The field of eukaryotic DNA repair is enjoying a period of remarkable growth and discovery, fueled by technological advances in molecular bi- ogy, protein biochemistry, and genetics. Notable achievements include the molecular cloning of multiple genes associated with classical human repair disorders, such as xeroderma pigmentosum, Cockayne syndrome, and ataxia telangiectasia; elucidation of the core reaction of nucleotide excision repair (NER); the discovery that certain NER proteins participate not only in repair, but also in transcription; recognition of the crucial role played by mismatch repair processes in maintenance of genome stability and avoidance of cancer; the findings that the tumor suppressor protein p53 is mutated in many types of cancer, and has a key role in directing potentially malignant, genotoxin-d- aged cells towards an apoptotic fate; and the discovery and elaboration of DNA damage (and replication) checkpoints, which placed repair phenomen- ogy firmly within a cell-cycle context. Of course, much remains to be learned about DNA repair. To that end, DNA Repair Protocols: Eukaryotic Systems is about the tools and techniques that have helped propel the DNA repair field into the mainstream of biological research. DNA Repair Protocols: Eukaryotic Systems provides detailed, step-- step instructions for studying manifold aspects of the eukaryotic response to genomic injury. The majority of chapters describe methods for analyzing DNA repair processes in mammalian cells. However, many of those techniques can be applied with only minor modification to other systems, and vice versa.

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 Günter 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 Mitochondrial 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-Dama ...