DNA Topoisomerases Methods and Protocols
Due to their importance to cell biology, DNA topology-altering enzymes, collectively DNA topoisomerases and gyrases, have been studied thoroughly from a biochemical perspective, yet the expansion of research at the molecular and cellular levels continues
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M O L E C U L A R B I O L O G Y TM
Series Editor John M. Walker School of Life Sciences University of Hertfordshire Hatfield, Hertfordshire, AL10 9AB, UK
For other titles published in this series, go to www.springer.com/series/7651
DNA Topoisomerases Methods and Protocols
Edited by
Duncan J. Clarke University of Minnesota Medical School, Minneapolis, MN, USA
Editor Duncan J. Clarke Department of Genetics, Cell Biology & Development University of Minnesota Medical School Minneapolis, MN 55455 USA [email protected]
ISSN 1064-3745 e-ISSN 1940-6029 ISBN 978-1-60761-339-8 e-ISBN 978-1-60761-340-4 DOI 10.1007/978-1-60761-340-4 Library of Congress Control Number: 2009933621 # Humana Press, a part of Springer ScienceþBusiness Media, LLC 2009 All rights reserved. This work may not be translated or copied in whole or in part without the written permission of the publisher (Humana Press, c/o Springer ScienceþBusiness Media, LLC, 233 Spring Street, New York, NY 10013, USA), except for brief excerpts in connection with reviews or scholarly analysis. Use in connection with any form of information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed is forbidden. The use in this publication of trade names, trademarks, service marks, and similar terms, even if they are not identified as such, is not to be taken as an expression of opinion as to whether or not they are subject to proprietary rights. Printed on acid-free paper springer.com
Preface Enzymes that alter the topology of DNA, collectively DNA topoisomerases and gyrases, arose early in the evolution of the DNA-based cells of archaea, bacteria, and eukaryotes. Together, they perform essential functions that are required for the basic processes of cell division: DNA replication, transcription, recombination, chromosome condensation, and chromosome segregation. Previous volumes in the Methods in Molecular Biology series have covered in great depth the methodologies needed to study topoisomerases from a biochemical perspective, including the topoisomerase– drug interactions relevant to clinical applications, and have provided indispensable protocols to topoisomerase researchers that cover almost every aspect of topoisomerase enzymology. However, the past decade has seen an expansion in topoisomerase research at the molecular and cellular levels, and this activity will doubtless continue to increase. With a greater understanding of the cellular functions performed by topoisomerases, there now is a clear need for a compendium of protocols that extends into the new areas of research that have been recently uncovered. Thus, this volume is not an updated republication of methods, nor does it aim to be all-inclusive, but rather the methods provided here add new approaches to the study of topoisomerase functions that are relevant in what is a rapidly changing field of research. First in this volume is a series of chapters that describe methods to analyze DNA topologies and the interacti
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