DNA Replication, 2009 Methods and Protocols Methods in Molecular Biology Series, Vol. 521

Reviews.- DNA Replication Initiation.- DNA Replication Fork Proteins.- Random and Site-Specific Replication Termination.- Checkpoint Regulation of DNA Replication.- to Molecular Combing: Genomics, DNA Replication, and Cancer.- Methods for Analysis of Replication of a Single Locus.- Replication Initiation Point Mapping: Approach and Implications.- Purification of Restriction Fragments Containing Replication Intermediates from Complex Genomes for 2-D Gel Analysis.- Topological Analysis of Plasmid DNA Replication Intermediates Using Two-Dimensional Agarose Gels.- Analysis of Telomeric DNA Replication Using Neutral–Alkaline Two-Dimensional Gel Electrophoresis.- Chromatin Immunoprecipitation of Replication Factors Moving with the Replication Fork.- Density Transfer as a Method to Analyze the Progression of DNA Replication Forks.- High-Resolution Mapping of Points of Site-Specific Replication Stalling.- DNA Replication in Nucleus-Free Xenopus Egg Extracts.- Genome-Wide Analysis Methods.- ChIP-Chip to Analyze the Binding of Replication Proteins to Chromatin Using Oligonucleotide DNA Microarrays.- Analyzing Origin Activation Patterns by Copy Number Change Experiments.- Detection of Replication Origins Using Comparative Genomics and Recombinational ARS Assay.- Isolation of Restriction Fragments Containing Origins of Replication from Complex Genomes.- Application of Alkaline Sucrose Gradient Centrifugation in the Analysis of DNA Replication After DNA Damage.- Biochemistry and Biophysics Methods.- Isolation of Recombinant DNA Elongation Proteins.- In Vitro Assays for Studying Helicase Activities.- The Use of 2-Aminopurine Fluorescence to Study DNA Polymerase Function.- Single-Molecule Observation of Prokaryotic DNA Replication.- Cell Biology and Genetic Methods.- Visualizationof DNA Replication Sites in Mammalian Nuclei.- Cell-Cycle Synchrony for Analysis of S. pombe DNA Replication.- Measuring DNA Content by Flow Cytometry in Fission Yeast.- Microscopy Techniques to Examine DNA Replication in Fission Yeast.- Using the DHFR Heat-Inducible Degron for Protein Inactivation in Schizosaccharomyces pombe.- Assays Used to Study the DNA Replication Checkpoint in Fission Yeast.- Incorporation of Thymidine Analogs for Studying Replication Kinetics in Fission Yeast.- The Fast-Halo Assay for the Assessment of DNA Damage at the Single-Cell Level.- Monitoring Homologous Recombination Following Replication Fork Perturbation in the Fission Yeast Schizosaccharomyces pombe.- DNA Fiber Analysis Methods.- Computational Methods to Study Kinetics of DNA Replication.- Use of DNA Combing to Study DNA Replicationin Xenopus and Human Cell-Free Systems.- Electron Microscopy Methods for Studying In Vivo DNA Replication Intermediates.- Determining the Replication Dynamics of Specific Gene Loci by Single-Molecule Analysis of Replicated DNA.- Use of DNA Combing for Studying DNA Replication In Vivo in Yeast and Mammalian Cells.

Presents a collection of methods described by the experts in the field of DNA replication Contains overview chapters as an introduction to the field of DNA replication and as a guide in selecting the methods to use Covers techniques for various biological systems, including viral, bacterial, yeast and mammalian DNA replication Describes assays based on different technical approaches, including, among others, whole cell microscopy, genetics, in vitro biochemistry and DNA fiber analysis Provides detailed, step-by-step protocols for setting up a technique Includes supplementary material: sn.pub/extras