DNA Topoisomerases Methods and Protocols

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

Type IA DNA Topoisomerases: A Universal Core and Multiple Activities.- Topoisomerase I and Genome Stability: The Good and The Bad.- DNA Topoisomerases as Targets for Antibacterial Agents.- DNA Supercoiling Measurement in Bacteria.- DNA Catenation Reveals the Dynamics of DNA Topology during Replication.- Mapping E. coli Topoisomerase IV Binding and Activity Sites.- The Use of Psoralen Photobinding to Study Transcription-Induced Supercoiling.- Immunoprecipitation of RNA:DNA Hybrids from Budding Yeast.- Detection of oriC-Independent Replication in Escherichia coli Cells.- Single-Molecule Magnetic Tweezer Analysis of Topoisomerases.- Synthesis of Hemicatenanes for the Study of Type IA Topoisomerases.- An Assay for Detecting RNA Topoisomerase Activity.- Studying TDP1 Function in DNA Repair.- Topoisomerase II Chromatin Immunoprecipitation.- Analyzing Mitotic Chromosome Structural Defects after Topoisomerase II Inhibition or Mutation.- Monitoring the DNA Topoisomerase II Checkpoint inSaccharomyces cerevisiae.- Studying Topoisomerase 1-Mediated Damage at Genomic Ribonucleotides.- A Fluorescence-Based Assay for Identification of Bacterial Topoisomerase I Poisons.- Fluoroquinolone-Gyrase-DNA Cleaved Complexes.- Detection of Topoisomerase Covalent Complexes in Eukaryotic Cells.- Visualization and Quantification of Topoisomerase-DNA Covalent Complexes Using the Trapped in Agarose Immunostaining (TARDIS) Assay.- Study of Plasmid-Mediated Quinolone Resistance in Bacteria.