This volume looks at the evolution of the topo field over the last year and discusses how DNA topoisomerases are directly and indirectly involved in numerous cellular processes. The chapters in this book cover various topics, such as type 1 topos with an evolutionary perspective; antimicrobial agents targeting topos; experimental protocols related to DNA topology, including a basic technique to measure DNA supercoiling in bacteria; protocols for in vitro studies, including assays to detect RNA topo activity; topo inhibitors; and a study of plasmid-mediated quinolone resistance in bacteria. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and comprehensive, DNA Topoisomerases: Methods and Protocols is intended for specialists and non-specialists with an overview of selected hot topics in the field, and the latest protocols to study DNA topology, topoisomerases functions and inhibition by various compounds.
Preface...Table of Contents...Contributing Authors...1- Type IA DNA Topoisomerases: A Universal Core and Multiple ActivitiesFlorence Garnier, Helene Debat, and Marc Nadal2- Topoisomerase I and Genome Stability: The Good and The BadJang-Eun Cho and Sue Jinks-Robertson3- DNA Topoisomerases as Targets for Antibacterial AgentsHiroshi Hiasa4- DNA Supercoiling Measurement in BacteriaYingting Liu, Zhi-Chun Hua, and Fenfei Leng5- DNA Catenation Reveals the Dynamics of DNA Topology during ReplicationAlicia Castan, Pablo Hernandez, Dora B. Krimer, and Jorge B. Schvartzman6- Mapping E. coli Topoisomerase IV Binding and Activity SitesHafez El Sayyed and Olivier Espeli7- The Use of Psoralen Photobinding to Study Transcription-Induced SupercoilingFedor Kouzine, Laura Baranello, and David Levens8- Immunoprecipitation of RNA:DNA Hybrids from Budding YeastAziz El Hage and David Tollervey9- Detection of oriC-Independent Replication in Escherichia coli CellsMakisha Martel, Aurelien Balleydier, Julien Brochu, and Marc Drolet10- Single-Molecule Magnetic Tweezer Analysis of TopoisomerasesKathryn H. Gunn, John F. Marko, and Alfonso Mondragon11- Synthesis of Hemicatenanes for the Study of Type IA TopoisomerasesShun-Hsiao Lee, Tao-shih Hsieh, and Grace Ee-Lu Siaw12- An Assay for Detecting RNA Topoisomerase ActivityMuzammil Ahmad, Dongyi Xu, and Weidong Wang13- Studying TDP1 Function in DNA RepairShih-Chieh Chiang, Kirsty Liversidge, and Sherif F. El-Khamisy14- Topoisomerase II Chromatin ImmunoprecipitationKayleigh A. Smith, Ian G. Cowell, and Caroline A. Austin15- Analyzing Mitotic Chromosome Structural Defects after Topoisomerase II Inhibition or MutationJuan F. Gimenez-Abian, Andrew B. Lane, and Duncan J. Clarke16- Monitoring the DNA Topoisomerase II Checkpoint in Saccharomyces cerevisiaeKatherine Furniss, Amit C. J. Vas, Andrew Lane, and Duncan J. Clarke17- Studying Topoisomerase 1-Mediated Damage at Genomic RibonucleotidesJessica S. Williams and Thomas A. Kunkel18- A Fluorescence-Based Assay for Identification of Bacterial Topoisomerase I PoisonsThirunavukkarasu Annamalai, Bokun Cheng, and Yuk-Ching Tse-Dinh19- Fluoroquinolone-Gyrase-DNA Cleaved ComplexesGan Luan and Karl Drlica20- Detection of Topoisomerase Covalent Complexes in Eukaryotic CellsJay Anand, Yilun Sun, Yang Zhao, Karin C. Nitiss, and John L. Nitiss21- Visualization and Quantification of Topoisomerase-DNA Covalent Complexes Using the Trapped in Agarose Immunostaining (TARDIS) AssayIan G. Cowell and Caroline A. Austin22- Study of Plasmid-Mediated Quinolone Resistance in BacteriaGeorge A. Jacoby