DNA Repair Protocols: (113 Methods in Molecular Biology)

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 Protocols: Eukaryotic Systems offers the most comprehensive collection of DNA repair protocols 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.

Table of Contents:
Mutant Isolation and Gene Cloning.- Isolation of DNA Structure-Dependent Checkpoint Mutants in S. pombe.- Isolating Mutants of the Nematode Caenorhabditis elegans That Are Hypersensitive to DNA-Damaging Agents.- Isolating DNA Repair Mutants of Drosophila melanogaster.- Generation, Identification, and Characterization of Repair-Defective Mutants of Arabidopsis.- Screening for ?-Ray Hypersensitive Mutants of Arabidopsis.- Isolation of Mutagen-Sensitive Chinese Hamster Cell Lines by Replica Plating.- Strategies for Cloning Mammalian DNA Repair Genes.- Novel Complementation Assays for DNA Repair-Deficient Cells.- Recognition and Removal of Inappropriate or Damaged DNA Bases.- The Use of Electrophoretic Mobility Shift Assays to Study DNA Repair.- Mismatch Repair Assay.- Measurement of Activities of Cyclobutane-Pyrimidine-Dimer and (6-4)-Photoproduct Photolyases.- A Dot Blot Immunoassay for UV Photoproducts.- Measurement of UV Radiation-Induced DNA Damage Using Specific Antibodies.- Quantification of Photoproducts in Mammalian Cell DNA Using Radioimmunoassay.- Monitoring Removal of Cyclobutane Pyrimidine Dimers in Arabidopsis.- DNA Damage Quantitation by Alkaline Gel Electrophoresis.- The Comet Assay (Single-Cell Gel Test).- Measuring the Formation and Repair of UV Photoproducts by Ligation-Mediated PCR.- PCR-Based Assays for Strand-Specific Measurement of DNA Damage and Repair I.- PCR-Based Assays for Strand-Specific Measurement of DNA Damage and Repair II.- Gene-Specific and Mitochondrial Repair of Oxidative DNA Damage.- Characterization of DNA Strand Cleavage by Enzymes That Act at Abasic Sites in DNA.- Base Excision Repair Assay Using Xenopus laevis Oocyte Extracts.- In Vitro Base Excision Repair Assay Using Mammalian Cell Extracts.- Nucleotide Excision Repair inSaccharomyces cerevisiae Whole-Cell Extracts.- In Vitro Excision Repair Assay in Schizosaccharomyces pombe.- Nucleotide Excision Repair Assay in Drosophila melanogaster Using Established Cell Lines.- Nucleotide Excision Repair in Nuclear Extracts from Xenopus Oocytes.- Assay for Nucleotide Excision Repair Protein Activity Using Fractionated Cell Extracts and UV-Damaged Plasmid DNA.- Dual-Incision Assays for Nucleotide Excision Repair Using DNA with a Lesion at a Specific Site.- DNA Strand Breakage and Repair.- In Vitro Chemiluminescence Assay to Measure Excision Repair in Cell Extracts.- Physical Monitoring of HO-Induced Homologous Recombination.- Use of P Element Transposons to Study DNA Double-Strand Break Repair in Drosophila melanogaster.- Analyzing Double-Strand Repair Events in Drosophila.- Expression of I-Sce I in Drosophila to Induce DNA Double-Strand Breaks.- Use of I-Sce I to Induce DNA Double-Strand Breaks in Nicotiana.- Chromosomal Double-Strand Breaks Introduced in Mammalian Cells by Expression of I-Sce I Endonuclease.- Induction of DNA Double-Strand Breaks by Electroporation of Restriction Enzymes into Mammalian Cells.- In Vitro Rejoining of Double-Strand Breaks in Genomic DNA.- Extrachromosomal Assay for DNA Double-Strand Break Repair.- Use of Gene Targeting to Study Recombination in Mammalian DNA Repair Mutants.- DNA Damage Tolerance Mechanisms and Regulatory Responses.- Measurement of Low-Frequency DNA Breaks Using Nucleoid Flow Cytometry.- Live Analysis of the Division Cycles in X-Irradiated Drosophila Embryos.- Inhibition of DNA Synthesis by Ionizing Radiation.- Analysis of Inhibition of DNA Replication in Irradiated Cells Using the SV40-Based In Vitro Assay of DNA Replication.- Assays of Bypass Replication of Genotoxic Lesions in Mammalian Disease and Mutant Cell-Free Extracts.- Detection of Chromatin-Bound PCNA in Cultured Cells Following Exposure to DNA-Damaging Agents.- Induction of p53 Protein as a Marker for Ionizing Radiation Exposure In Vivo.- Activation of p53 Protein Function in Response to Cellular Irradiation.- Selective Extraction of Fragmented DNA from Apoptotic Cells for Analysis by Gel Electrophoresis and Identification of Apoptotic Cells by Flow Cytometry.- Detection of DNA Strand Breakage in the Analysis of Apoptosis and Cell Proliferation by Flow and Laser Scanning Cytometry.- Immunoassay for Single-Stranded DNA in Apoptotic Cells.

Review :
"...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 protocols 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...Protocols 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