA preparation for PCR analysis of nascent strands 21 Size fractionation of DNA 24 Purification of BUdR labelled nascent DNA 26 PCR amplification and Southern blot hybridization 28 Analysis of PCR results 30 4. Replication initiation point (RIP) mapping 31 Background 31 Labelling and isolation of DNA for RIP mapping 32 Enrichment of replication intermediate (RI) DNA on BND cellulose 35 Phosphorylation of RI DNA by T4 polynucleotide kinase 35 \-exonuclease treatment of RI DNA 36 Primer extension reaction 37 Acknowledgements 40 References 40
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