DNA Topoisomerases

DNA topoisomerases and gyrases have been studied thoroughly from a biochemical perspective, and expanding research at the molecular and cellular level shows great promise. This book gives a compendium of protocols that extends into such new areas of research.

Due to their importance to cell biology, DNA topology-altering enzymes, collectively DNA topoisomerases and gyrases, have been studied thoroughly from a biochemical perspective, yet the expansion of research at the molecular and cellular levels continues to show a great deal of promise. In DNA Topoisomerases: Methods and Protocols , experts in the field present a compendium of protocols that extends into the new areas of research that have been recently uncovered in order to elucidate the methodology needed to study topoisomerases in the molecular and cellular context. The volume examines subjects such as the analysis of DNA topologies and the interaction of topoisomerases with DNA as tools to measure topoisomerase functions, the binding of topoisomerases to specific sites in the genomes of eukaryotes, including origins of DNA replication, as well as exploration of perturbed topoisomerase function. As a volume in the highly successful Methods in Molecular Biology™ series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, laboratory protocols, and notes on trouble-shooting and avoiding known pitfalls.

Cutting-edge and easy-to-use, DNA Topoisomerases: Methods and Protocols provides key content which reflects an expanded understanding of the functions of these essential enzymes in the hope of inspiring researchers to further important discoveries in this dynamic field.

Provides an easily accessible reference volume for topoisomerase protocols written by leading researchers in the field Covers a wide range of assays from cell-based methods and molecular analysis of topoisomerases, to biochemical and biophysical studies Presents diverse approaches to experimental design, covering model biological systems including yeast and mammalian cells as well as cell-free systems and purified components Comprehensive guide detailing topoisomerase research from its enzymology to its function at the cytological level Provides tools for the future of the topoisomerase research field Includes supplementary material: sn.pub/extras

Inhalt

1. Introduction: Emerging Themes in DNA Topoisomerase Research.- 2. Analysis of DNA Topoisomers, Knots, and Catenanes by Agarose Gel Electrophoresis.- 3. Two-Dimensional Agarose Gel Electrophoresis of DNA Topoisomers.- 4. Cleavage of Plasmid DNA by Eukaryotic Topoisomerase II.- 5. Assays for the Preferential Binding of Human Topoisomerase I to Supercoiled DNA.- 6. Monitoring the Topoisomerase II DNA Gate Conformational Change with Fluorescence Resonance Energy Transfer.- 7. Single-Molecule Magnetic Tweezers Studies of Type IB Topoisomerases.- 8. Dissolution of Double Holliday Junctions by the Concerted Action of BLM and Topoisomerase III?.- 9. ChIP-on-Chip Analysis of DNA Topoisomerases.- 10. Analyzing Top2 Distribution on Yeast Chromosomes by Chromatin Immunoprecipitation.- 11. Binding of DNA Topoisomerases I and II to Replication Origins.- 12. Cytometric Assessment of DNA Damage Induced by DNA Topoisomerase Inhibitors.- 13. Analysis of the Topoisomerase II-Dependent Decatenation G2 Checkpoint and Checkpoint Kinases in Human Cells.- 14. Assaying Topoisomerase II Checkpoints in Yeast.- 15. Cytological Analysis of Chromosome Structural Defects that Result from Topoisomerase II Dysfunction.- 16. Top2 SUMO Conjugation in Yeast Cell Lysates.- 17. Analysis of SUMOylation of Topoisomerase II? with Xenopus Egg Extracts.- 18. The Dynamics of DNA Topoisomerase II? in Living Cells.- 19. Depletion and Mutation of Topoisomerase II in Animal Cells.