DNA Topoisomerases: Methods and Protocols

Description

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 Protoc ols 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. Front Matter ....Pages i-xi Type IA DNA Topoisomerases: A Universal Core and Multiple Activities (Florence Garnier, Hélène Debat, Marc Nadal)....Pages 1-20 Topoisomerase I and Genome Stability: The Good and the Bad (Jang-Eun Cho, Sue Jinks-Robertson)....Pages 21-45 DNA Topoisomerases as Targets for Antibacterial Agents (Hiroshi Hiasa)....Pages 47-62 DNA Supercoiling Measurement in Bacteria (Yingting Liu, Zhi-Chun Hua, Fenfei Leng)....Pages 63-73 DNA Catenation Reveals the Dynamics of DNA Topology During Replication (Alicia Castán, Pablo Hernández, Dora B. Krimer, Jorge B. Schvartzman)....Pages 75-86 Mapping E. coli Topoisomerase IV Binding and Activity Sites (Hafez El Sayyed, Olivier Espéli)....Pages 87-94 The Use of Psoralen Photobinding to Study Transcription-Induced Supercoiling (Fedor Kouzine, Laura Baranello, David Levens)....Pages 95-108 Immunoprecipitation of RNA:DNA Hybrids from Budding Yeast (Aziz El Hage, David Tollervey)....Pages 109-129 Detection of oriC-Independent Replication in Escherichia coli Cells (Makisha Martel, Aurélien Balleydier, Julien Brochu, Marc Drolet)....Pages 131-138 Single-Molecule Magnetic Tweezer Analysis of Topoisomerases (Kathryn H. Gunn, John F. Marko, Alfonso Mondragón)....Pages 139-152 Synthesis of Hemicatenanes for the Study of Type IA Topoisomerases (Shun-Hsiao Lee, Tao-shih Hsieh, Grace Ee-Lu Siaw)....Pages 153-159 An Assay for Detecting RNA Topoisomerase Activity (Muzammil Ahmad, Dongyi Xu, Weidong Wang)....Pages 161-172 Studying TDP1 Function in DNA Repair (Shih-Chieh Chiang, Kirsty Liversidge, Sherif F. El-Khamisy)....Pages 173-181 Topoisomerase II Chromatin Immunoprecipitation (Kayleigh A. Smith, Ian G. Cowell, Caroline A. Austin)....Pages 183-189 Analyzing Mitotic Chromosome Structural Defects After Topoisomerase II Inhibition or Mutation (Juan F. Giménez-Abián, Andrew B. Lane, Duncan J. Clarke)....Pages 191-215 Monitoring the DNA Topoisomerase II Checkpoint in Saccharomyces cerevisiae (Katherine Furniss, Amit C. J. Vas, Andrew B. Lane, Duncan J. Clarke)....Pages 217-240 Studying Topoisomerase 1-Mediated Damage at Genomic Ribonucleotides (Jessica S. Williams, Thomas A. Kunkel)....Pages 241-257 A Fluorescence-Based Assay for Identification of Bacterial Topoisomerase I Poisons (Thirunavukkarasu Annamalai, Bokun Cheng, Neelam Keswani, Yuk-Ching Tse-Dinh)....Pages 259-268 Fluoroquinolone-Gyrase-DNA Cleaved Complexes (Gan Luan, Karl Drlica)....Pages 269-281 Detection of Topoisomerase Covalent Complexes in Eukaryotic Cells (Jay Anand, Yilun Sun, Yang Zhao, Karin C. Nitiss, John L. Nitiss)....Pages 283-299 Visualization and Quantification of Topoisomerase–DNA Covalent Complexes Using the Trapped in Agarose Immunostaining (TARDIS) Assay (Ian G. Cowell, Caroline A. Austin)....Pages 301-316 Study of Plasmid-Mediated Quinolone Resistance in Bacteria (George A. Jacoby)....Pages 317-325 Back Matter ....Pages 327-328