DNA Repair Protocols

ISBN-13: 9781617371967 / Angielski / Miękka / 2010 / 642 str.

Daryl S. Henderson

Opis

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.

Recenzje

"...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

Spis treści

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-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.

Blurb

In DNA Repair Protocols: Eukaryotic Systems, 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 on troubleshooting and avoiding pitfalls. 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.