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PCR Guru: An Ultimate Benchtop Reference for Molecular Biologists
PCR Guru: An Ultimate Benchtop Reference for Molecular Biologists
PCR Guru: An Ultimate Benchtop Reference for Molecular Biologists
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PCR Guru: An Ultimate Benchtop Reference for Molecular Biologists

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PCR Guru: An Ultimate Benchtop Reference for Molecular Biologists is provides researchers in molecular biology with a handy reference for approaching and solving challenging problems associated with PCR setup and optimization. As a laboratory guide, it emphasizes the technical aspects of employing PCR as a tool in molecular biology laboratories. The book covers the history of PCR and the basic science underlying it. It then discusses PCR at the bench level, starting with detailed description and tips on primer design, and continuing with the standard protocols used to perform PCR.

  • Provides troubleshooting tips for various types of modifications of standard protocols
  • Contains unique “Good Practices and Tips that are indispensable for the beginner and expert alike
  • Features “Special Cases with applications of PCR, optimization, and troubleshooting
  • Includes detailed appendices with tables, figures, and key protocols
  • Organized as a systematic, concentrated resource to save time when addressing a PCR problem
LanguageEnglish
Release dateNov 28, 2016
ISBN9780128042465
PCR Guru: An Ultimate Benchtop Reference for Molecular Biologists
Author

Ayaz Najafov

Ayaz was born in Baku, Azerbaijan. He obtained his BSc and MSc degrees in Molecular Biology and Genetics from Bosphorus University, Istanbul, Turkey and got a 2-year training in Biochemistry as an intern at Baylor College of Medicine, Houston, Texas, USA. Ayaz pursued his PhD in Biochemistry at MRC Protein Phosphorylation Unit at Dundee University, Scotland, UK in Prof. Dario Alessi’s lab. Ayaz is currently a postdoctoral fellow in Prof. Junying Yuan’s lab at Harvard Medical School, Cell Biology Department.

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    Book preview

    PCR Guru - Ayaz Najafov

    PCR Guru

    An Ultimate Benchtop Reference for Molecular Biologists

    Ayaz Najafov

    Harvard Medical School, Department of Cell Biology, Boston, MA, United States

    Gerta Hoxhaj

    Harvard T.H. Chan School of Public Health, Department of Genetics and Complex Diseases, Boston, MA, United States

    Table of Contents

    Cover

    Title page

    Copyright

    Dedications

    Biography

    Preface

    Acknowledgments

    Note to the Reader

    Chapter 1: Introduction

    Abstract

    1.1. A bit of history

    1.2. What is PCR?

    1.3. PCR components

    1.4. Exponential nature of PCR

    1.5. Popularity of PCR

    Chapter 2: Procedure

    Abstract

    2.1. Primer design

    2.2. Standard PCR setup

    2.3. Controls

    2.4. Cycling parameters

    Chapter 3: Good PCR Practices

    Abstract

    Chapter 4: Optimization and Troubleshooting

    Abstract

    4.1. Optimization rules

    4.2. General optimization strategies

    4.3. Troubleshooting specific problems

    Chapter 5: Tips and Tricks

    Abstract

    Chapter 6: Special Cases

    Abstract

    Glossary and Abbreviations

    Appendix A: Agarose Gel Electrophoresis Protocol

    Appendix B: Silver Staining of DNA Gels

    Appendix C: Plasmid Miniprep Protocol (by using QIAprep Spin Miniprep Kit)

    Appendix D: Restriction Enzyme Digestion Protocol

    Appendix E: Protocol for DNA Concentration Estimation Using Hoechst 33258

    Appendix F: Formulas

    Appendix G: Common Primers for Sequencing, Promoters, Housekeeping Genes, and Reporters

    Appendix H: Tags

    Appendix I: Thermostable DNA polymerases

    Appendix J: Example of a Daily PCR Log

    Appendix K: Common Buffers and Solutions

    Appendix L: Useful Numbers

    Appendix M: Yeast Colony PCR

    Useful Websites

    References

    Index

    Copyright

    Academic Press is an imprint of Elsevier

    125 London Wall, London EC2Y 5AS, United Kingdom

    525 B Street, Suite 1800, San Diego, CA 92101-4495, United States

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    Copyright © 2017 Elsevier Inc. All rights reserved.

