DNA Repair Protocols

Overview

Daryl S. Henderson and a team of hands-on experts give time-tested instructions for analyzing a wide range of DNA repair processes and cellular responses to DNA damage, including nucleotide and base excision repair, DNA strand break repair, and mismatch repair. The methods focus on eukaryotic model systems that have made, or have the potential to make, important contributions to our understanding of cellular responses to DNA damage in relation to mutagenesis, carcinogenesis, and the cell cycle. Although mammalian...

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Overview

Daryl S. Henderson and a team of hands-on experts give time-tested instructions for analyzing a wide range of DNA repair processes and cellular responses to DNA damage, including nucleotide and base excision repair, DNA strand break repair, and mismatch repair. The methods focus on eukaryotic model systems that have made, or have the potential to make, important contributions to our understanding of cellular responses to DNA damage in relation to mutagenesis, carcinogenesis, and the cell cycle. Although mammalian cells predominate, consideration is also given to such important nonmammalian model systems as yeast, C. elegans (nematode), Drosophila (fruitfly), Xenopus (amphibian), and plants. DNA Repair Prools: Eukaryotic Systems offers the most comprehensive collection of DNA repair prools available, all step-by-step, optimized, and eminently reproducible with tips. It will serve as the gold-standard reference for both the practical and theoretical aspects of DNA repair studies, encourage the transfer of methodologies between model systems, and stimulate the development of new approaches.

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Editorial Reviews

From the Publisher
"...a comprehensive series of technique-oriented chapters focusing on eukaryotic DNA repair methodology. ...this text succeeds admirably...The scope of the text is fairly broad and encompasses not only in vitro biochemistry and enzymology, but also cell biology and genetics and even signal transduction....In vitro biochemical assays are well covered,...A particularly nice feature of the book is that the chapters have undergone uniform editing and formatting. All provide a nice overview of the topic, including a brief review of the pertinent literature, followed by step-by-step methods sections. The methods are clearly presented in annotated outline form with cross referencing and high level of detail. Each chapter has a particularly valuable section at the end, called "Notes" in which the authors present some of the nitty-gritty details and tricks of the trade needed to make the techniques work....Overall, this book should provide a valuable laboratory companion for researchers in the area of DNA repair. It serves to provide useful and readable introductions to various topics, along with techniques prools sufficient for reproducibility....this text will have substantial appeal to the readers of Radiation Research."-Radiation Research

"The list of authors contains many of the leading scientists within the field...Prools for most experimental eukaryotic organisms are described, from yeast through plants, worms, flies and frogs to mammals. Another laudable quality of this book is the standardization of the descriptions in Materials and methods. Since (almost) all articles are organized similarly, it is relatively easy to find what you want. Also, technical details have been standardized....At the end of each article , there is a 'Notes' section with detailed explanation of specific technical points. For a novice it is good to be reminded that ethidium bromide is a mutagen and that lids should be loosened before putting flasks in the microwave oven. I particularly liked the description, written by the editor, of how to squash Drosophila larvae on a microscope slide by"standing on it with the ball of your foot or your heel. If using the foot method, place the slide (sandwiched in 3 MED MER) on a hard clean floor, cover it carefully with a piece of wood, and stand on that". ...this book keeps up the reputation of the 'Methods in Molecular Biology' series and I would recommend if for labs working with DNA repair, in particular for use by students and technicians."-FEBS Letters

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Product Details

  • ISBN-13: 9781617371967
  • Publisher: Springer-Verlag New York, LLC
  • Publication date: 11/10/2010
  • Series: Methods in Molecular Biology Series , #113
  • Edition description: Softcover reprint of hardcover 1st ed. 1999
  • Edition number: 1
  • Pages: 642
  • Product dimensions: 6.00 (w) x 9.00 (h) x 1.34 (d)

Table of Contents

Part I. Mutant Isolation and Gene Cloning

Isolation of DNA Structure-Dependent Checkpoint Mutants in S. pombe
Rui G. Martinho and Antony M. Carr

Isolating Mutants of the Nematode Caenorhabditis elegans That Are Hypersensitive to DNA-Damaging Agents
Phil S. Hartman and Naoaki Ishii

