Protocols Vol I

DNA Topoisomerase Protocols Volume I

DNA Topology and Enzymes

Eds. M.Bjornsti and N.Osheroff

DNA Topoisomerase Protocols is an unprecedented collection of cutting-edge experimental protocols for investigating DNA structure, topology, and DNA topoisomerase function. Described by expert experimentalists who have perfected the techniques, these time-proven methods utilize new approaches to study changes in DNA topology (linking number, knotting, catenation, and relaxation) and DNA structure (bending), as well as to assess chromosome structure through FLP-mediated recombination and to analyze bacterial nucleoid structure. State-of-the-art protocols also detail the expression and purification of bacterial, viral, and eukaryotic DNA topoisomerases from a variety of sources, including baculovirus, bacterial, yeast, and mammalian expression systems.

Table of Contents

Introduction to DNA Topoisomerases, Mary-Ann Bjornsti and Neil Osheroff. Resolution of DNA Molecules by One-Dimensional Agarose-Gel Electrophoresis,Mary-Ann Bjornsti and Maureen D. Megonigal. Two-Dimensional Agarose-Gel Electrophoresis of DNA Topoisomers, Ryo Hanai and Joaquim Roca. Analysis of Altered DNA Structures: Cruciform DNA, Albert J. Courey. Purification of Supercoiled Plasmid DNA, Kelly L. Jordan, Devon L. Evans, and David J. Hall. Purification and Use of DNA Minicircles with Different Linking Numbers, Giorgio Camilloni, Rodolfo Negri, Micaela Caserta, and Ernesto Di Mauro. Isolation of Kinetoplast DNA, Theresa A. Shapiro, Viiu A. Klein, and Paul T. Englund. Isolation of Knotted DNA from Coliphage P4, Morten Isaksen, Bryan Julien, Richard Calendar, and Björn H. Lindqvist. Analysis of DNA Knots and Catenanes by Agarose-Gel Electrophoresis, Stephen D. Levene and Hua Tsen. Sedimentation Analysis of Bacterial Nucleoid Structure, Karl Drlica, Chang-Rung Chen, and Samuel Kayman. Coating DNA with RecA Protein to Distinguish DNA Path by Electron Microscopy, E. Lynn Zechiedrich and Nancy J. Crisona. Methods for Analyzing DNA Bending, Jason D. Kahn. Formation of Extrachromosomal DNA Rings in Saccharomyces cerevisiae Using Site-Specific Recombination, Marc R. Gartenburg. Overexpression and Purification of Bacterial DNA Gyrase, Anthony Maxwell and Alison J. Howells. Overexpression and Purification of Bacterial DNA Topoisomerase I, Chang-Xi Zhu and Yuk-Ching Tse-Dinh. Overexpression and Purification of Escherichia coli DNA Topoisomerase III, Russell J. DiGate. Overexpression and Purification of Bacterial DNA Topoisomerase IV, Hong Peng and Kenneth J. Marians. Purification of Bacteriophage T4 Type II DNA Topoisomerase, Kenneth N. Kreuzer and Sue H. Neece. Overexpression and Purification of DNA Topoisomerase I from Yeast,Mary-Ann Bjornsti and Jolanta Fertala. Overexpression and Purification of Saccharomyces cerevisiae DNA Topoisomerase II from Yeast, Janet E. Lindsley. Purification of DNA Topoisomerase II from Drosophilamelanogaster, Stacie J. Froelich-Ammon, Paul S. Kingma, and Neil Osheroff. Purification of DNA Topoisomerase I from Human Placenta, Joseph A. Holden. Purification of Baculovirus-Expressed Human DNA Topoisomerase I, Lance Stewart and James J. Champoux. Rapid Purification of DNA Topoisomerase II Containing a Hexahistidine Tag by Metal Ion Affinity Chromatography, Harald Biersack, Sanne Jensen, and Ole Westergaard. Metabolic Labeling, Immunoprecipitation, and Two-Dimensional Tryptic Phosphopeptide Mapping of Human Topoisomerase II, Nicholas J. Wells and Ian D. Hickson. Immunoblot Analysis and Band Depletion Assays, Scott H. Kaufmann and Phyllis A. Svingen. Visualization of DNA Topoisomerases by Electron Microscopy, Piero Benedetti and Alessandra Silvestri. Appendix: Compendium of DNA Topoisomerase Sequences, Paul R. Caron.

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