DNA Topoisomerases: Methods and Protocols

1. Introduction: Emerging Themes in DNA Topoisomerase Research Duncan J. Clarke and Andrew Lane 2. Analysis of DNA Topoisomers, Knots, and Catenanes by Agarose-Gel Electrophoresis Stephen D. Levene 3. Two-Dimensional Agarose-Gel Electrophoresis of DNA Topoisomers Joaquim Roca 4. Cleavage of Plasmid DNA by Eukaryotic Topoisomerase II Omari J. Bandele and Neil Osheroff 5. Assays for the Preferential Binding of Human Topoisomerase I to Supercoiled DNA Zheng Yang and James J. Champoux 6. Monitoring the Topoisomerase II DNA Gate Conformational Change with Fluorescence Resonance Energy Transfer Tammy R. L. Collins and Tao-shih Hsieh 7. Single Molecule Magnetic Tweezers Studies of Type IB Topoisomerases Jan Lipfert, Daniel A. Koster, Igor D. Vilfan, Susanne Hage, and Nynke H. Dekker 8. Dissolution of Double Holliday Junctions by the Concerted Action of BLM and Topoisomerase IIIa Csanád Z. Bachrati and Ian D. Hickson 9. ChIP-on-Chip Analysis of DNA Topoisomerases Rodrigo Bermejo, Yuki-Mori Katou, Katsuhiko Shirahige, and Marco Foiani 10. Analyzing Top2 Distribution on Yeast Chromosomes by Chromatin Immunoprecipitation Melissa Baldwin, Tariq Warsi, and Jeff Bachant 11. Binding of DNA Topoisomerases I and II to Replication Origins Arturo Falaschi 12. Cytometric Assessment of DNA Damage Induced by DNA Topoisomerase Inhibitors Zbigniew Darzynkiewicz, H. Dorota Halicka, and Toshiki Tanaka 13. Analysis of the Topoisomerase II-Dependent Decatenation G2 Checkpoint and Checkpoint Kinases in Human Cells William K. Kaufmann 14. Assaying Topoisomerase II Checkpoints in Yeast Katherine Furniss, Amit C. J. Vas, Andrew Lane, and Duncan J.Clarke 15. Cytological Analysis of Chromosome Structural Defects that Result from Topoisomerase II Dysfunction Juan F. Giménez-Abián and Duncan J. Clarke 16. Top2 SUMO Conjugation in Yeast Cell Lysates Melissa Baldwin and Jeff Bachant 17. Analysis of SUMOylation of Topoisomerase IIa with Xenopus Egg Extracts Yoshiaki Azuma 18. The Dynamics of DNA Topoisomerase IIa in Living Cells John R. Daum, Yin Yuan Mo, and Gary J. Gorbsky 19. Depletion and Mutation of Topoisomerase II in Animal Cells Andrew C. G. Porter