Isolating DNA Repair Mutants of Drosophila melanogaster, Daryl S. Henderson

Generation, Identification, and Characterization of Repair-Defective Mutants of Arabidopsis
Anne Britt and Cai-Zhong Jiang

Screening for g-Ray Hypersensitive Mutants of Arabidopsis
Corinne S. Davies

Isolation of Mutagen-Sensitive Chinese Hamster Cell Lines by Replica Plating
Malgorzata Z. Zdzienicka

Strategies for Cloning Mammalian DNA Repair Genes
Larry H. Thompson

Novel Complementation Assays for DNA Repair-Deficient Cells: Transient and Stable Expression of DNA Repair Genes
Lin Zeng, Alain Sarasin, and Mauro Mezzina

Part II. Recognition and Removal of Inappropriate or Damaged DNA Bases

The Use of Electrophoretic Mobility Shift Assays to Study DNA Repair
Byung Joon Hwang,Vaughn Smider, and Gilbert Chu

Mismatch Repair Assay
Stephanie E. Corrette-Bennett and Robert S. Lahue

Measurement of Activities of Cyclobutane-Pyrimidine-Dimer and (6-4)-Photoproduct Photolyases
John B. Hays and Peter Hoffman

A Dot Blot Immunoassay for UV Photoproducts
Shirley McCready

Measurement of UV Radiation-Induced DNA Damage Using Specific Antibodies
Ann E. Stapleton

Quantification of DNA Photoproducts in Mammalian Cell DNA Using Radioimmunoassay
David L. Mitchell

Monitoring Removal of Cyclobutane Pyrimidine Dimers in Arabidopsis
John B. Hays and Qishen Pang

DNA Damage Quantitation by Alkaline Gel Electrophoresis
Betsy M. Sutherland, Paula V. Bennett, and John C. Sutherland

The Comet Assay (Single-Cell Gel Test): A Sensitive Genotoxicity Test for the Detection of DNA Damage and Repair
G√ľnter Speit and Andreas Hartmann

Measuring the Formation and Repair of UV Photoproducts by Ligation-Mediated PCR
Gerd P. Pfeifer and Reinhard Dammann

PCR-Based Assays for Strand-Specific Measurement of DNA Damage and Repair I: Strand-Specific Quantitative PCR
Keith A. Grimaldi, John P. Bingham, and John A. Hartley

PCR-Based Assays for Strand-Specific Measurement of DNA Damage and Repair II: Single-Strand Ligation-PCR
Keith A. Grimaldi, Simon R. McAdam, and John A. Hartley

Gene-Specific and Mihondrial Repair of Oxidative DNA Damage
R. Michael Anson and Vilhelm A. Bohr

Characterization of DNA Strand Cleavage by Enzymes That Act at Abasic Sites in DNA
Walter A. Deutsch and Adly Yacoub

Base Excision Repair Assay Using Xenopus laevis Oocyte Extracts
Yoshihiro Matsumoto

In Vitro Base Excision Repair Assay Using Mammalian Cell Extracts
Guido Frosina, Enrico Cappelli, Paola Fortini, and Eugenia Dogliotti

Nucleotide Excision Repair in Saccharomyces cerevisiae Whole-Cell Extracts
Johnson M. S. Wong, Zhigang He, and C. James Ingles

In Vitro Excision Repair Assay in Schizosaccharomyces pombe
Bernard Salles and Patrick Calsou

Nucleotide Excision Repair Assay in Drosophila melanogaster Using Established Cell Lines
Kenji Kohno and Takuya Shimamoto

Nucleotide Excision Repair in Nuclear Extracts from Xenopus Oocytes
Eric J. Ackerman, Lilia K. Koriazova, Jitendra K. Saxena, and Alexander Y. Spoonde

Assay for Nucleotide Excision Repair Protein Activity Using Fractionated Cell Extracts and UV-Damaged Plasmid DNA
Maureen Biggerstaff and Richard D. Wood

Dual-Incision Assays for Nucleotide Excision Repair Using DNA with a Lesion at a Specific Site
Mahmud K.

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