    No part of this publication may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, recording, or any information storage and retrieval system, without permission in writing from the publisher. Details on how to seek permission, further information about the Publisher’s permissions policies and our arrangements with organizations such as the Copyright Clearance Center and the Copyright Licensing Agency, can be found at our website: www.elsevier.com/permissions.

    This book and the individual contributions contained in it are protected under copyright by the Publisher (other than as may be noted herein).

    Notices

    Knowledge and best practice in this field are constantly changing. As new research and experience broaden our understanding, changes in research methods, professional practices, or medical treatment may become necessary.

    Practitioners and researchers must always rely on their own experience and knowledge in evaluating and using any information, methods, compounds, or experiments described herein. In using such information or methods they should be mindful of their own safety and the safety of others, including parties for whom they have a professional responsibility.

    To the fullest extent of the law, neither the Publisher nor the authors, contributors, or editors, assume any liability for any injury and/or damage to persons or property as a matter of products liability, negligence or otherwise, or from any use or operation of any methods, products, instructions, or ideas contained in the material herein.

    Library of Congress Cataloging-in-Publication Data

    A catalog record for this book is available from the Library of Congress

    British Library Cataloguing-in-Publication Data

    A catalogue record for this book is available from the British Library

    ISBN: 978-0-12-804231-1

    For information on all Academic Press publications visit our website at https://www.elsevier.com/

    Publisher: Sara Tenney

    Acquisitions Editor: Sara Tenney

    Editorial Project Manager: Fenton Coulthurst

    Production Project Manager: Chris Wortley

    Designer: Christian Bilbow

    Typeset by Thomson Digital

    Dedications

    I dedicate this book to my father, Azad Najafov, who introduced me to the world of molecular biology and to my friend and mentor, İbrahim Barış, who taught me how to do my first PCR.

    Ayaz Najafov

    I dedicate this book to my family to whom I am eternally grateful for their constant support and care for me and my academic career.

    Gerta Hoxhaj

    Biography

    Ayaz Najafov

    Ayaz was born in Baku, Azerbaijan and as a high school student, participated in local and international biology Olympiads, where he had won several gold, silver, and bronze medals. He obtained his BSc and MSc degrees in Molecular Biology and Genetics from Bosphorus University, Istanbul, Turkey, and got a 2-year training in Biochemistry as an intern at Baylor College of Medicine, Houston, TX, United States. Ayaz pursued his PhD in Biochemistry at MRC Protein Phosphorylation Unit at Dundee University, Scotland, United Kingdom in Prof. Dario Alessi’s lab. Ayaz is currently a postdoctoral fellow in Prof. Junying Yuan’s lab at Harvard Medical School, Cell Biology Department.

    Gerta Hoxhaj

    Gerta was born in Fier, Albania. She obtained her BSc degree in Molecular Biology and Genetics, as well as a second major in Chemistry from Bosphorus University, Istanbul, Turkey. Gerta pursued her PhD in Biochemistry at MRC Protein Phosphorylation Unit at Dundee University, Scotland, United Kingdom in Prof. Carol MacKintosh’s lab. Gerta is currently a postdoctoral fellow in Prof. Brendan Mannings’s lab at Harvard T.H. Chan School of Public Health, Department of Genetics and Complex Diseases.

    Preface

    This book was written with an aim of providing researchers practicing molecular biology, whether at their beginner or expert stage, with a handy tool and reference for setting up, performing, optimizing, and troubleshooting polymerase chain reaction (PCR). We believe that this book will provide tremendous assistance for solving problems associated with challenging cases of PCR.

    This book does not provide the reader with vast details of the PCR theory and the multiple applications of the technique. As this book is a laboratory guide, the emphasis here was made on the technical aspects of employing PCR as a tool in molecular biology laboratories and the issues were described in bench terms, which makes the book more comprehendible to the end users of the technique.

    General optimization and troubleshooting strategies, as well as a detailed

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