Mutation Detection: A Practical Approach PDF
Preview Mutation Detection: A Practical Approach
Mutation Detection The Practical Approach Series SERIES EDITOR B. D. HAMES Department of Biochemistry and Molecular Biology University of Leeds, Leeds LS2 9JT, UK indicates new and forthcoming titles Affinity Chromatography Cellular Interactions in * Affinity Separations Development Anaerobic Microbiology Cellular Neurobiology Animal Cell Culture * Chromatin (2nd edition) Clinical Immunology Animal Virus Pathogenesis if Complement Antibodies I and II Crystallization of Nucleic if Antibody Engineering Acids and Proteins * Antisense Technologies Cytokines (2nd edition) if Applied Microbial The Cytoskeleton Physiology Diagnostic Molecular Pathology Basic Cell Culture I and II Behavioural Neuroscience * DNA and Protein Sequence Analysis Bioenergetics DNA Cloning 1: Core Biological Data Analysis Techniques (2nd edition) Biomechanics—Materials DNA Cloning 2: Expression Biomechanics—Structures and Systems (2nd edition) Systems if DNA Cloning 3: Complex Biosensors Genomes (2nd edition) Carbohydrate Analysis if DNA Cloning 4: Mammalian (2nd edition) Systems (2nd edition) Cell-Cell Interactions Electron Microscopy in The Cell Cycle Biology Cell Growth and Apoptosis Electron Microscopy in Cellular Calcium Molecular Biology Electrophysiology Lipid Analysis Enzyme Assays Liposomes * Epithelial Cell Culture Mammalian Cell Biotechnology Essential Developmental Medical Parasitology Biology Medical Virology Essential Molecular Biology I * MHC Volumes 1 and 2 and II Molecular Genetic Analysis of Experimental Neuroanatomy Populations Extracellular Matrix Molecular Genetics of Yeast Flow Cytometry (2nd edition) Molecular Imaging in * Free Radicals Neuroscience Gas Chromatography Molecular Neurobiology Gel Electrophoresis of Nucleic Molecular Plant Pathology Acids (2nd edition) I and II Gel Electrophoresis of Proteins Molecular Virology (2nd edition) Monitoring Neuronal Activity Gene Probes 1 and 2 Mutagenicity Testing Gene Targeting * Mutation Detection Gene Transcription Neural Cell Culture * Genome Mapping Neural Transplantation Glycobiology if Neurochemistry (2nd edition) Growth Factors Neuronal Cell Lines Haemopoiesis NMR of Biological Histocompatibility Testing Macromolecules HIV Volumes 1 and 2 Non-isotopic Methods in Molecular Biology Human Cytogenetics I and II (2nd edition) Nucleic Acid Hybridization Human Genetic Disease Oligonucleotides and Analysis Analogues if Immunochemistry 1 Oligonucleotide Synthesis * Immunochemistry 2 PCR1 Immunocytochemistry PCR 2 In Situ Hybridization *PCR3:PCR In Situ lodinated Density Gradient Hybridization Media Peptide Antigens Ion Channels Photosynthesis: Energy Lipid Modification of Proteins Transduction Plant Cell Culture Protein Purification Methods (2nd edition) Protein Sequencing Plant Molecular Biology * Protein Structure Plasmids (2nd edition) (2nd edition) * Platelets * Protein Structure Prediction Postimplantation Mammalian Protein Targeting Embryos Proteolytic Enzymes Preparative Centrifugation Pulsed Field Gel Electrophoresis Protein Blotting RNA Processing I and II Protein Engineering * Signalling by Inositides if Protein Function (2nd edition) * Subcellular Fractionation Protein Phosphorylation Signal Transduction Transcription Factors Protein Purification Applications Tumour Immunobiology Mutation Detection A Practical Approach Edited by R. G. H. COTTON Mutation Research Centre Victoria, Australia E. EDKINS Joint Women's and Children's Hospital Perth, Australia and S. FORREST Murdoch Institute Victoria, Australia Oxford University Press, Great Clarendon Street, Oxford OX2 6DP Oxford New York Athens Auckland Bangkok Bogota Bombay Buenos Aires Calcutta Cape Town Dar es Salaam Delhi Florence Hong Kong Istanbul Karachi Kuala Lumpur Madras Madrid Melbourne Mexico City Nairobi Paris Singapore Taipei Tokyo Toronto Warsaw and associated companies in Berlin Ibadan Oxford is a trade mark of Oxford University