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DNA replication : methods and protocols / edited by Sonya Vengrova and Jacob Z. Dalgaard. — [New York] : Humana, c2009. – (58.17/M592/v.521)

Contents

    Contents
    
    Preface
    Contributors
    PART I: REVIEWS
    1 DNA Replication Initiation
    2 DNA Replication Fork Proteins
    3 Random and Site-Specific Replication Termination 35
    4 Checkpoint Regulation of DNA Replication 55
    5 Introduction to Molecular Combing: Genomics, DNA Replication, and Cancer 71
    PART II: METHODS FOR ANALYSIS OF REPLICATION OF A SINGLE LOCUS
    6 Replication Initiation Point Mapping: Approach and Implications 105
    7 Purification of Restriction Fragments Containing Replication Intermediates from Complex Genomes for 2-D Gel Analysis 121
    8 Topological Analysis of Plasmid DNA Replication Intermediates Using Two-Dimensional Agarose Gels 139
    9 Analysis of Telomeric DNA Replication Using Neutral-Alkaline Two-Dimensional Gel Electrophoresis 169
    10 Chromatin Irnmunoprecipitation of Replication Factors Moving with the Replication Fork 191
    11 Density Transfer as a Method to Analyze the Progression of DNA Replication Forks 203
    12 High-Resolution Mapping of Points of Site-Specific Replication Stalling 215
    13 DNA Replication in Nucleus-Free Xenopus Egg Extracts
    PART III: GENOME - WIDE ANALYSIS METHODS
    14 ChIP-Chip to Analyze the Binding of Replication Proteins to Chromatin Using Oligonucleotide DNA Microarrays 255
    15 Analyzing Origin Activation Patterns by Copy Number Change Experiments 279
    16 Detection of Replication Origins Using Comparative Genomics and Recombinational ARS Assay 295
    17 Isolation of Restriction Fragments Containing Origins of Replication from Complex Genomes 315
    18 Application of Alkaline Sucrose Gradient Centrifugation in the Analysis of DNA Replication After DNA Damage
    PART IV: BIOCHEMISTRY AND BIOPHYSICS METHODS
    19 Isolation of Recombinant DNA Elongation Proteins
    20 In Vitro Assays for Studying Helicase Activities
    21 The Use of 2-Aminopurine Fluorescence to Study DNA Polymerase Function
    22 Single-Molecule Observation of Prokaryotic DNA Replication
    PART V: CELL BIOLOGY AND GENETIC METHODS
    23 Visualization of DNA Replication Sites in Mammalian Nuclei
    24 Cell-Cycle Synchrony for Analysis of S. pombe DNA Replication 437
    25 Measuring DNA Content by Flow Cytometry in Fission Yeast 449
    26 Microscopy Techniques to Examine DNA Replication in Fission Yeast 463
    27 Using the DHFR Heat-Inducible Degron for Protein Inactivation in Schizosaccharomyces pombe 483
    28 Assays Used to Study the DNA Replication Checkpoint in Fission Yeast 493
    29 Incorporation of Thymidine Analogs for Studying Replication Kinetics in Fission Yeast 509
    30 The Fast-Halo Assay for the Assessment of DNA Damage at the Single-Cell Level
    31 Monitoring Homologous Recombination Following Replication Fork Perturbation in the Fission Yeast Schizosaccharomyces pombe 535
    PART VI: DNA FIBER ANALYSIS METHODS
    32 Computational Methods to Study Kinetics of DNA Replication
    33 Use of DNA Combing to Study DNA Replication in Xenopus and Human Cell-Free Systems 575
    34 Electron Microscopy Methods for Studying In Vivo DNA Replication Intermediates 605
    35 Determining the Replication Dynamics of Specific Gene Loci by Single-Molecule Analysis of Replicated DNA 633
    36 Use of DNA Combing for Studying DNA Replication In Vivo in Yeast and Mammalian Cells 673
    Index