Main 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.

Contents:

Preface...
Table of Contents...
Contributing Authors...

1- Type IA DNA Topoisomerases: A Universal Core and Multiple Activities
Florence Garnier, Helene Debat, and Marc Nadal

2- Topoisomerase I and Genome Stability: The Good and The Bad
Jang-Eun Cho and Sue Jinks-Robertson

3- DNA Topoisomerases as Targets for Antibacterial Agents
Hiroshi Hiasa

4- DNA Supercoiling Measurement in Bacteria
Yingting Liu, Zhi-Chun Hua, and Fenfei Leng

5- DNA Catenation Reveals the Dynamics of DNA Topology during Replication
Alicia Castan, Pablo Hernandez, Dora B. Krimer, and Jorge B. Schvartzman

6- Mapping E. coli Topoisomerase IV Binding and Activity Sites
Hafez El Sayyed and Olivier Espeli

7- The Use of Psoralen Photobinding to Study Transcription-Induced Supercoiling
Fedor Kouzine, Laura Baranello, and David Levens

8- Immunoprecipitation of RNA:DNA Hybrids from Budding Yeast
Aziz El Hage and David Tollervey

9- Detect

ion of oriC-Independent Replication in Escherichia coli Cells
Makisha Martel, Aurelien Balleydier, Julien Brochu, and Marc Drolet

10- Single-Molecule Magnetic Tweezer Analysis of Topoisomerases
Kathryn H. Gunn, John F. Marko, and Alfonso Mondragon

11- Synthesis of Hemicatenanes for the Study of Type IA Topoisomerases
Shun-Hsiao Lee, Tao-shih Hsieh, and Grace Ee-Lu Siaw

12- An Assay for Detecting RNA Topoisomerase Activity
Muzammil Ahmad, Dongyi Xu, and Weidong Wang

13- Studying TDP1 Function in DNA Repair
Shih-Chieh Chiang, Kirsty Liversidge, and Sherif F. El-Khamisy

14- Topoisomerase II Chromatin Immunoprecipitation
Kayleigh A. Smith, Ian G. Cowell, and Caroline A. Austin

15- Analyzing Mitotic Chromosome Structural Defects after Topoisomerase II Inhibition or Mutation
Juan F. Gimenez-Abian, Andrew B. Lane, and Duncan J. Clarke

16- Monitoring the DNA Topoisomerase II Checkpoint in Saccharomyces cerevisiae
Katherine Furniss, Amit C. J. Vas, Andrew Lane, and Duncan J. Clarke

17- Studying Topoisomerase 1-Mediated Damage at Genomic Ribonucleotides
Jessica S. Williams and Thomas A. Kunkel

18- A Fluorescence-Based Assay for Identification of Bacterial Topoisomerase I Poisons
Thirunavukkarasu Annamalai, Bokun Cheng, and Yuk-Ching Tse-Dinh

19- Fluoroquinolone-Gyrase-DNA Cleaved Complexes
Gan Luan and Karl Drlica

20- Detection of Topoisomerase Covalent Complexes in Eukaryotic Cells
Jay Anand, Yilun Sun, Yang Zhao, Karin C. Nitiss, and John L. Nitiss

21- Visualization and Quantification of Topoisomerase-DNA Covalent Complexes Using the Trapped in Agarose Immunostaining (TARDIS) Assay
Ian G. Cowell and Caroline A. Austin

22- Study of Plasmid-Mediated Quinolone Resistance in Bacteria
George A. Jacoby