DNA Topoisomerase Protocols: Volume II: Enzymology and Drugs

ISBN-13: 9781617370571 / Angielski / Miękka / 2010 / 334 str.

Neil Osheroff; Mary-Ann Bjornsti

Opis

Beginning with the Escherichia coli ? protein, or bacterial DNA topoisomerase I, an ever-increasing number of enzymes have been identified that catalyze changes in the linkage of DNA strands. DNA topoisomerases are ubiquitous in nature and have been shown to play critical roles in most p- cesses involving DNA, including DNA replication, transcription, and rec- bination. These enzymes further constitute the cellular targets of a number of clinically important antibacterial and anticancer agents. Thus, further studies of DNA topology and DNA topoisomerases are critical to advance our und- standing of the basic biological processes required for cell cycle progression, cell division, genomic stability, and development. In addition, these studies will continue to provide critical insights into the cytotoxic action of drugs that target DNA topoisomerases. Such mechanistic studies have already played an important role in the development and clinical application of antimicrobial and chemotherapeutic agents. The two volumes of DNA Topoisomerase Protocols are designed to help new and established researchers investigate all aspects of DNA topology and the function of these enzymes. The chapters are written by prominent investigators in the field and provide detailed background information and st- by-step experimental protocols. The topics covered in Part I: DNA Topology and Enzymes, range from detailed methods to analyze various aspects of DNA structure, from linking number, knotting/unknotting, site-specific recombi- tion, and decatenation to the overexpression and purification of bacterial and eukaryotic DNA topoisomerases from a variety of cell systems and tissues.

Recenzje

"This book completes a comprehensive collection of assays, including the weird and wonderful, that can be used to investigate the enzymology and drug inhibition of topoisomerases...I recommend any students about to undertake a PhD degree in this area to buy a copy. Even those who are well versed in the biology of topoisomerases should consider buying both volumes of this book, they will surely find some things they didn't know - I did!" - MicroBiology Today

"Described by expert experimentalists who have perfected the techniques, these reproducible methods include assays for enzyme-catalyzed DNA relaxation/supercoiling, DNA cleavage, DNA nicking, DNA decatentaion, and ATP hydrolysis." - Anticancer Research

"An unprecedented collection of cutting-edge experimental protocols for investigating the catalytic activities of DNA topoisomerases, as well as their specific interactions with topoisomerase-targeted antitumor and antibacterial drugs." -Tumori

