Preface ......................................................... v
Contributors ................................................... xi
Part I: Reviews
1 DNA Replication Initiation ................................... 3
Stephen J. Aves
2 DNA Replication Fork Proteins ............................... 19
Ulrich Hübscher
3 Random and Site-Specific Replication Termination ............ 35
Jacob Z. Dalgaard, Trevor Eydmann, Milana Koulintchenko,
Suha Sayrac, Sonya Vengrova, and Tomoko Yamada-Inagawa
4 Checkpoint Regulation of DNA Replication .................... 55
Erik Boye, Henriette С. Skjølberg, and Beáta Grallert
5 Introduction to Molecular Combing: Genomics, DNA
Replication, and Cancer ..................................... 71
John Herrick and Aaron Bensimon
Part II: Methods for Analysis of Replication of a Single locus
6 Replication Initiation Point Mapping: Approach and
Implications ............................................... 105
Sapna Das-Bradoo and Anja-Katrin Bielinsky
7 Purification of Restriction Fragments Containing
Replication Intermediates from Complex Genomes for 2-D
Gel Analysis ............................................... 121
Larry D. Mesner, Pieter A. Dijkwel, and Joyce L. Hamlin
8 Topological Analysis of Plasmid DNA Replication
Intermediates Using Two-Dimensional Agarose Gels ........... 139
Olivier Hyrien
9 Analysis of Telomeric DNA Replication Using Neutral-
Alkaline Two-Dimensional Gel Electrophoresis ............... 169
Svetlana Makovets
10 Chromatin Immunoprecipitation of Replication Factors
Moving with the Replication Fork ........................... 191
Jordan B. Rapp, Alison B. Ansbach, Chiaki Noguchi, and
Eishi Noguchi
11 Density Transfer as a Method to Analyze the Progression
of DNA Replication Forks ................................... 203
José Antonio Tercero
12 High-Resolution Mapping of Points of Site-Specific
Replication Stalling ....................................... 215
Sonya Vengrova and Jacob Z. Dalgaard
13 DNA Replication in Nucleus-Free Xenopus Egg Extracts ....... 229
Ronald Lebofiky, Tatsuro Takahashi, and Johannes
C. Walter
Part III: Genome - Wide Analysis Methods
14 ChlP-Chip to Analyze the Binding of Replication
Proteins to Chromatin Using Oligonucleotide DNA
Microarrays ................................................ 255
Christopher J. Viggiani, Jennifer G. Aparicio, and Oscar
M. Aparicio
15 Analyzing Origin Activation Patterns by Copy Number
Change Experiments ......................................... 279
Miruthubashini Raveendranathan and Anja-Katrin Bielinsky
16 Detection of Replication Origins Using Comparative
Genomics and Recombinational ARS Assay ..................... 295
Conrad A. Nieduszynski and Anne D. Donaldson
17 Isolation of Restriction Fragments Containing Origins
of Replication from Complex Genomes ........................ 315
Larry D. Mesner and Joyce L. Hamlin
18 Application of Alkaline Sucrose Gradient Centrifugation
in the Analysis of DNA Replication After DNA Damage ........ 329
Sascha Raschke, Jun Guan, and George Iliakis
Part IV: Biochemistry and Biophysics Methods
19 Isolation of Recombinant DNA Elongation Proteins ........... 345
Barbara van Loon, Elena Ferrari, and Ulrich Hübscher
20 In Vitro Assays for Studying Helicase Activities ........... 361
Jeong-Hoon Kim and Yeon-Soo Seo
21 The Use of 2-Aminopurine Fluorescence to Study DNA
Polymerase Function ........................................ 381
Linda J. Reha-Krantz
22 Single-Molecule Observation of Prokaryotic DNA
Replication ................................................ 397
Nathan A. Tanner and Antoine M. van Oijen
Part V: Cell Biology and Genetic Methods
23 Visualization of DNA Replication Sites in Mammalian
Nuclei ..................................................... 413
Daniela S. Dimitrova
24 Cell-Cycle Synchrony for Analysis of S. pombe DNA
Replication ................................................ 437
Douglas D. Luche, and Susan L. Forsburg
25 Measuring DNA Content by Flow Cytometry in Fission Yeast ... 449
Sarah A. Sabatinos and Susan L. Forsburg
26 Microscopy Techniques to Examine DNA Replication in
Fission Yeast .............................................. 463
Marc D. Green, Sarah A. Sabatinos, and Susan L. Forsburg
27 Using the DHFR Heat-Inducible Degron for Protein
Inactivation in Schizosaccharomyces pombe .................. 483
Stephen E. Kearsey and Juraj Gregan
28 Assays Used to Study the DNA Replication Checkpoint in
Fission Yeast .............................................. 493
Eishi Noguchi, Alison B. Ansbach, Chiaki Noguchi, and
Paul Russell
29 Incorporation of Thymidine Analogs for Studying
Replication Kinetics in Fission Yeast ...................... 509
Nicholas Rhind
30 The Fast-Halo Assay for the Assessment of DNA Damage at
the Single-Cell Level ...................................... 517
Piero Sestili
31 Monitoring Homologous Recombination Following Replication
Fork Perturbation in the Fission Yeast
Schizosaccharomyces pombe .................................. 535
Fekret Osman and Matthew C. Whitby
Part VI: DNA Fiber Analysis Methods
32 Computational Methods to Study Kinetics of DNA
Replication ................................................ 555
Scott Cheng-Hsin Yang, Michel G. Gauthier, and John
Bechhoefer
33 Use of DNA Combing to Study DNA Replication in Xenopus
and Human Cell-Free Systems ................................ 575
Kathrin Marheineke, Arach Goldar, Torsten Krude, and
Olivier Hyrien
34 Electron Microscopy Methods for Studying In Vivo DNA
Replication Intermediates .................................. 605
Massimo Lopes
35 Determining the Replication Dynamics of Specific Gene
Loci by Single-Molecule Analysis of Replicated DNA ......... 633
Agnieszka Demczuk and Paolo Norio
36 Use of DNA Combing for Studying DNA Replication In Vivo
in Yeast and Mammalian Cells ............................... 673
Etienne Schwob, Christelle de Renty, Vincent Coulon,
Thierry Gostan, Cécile Boyer, Linda Camet-Gabut, and
Claire Amato
Index ......................................................... 689
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