DNA Replication Methods and Protocols

About this book

Since the discovery of DNA structure and throughout the ensuing "DNA era," the field of DNA replication has expanded to cover a vast number of experimental systems. In DNA Replication: Methods and Protocols, expert researchers present a collection of techniques and approaches used to investigate DNA replication with an emphasis on the most recent technological developments.

Beginning with several informative introductory review chapters, this extensive volume is organized for clarity while fully encouraging innovation by the mixing of methods to create new techniques. Written in the highly successful Methods in Molecular Biologya" series format, chapters contain brief introductions to the topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting and avoiding known pitfalls. Comprehensive and cutting-edge, DNA Replication: Methods and Protocols provides an excellent tool for both established laboratories and individuals new to this exciting field of research.

Contents

Part I: Reviews1. DNA Replication InitiationStephen J. Aves2. DNA Replication Fork ProteinsUlrich Hubscher3. Random and Site-Specific Replication TerminationJacob Z. Dalgaard, Trevor Eydmann, Milana Koulintchenko, Suha Sayrac, Sonya Vengrova, and Tomoko Yamada-Inagawa4. Checkpoint Regulation of DNA ReplicationErik Boye, Henriette C. SkjA lberg, and Beata Grallert5. Introduction to Molecular Combing: Genomics, DNA Replication and CancerJohn Herrick and Aaron Bensimon Part II: Methods for Analysis of Replication of a Single Locus 6. Replication Initiation Point Mapping: Approach and ImplicationsSapna Das-Bradoo and Anja-Katrin Bielinsky7. Purification of Restriction Fragments Containing Replication Intermediates from Complex Genomes for 2-D Gel AnalysisLarry D. Mesner, Pieter A. Dijkwel, and Joyce L. Hamlin8. Topological Analysis of Plasmid DNA Replication Intermediates Using Two-Dimensional Agarose GelsOlivier Hyrien9. Analysis of Telomeric DNA Replication Using Neutral-Alkaline Two-Dimensional Gel ElectrophoresisSvetlana Makovets10. Chromatin Immunoprecipitation of Replication Factors Moving with the Replication ForkJordan B. Rapp, Alison B. Ansbach, Chiaki Noguchi, and Eishi Noguchi11. Density Transfer as a Method to Analyze the Progression of DNA Replication ForksJose Antonio Tercero12. High-Resolution Mapping of Points of Site-Specific Replication StallingSonya Vengrova and Jacob Z. Dalgaard13. DNA Replication in Nucleus-Free Xenopus Egg ExtractsRonald Lebofsky, Tatsuro Takahashi, and Johannes C. Walter Part III: Genome-Wide Analysis Methods14. ChIP-Chip to Analyze the Binding of Replication Proteins to Chromatin Using Oligonucleotide DNA MicroarraysChristopher J. Viggiani, Jennifer G. Aparicio, and Oscar M. Aparicio15. Analyzing Origin Activation Patterns by Copy Number Change ExperimentsMiruthubashini Raveendranathan and Anja-Katrin Bielinsky16. Detection of Replication Origins Using Comparative Genomics and Recombinational ARS AssayConrad A. Nieduszynski and Anne D. Donaldson17. Isolation of Restriction Fragments Containing Origins of Replication from Complex GenomesLarry D. Mesner and Joyce L. Hamlin18. Application of Alkaline Sucrose Gradient Centrifugation in the Analysis of DNA Replication after DNA DamageSascha Raschke, Jun Guan, and George Iliakis Part IV: Biochemistry and Biophysics Methods19. Isolation of Recombinant DNA Elongation ProteinsBarbara Bohacek, Elena Ferrari, and Ulrich Hubscher20. In vitro Assays for Studying Helicase ActivitiesJeong-Hoon Kim and Yeon-Soo Seo21. The Use of 2-Aminopurine Fluorescence to Study DNA Polymerase FunctionLinda J. Reha-Krantz22. Single-Molecule Observation of Prokaryotic DNA ReplicationNathan A. Tanner and Antoine M. van Oijen Part V: Cell Biology and Genetic Methods23. Visualization of DNA Replication Sites in Mammalian NucleiDaniela S. Dimitrova24. Cell Cycle Synchrony for Analysis of S. pombe DNA ReplicationDouglas D. Luche and Susan L. Forsburg25. Measuring DNA Content by Flow Cytometry in Fission YeastSarah A. Sabatinos and Susan L. Forsburg 26. Microscopy Techniques to Examine DNA Replication in Fission YeastMarc D. Green, Sarah A. Sabatinos and Susan L. Forsburg27. Using the DHFR Heat-Inducible Degron for Protein Inactivation in Schizosaccharomyces pombe Stephen E. Kearsey and Juraj Gregan28. Assays Used to Study the DNA Replication Checkpoint in Fission YeastEishi Noguchi, Alison B. Ansbach, Chiaki Noguchi, and Paul Russell29. Incorporation of Thymidine Analogs for Studying Replication Kinetics in Fission YeastNicholas Rhind30. The Fast-Halo Assay (FHA) for the Assessment of DNA Damage at the Single-Cell LevelPiero Sestili31. Monitoring Homologous Recombination Following Replication Fork Perturbation in the Fission Yeast Schizosaccharomyces pombeFekret Osman and Matthew C. Whitby Part VI: DNA Fiber Analysis Methods32. Computational Methods to Study Kinetics of DNA ReplicationScott Cheng-Hsin Yang, Michel G. Gauthier, and John Bechhoefer 33. Use of DNA Combing to Study DNA Replication in Xenopus and Human Cell-Free SystemsKathrin Marheineke, Arach Goldar, Torsten Krude, and Olivier Hyrien34. Electron Microscopy Methods for Studying in vivo DNA Replication Intermediates Massimo Lopes35. Determining the Replication Dynamics of Specific Gene Loci by Single-Molecule Analysis of Replicated DNAAgnieszka Demczuk and Paolo Norio36. Use of DNA Combing for Studying DNA Replication in vivo in Yeast and Mammalian Cells Etienne Schwob, Christelle de Renty, Vincent Coulon, Thierry Gostan, Cecile Boyer, Linda Camet-Gabut, and Claire Amato

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