DNA Electrophoresis Methods and Protocols

This volume explores the latest techniques used by researchers to study DNA electrophoresis, with focus on various species including bacteria, yeasts, and mammalian cells. The chapters in this book cover topics such as two-dimensional gel electrophoresis; DNA replication; pulsed-field gel electrophoresis; ChIP; and post-labeling/PAGE method for detection of DNA adducts. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

Cutting-edge and authoritative, DNA Electrophoresis: Methods and Protocols is a valuable resource for any researchers looking to learn more about this developing field.

Preface…
Table of Contents…
Contributing Authors…

1.  Introduction and Perspectives of DNA Electrophoresis
Katsuhiro Hanada

2.  Two-Dimensional Gel Electrophoresis to Resolve DNA Topoisomers
Elizabeth G. Gibson, Alexandria A. Oviatt, and Neil Osheroff

3.  Using Two-Dimensional Intact Mitochondrial DNA (mtDNA) Agarose Gel Electrophoresis (2D-IMAGE) to Detect Changes in Topology Associated with Mitochondrial Replication, Transcription, and Damage
Jill E. Kolesar and Brett A. Kaufman 

4.  2D Gel Electrophoresis to Detect DNA Replication and Recombination Intermediates in Budding Yeast
Luca Zardoni, Eleonora Nardini, and Giordano Liberi

5.  Neutral-Neutral 2-Dimensional Agarose Gel Electrophoresis for Visualization of E. coli DNA Replication Structures
Karla A. Mettrick, Georgia M. Weaver, and Ian Grainge

6.  Alkali Comet Assay in Genotoxicity Tests
Maya Ueda

7.  The Analysis of DNA Interstrand Crosslinks and their Repair by the Modified Comet Assay
Lonnie P. Swift, Lianne Castle, and Peter J. McHugh

8.  Analysis of Chromosomal DNA Fragmentation in Apoptosis by Pulsed-Field Gel Electrophoresis
Takeshi Terabayashi, Asako Tokumaru, Toshimasa Ishizaki, and Katsuhiro Hanada

9.  Detection of DNA Damage-Induced DSBs by the Contour-Clamped Homogeneous Electric Field (CHEF) System in Mammalian Cells
Yuri Takiguchi, Ryo Kariyazono, and Kunihiro Ohta

10.  Investigation of DNA Double-Strand Breaks Induced in Host Cells following Infection with Genotoxic Bacteria
Rie Teshima

11.  Monitoring of DNA Replication and DNA Double-Strand Breaks in Saccharomyces cerevisiae by Pulsed-Field Gel Electrophoresis (PFGE)
Kenji Keyamura and Takashi Hishida

12. Pulsed-Field Gel Electrophoresis for Detecting Chromosomal DNA Breakage in Fission Yeast
Takatomi Yamada, Hiroshi Murakami, and Kunihiro Ohta

13. Detection of DNA Double-Strand Breaks by Pulsed-Field Gel Electrophoresis of Circular Bacterial Chromosomes
Ichizo Kobayashi and Hanada Katsuhiro 

14. Detection of Bleomycin-Induced DNA Double-Strand Breaks in Escherichia coli by Pulsed-Field Gel Electrophoresis using a Rotating Gel Electrophoresis System
Naomi Inoue, Hisashi Narahara, Yoshihiro Nishida, and Katsuhiro Hanada

15. Circle-Seq: Isolation and Sequencing of Chromosome-Derived Circular DNA Elements in Cells
Henrik D. Møller

16. Chromatin Pull-Down Methodology Based on DNA Triple Helix Formation
Asako Isogawa, Robert P. Fuchs, and Shingo Fujii

17.  DNA Fragments Agarose Gel Electrophoresis for Chromatin Immunoprecipitation (ChIP)
Mayu Isono and Satoru Hashimoto 

18. Post-Labeling/PAGE Method for Detection of DNA Adducts
Kazuhiro Shiizaki