Spis treści

Assaying DNA Topoisomerase I Relaxation Activity Lance Stewart and James J. Champoux DNA Topoisomerase II-Catalyzed DNA Decatenation Andrea Haldane and Daniel M. Sullivan Plasmid DNA Supercoiling by DNA Gyrase Penny J. Sayer, Martin L. Goble, Mark Oram, and L. Mark Fisher Analyzing Reverse Gyrase Activity Michel Duguet, Christine Jaxel, Anne-Céile Déclais, Fabrice Confalonieri, Janine Marsault, Claire Bouthier de la Tour, Marc Nadal, and Christiane Portemer Topoisomerase II-Catalyzed ATP Hydrolosis as Monitored by Thin-Layer Chromatography Paul S. Kingma, John M. Fortune, and Neil Osheroff Use of a Real-Time, Coupled Assay to Measure the ATPase Activity of DNA Topoisomerase II Janet E. Lindsley Analysis of Topoisomerase-DNA Interactions by Electrophoretic Mobility Shift Assay Stewart Shuman Filter Binding Assays for Topoisomerase-DNA Complexes Joaquim Roca DNA Topoisomerase I-Mediated Nicking of Circular Duplex DNA James J. Champoux Analysis of Cleavage Complexes Using Reactive Inhibitor Derivatives Kenneth N. Kreuzer, Catherine H. Freudenreich, and Yves Pommier Uncoupling of Topoisomerase-Mediated DNA Cleavage and Religation Anni H. Anderson, Kent Christiansen, and Ole Westergaard Synthesis and Use of DNA Containing a 5'-Bridging Phosphorothioate as a Suicide Substrate for Type I DNA Topoisomerases Alex B. Burgin, Jr Isolation of Covalent Enzyme-DNA Complexes Thomas C. Rowe, Dale Grabowski, and Ram Ganapathi ICE Bioassay: Isolating In Vivo Complexes of Enzyme to DNA Deepa Subramanian, Christine Sommer Furbee, and Mark T. Muller DNA Unwinding Test Using Eukaryotic DNA Topoisomerase I Linus L. Shen Drug-DNA Interactions David E. Graves Quinolone Interactions with DNA and DNA Gyrase Linus L.Shen Bactericidal Assays for Fluoroquinolones Thomas D. Gootz Drug Toxicity in E. coli Cells Expressing Human DNA Topoisomerase I Scott T. Taylor and Rolf Menzel Drug-Induced Cytotoxicity in Tissue Culture Cynthia E. Herzog and Leonard A. Zwelling Analysis of Drug Uptake-Flow Cytometry Grace Zoorob and Thomas Burke Cell Cycle Analysis of Drug-Treated Cells Frank Traganos, Gloria Juan, and Zbigniew Darzynkiewicz Assaying Drug-Induced Apoptosis Zbigniew Darzynkiewicz, Gloria Juan, and Frank Traganos Single-Strand Conformational Polymorphism Analysis of DNA Topoisomerases I and II Mary K. Danks PCR-Based Cloning of DNA Topoisomerase Genes Wai Mun Huang Topoisomerase II-Catalyzed Relaxation and Catenation of Plasmid DNA John M. Fortune and Neil Osheroff Topoisomerase II-Mediated Cleavage of Plasmid DNA D. Andrew Burden, Stacie J. Froelich-Ammon, and Neil Osheroff Drug-induced Stabilization of Covalent DNA Topoisomerase I-DNA Intermediates: DNA Cleavage Assays Paola Fiorani, Christine L. Hann, Piero Benedetti, and Mary-Ann Bjornsti Studying DNA Topoisomerase I-Targeted Drugs in the Yeast Saccharomyces cerevisiae Michael H. Woo, John R. Vance, and Mary-Ann Bjornsti Yeast Systems for Demonstrating the Transfer of Antitopoisomerase II Agents John L. Nitiss and Karen C. Nitiss Index

Blurb

DNA Topoisomerase Protocols, II: Enzymology and Drugs brings together an unprecedented collection of cutting-edge experimental protocols for investigating the catalytic activities of DNA topoisomerases, as well as their specific interactions with topoisomerase-targeted antitumor and antibacterial drugs. Described by expert experimentalists who have perfected the techniques, these unfailingly reproducible methods include assays for enzyme-catalyzed DNA relaxation/supercoiling, DNA cleavage, DNA nicking, DNA decatenation, and ATP hydrolysis. Several modified DNA substrates, used to dissect enzyme mechanisms by trapping intermediates, are also described. Methodologies to determine the action of topoisomerase-targeted drugs include biochemical assays of drug-induced enzyme-DNA complexes, methods for assaying drug uptake, and cell-based assays for determining drug specificity and mechanisms of resistance. A companion volume, DNA Topoisomerase Protocols, I: DNA Topology and Enzymes, provides state-of-the-art experimental protocols for investigating DNA structure, topology, and DNA topoisomerase function.

DNA Topoisomerase Protocols, II: Enzymology and Drugs provides, for the first time, a comprehensive description of the methods and experimental systems needed to investigate fully the catalytic mechanisms of DNA topoisomerases from bacterial, viral, and eukaryotic sources. For the many basic scientists and clinicians who want better to understand and to exploit the action of topoisomerase-targeted drugs in a variety of in vitro and in vivo systems, it will immediately develop immense value as the new standard reference in the field.