Press Published in the United States by Oxford University Press Inc., New York © Oxford University Press, 1998 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 licences 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 963657 5 (Hbk) ISBN 0 19 963656 7 (Pbk) Typeset by Footnote Graphics, Warminster, Wilts Printed in Great Britain by Information Press, Ltd, Eynsham, Oxon. CCoonntteennttss List of Contributors xix XV Abbreviations xix xix Introduction 1 1 Sue Forrest References 66 1. Single-strand conformation polymorphism analysis 7 7 Kenshi Hayashi, Youji Kukita, Masakazu Inazuka, and Tomoko Tahira 1. Introduction 77 2. PCR-SSCP using polyacrylamide slab gel 88 PCR Optimization and primer design 1100 Pre-amplification and isolation by agarose gel electrophoresis 1100 PCR using [32P]deoxynucleotide triphosphate 1111 Removal of 3' appendage 1122 SSCP gel electrophoresis 1133 Interpretation of autoradiogram 1155 Re-amplification and direct sequencing 1155 Gel matrices other than polyacrylamide 1166 Restriction endonuclease fingerprinting and dideoxy fingerprinting 1177 3. Fluorescent SSCP in an automated DNA sequencer 1177 Primer design in post-PCR fluorescent labelling 1188 Fluorescent labelling by 3' exchange reaction 1199 SSCP in capillary electrophoresis (CE-SSCP) 2211 Data processing 2233 Acknowledgements 2233 References 2233 2. Single-stranded conformation polymorphism and heteroduplex analysis 25 25 Bernard Gerrard and Michael Dean 1. Introduction 2255 CCoonntteennttss 2. Optimization of the PCR reaction 2277 3. SSCP sample prepration 2288 4. Optimization of SSCP/HA detection 2299 5. Multiplexing 3311 6. Interpretation of results 3322 7. Applications 3333 8. Other methods 3333 References 3333 3. Comprehensive mutation detection with denaturing gradient gel electrophoresis 35 35 L. S. Lerman and Cherif Beldjord 1. Introduction 3355 The scope of DGGE, its distinctive capabilities, and the nature of results 3355 2. Background 3388 3. Basic principle, the physical properties of DNA 3399 4. Overview of the procedures in searching for mutants 4400 Defining segments for scrutiny 4400 Sample preparation 4411 Gradient and velocity separations 4411 Features of the gel patterns 4422 Discrimination of zygozygosity 4422 Comments 4433 5. Use of the psoralen cross-link as a clamp 4433 The psoralen protocol 4444 6. Computational tools 4455 What is a meltmap? 4455 Meltmap protocol 4488 Predicting electrophoretic separations 5533 Computer operations for MUTRAV 5566 7. Other members of the DGGE family 5577 Gel separations in a uniform, partially denaturing environment 5577 Capillary electrophoresis 5577 The thermal gradient 5577 The temperature ramp 5588 2D length and gradient separations 5588 8. End notes 5599 Acknowledgments 5599 References 5599 vviiiiii CCoonntteennttss 4. Cleavage using RNase to detect mutations 63 63 H. Nagase and Y. Nakamura 1. Introduction 6633 2. RNase protection assay for mutation detection 6644 Evaluation of the sensitivity 6644 Source material 6677 PCR for RNase protection assay 6688 RNA probe preparation 6699 RNase protection 7733 Detection of digested probe 7755 Mutation detection by sequencing of the PCR products 7766 Other modified methodologies for mutation detection 7788 Acknowledgements 7799 References 7799 5. Cleavage of mismatched bases using chemical reagents 81 Francesco Giannelli, Peter M. Green, and Susan J. Ramus 1. Introduction 8811 2. Basic procedures 8833 Comments on the basic procedures 8899 3. Ultra fast chemical mismatch detection 9900 Labelling 9900 Solid phase 9900 Comments 9955 References 9966 6. Mutation detection using T4 endonuclease VII 99 99 Rima Youil 1. Introduction 9999 2. The biology of Endo VII 9999 The role of Endo VII in vivo 9999 Characterization of Endo VII 9999 Action of Endo VII on heteroduplex DNA 110000 3. Use of Endo VII for mutation detection 110022 Enzyme mismatch cleavage 110022 Amplification of reference and target DNA 110022 iixx
The list of books you might like
