Homologous recombination is important in various aspects of DNA metabolism, including damage repair, replication, telomere maintenance, and meiosis, and yeast genetics has successfully provided a framework for the mechanism of homologous recombination. Divided into four convenient sections, DNA Recombination: Methods and Protocols covers recent techniques that best utilize the advantages of the yeast system, prescribing to the belief that yeast will keep serving as a great model organism to study homologous recombination. Chapters have also been included for such exceptions as the group of genes involved in recombination that are found solely in higher eukaryotes, such as BRCA2. And looking forward, a necessary step in the direction of understanding the homologous recombination process is to isolate the machine and let it work in a test tube.  Understanding the design by studying the appearance and behavior of the machinery as a single molecule will be an important milestone toward understanding the mechanism of action of the machinery. Techniques covering these topics have also been included.  Written in the 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 protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and easily accessible, DNA Recombination: Methods and Protocols serves as an ideal guide to scientists of all backgrounds with its well-honed methodologies and strives to bring the reader to the next level of understanding regarding this vital subject.

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Part I. Genetic and Molecular Biological Approaches with Yeast   1. Methods to Study Mitotic Homologous Recombination and Genome Stability             Xiuzhong Zheng, Anastasiya Epstein, and Hannah L. Klein   2. Characterizing Resection at Random and Unique Chromosome Double-Strand Breaks and Telomere Ends             Wenjian Ma, Jim Westmoreland, Wataru Nakai, Anna Malkova, and Michael A. Resnick   3. Characterization of Meiotic Recombination Initiation Sites Using Pulsed-field Gel Electrophoresis             Sarah Farmer, Wing-Kit Leung, and Hideo Tsubouchi   4. Genome-Wide Detection of Meiotic DNA Double-Strand Break Hotspots Using Single-stranded DNA             Hannah G. Blitzblau and Andreas Hochwagen   5. Detection of Covalent DNA-Bound Spo11 and Topoisomerase Complexes             Edgar Hartsuiker   6. Molecular Assays to Investigate Chromatin Changes during DNA Double-Strand Break Repair in Yeast             Scott Houghtaling, Toyoko Tsukuda, and Mary Ann Osley   7. Analysis of Meiotic Recombination Intermediates by Two-Dimensional Gel Electrophoresis             Jasvinder A. Singh and G. Valentin Börner   8. Mapping of Crossover Sites Using DNA Microarrays             Stacy Y. Chen and Jennifer C. Fung   9. Using the Semi-Synthetic Epitope System to Identify Direct Substrates of the Meiosis-Specific Budding Yeast Kinase, Mek1             Hsiao-Chi Lo and Nancy M. Hollingsworth   10. Genetic and Molecular Analysis of Mitotic Recombination in Saccharomyces cerevisiae             Belen Gomez-Gonzalez, Jose F. Ruiz, and Andres Aguilera   11. In vivo Site-Specific Mutagenesis and Gene Collage Using the Delitto Perfetto System in Yeast Saccharomyces cerevisiae             Samantha Stuckey, Kuntal Mukherjee, and Francesca Storici   12. Detection of RNA-Templated Double-Strand Break Repair in Yeast             Ying Shen and Francesca Storici   Part II. Genetic and Molecular Biological Approaches with Higher Eukaryotes   13. SNP-Based Mapping of Crossover Recombination in C. elegans             Grace C. Bazan and Kenneth J. Hillers   14. Characterization of Meiotic Crossovers in Pollen from Arabidopsis thaliana             Jan Drouaud and Christine Mezard   15. Isolation of Meiotic Recombinants from Mouse Sperm             Francesca Cole and Maria Jasin   16. Homologous Recombination Assay for Interstrand Crosslink Repair             Koji Nakanishi, Francesca Cavallo, Erika Brunet, and Maria Jasin   17. Evaluation of Homologous Recombinational Repair in Chicken B Lymphoma Cell Line, DT40             Hiroyuki Kitao, Seiki Hirano, and Minoru Takata   18. Understanding the Immunoglobulin Locus Specificity of Hypermutation             Vera Batrak, Artem Blagodatski, and Jean-Marie Buerstedde   Part III.  In Vitro Reconstitution of Homologous Recombination Reactions and Single Molecular Analysis of Recombination Proteins   19. Quality Control of Purified Proteins Involved in Homologous Recombination             Xiao-Ping Zhang and Wolf-Dietrich Heyer   20. Assays for Structure-Selective DNA Endonucleases             William D. Wright, Kirk T. Ehmsen, and Wolf-Dietrich Heyer   21. In vitro Assays for DNA Pairing and  Recombination-Associated DNA Synthesis             Jie Liu, Jessica Sneeden, and Wolf-Dietrich Heyer   22. An In vitro Assay for Monitoring the Formation and Branch Migration of Holliday Junctions Mediated by a Eukaryotic Recombinase             Yasuto Murayama and Hiroshi Iwasaki   23. Reconstituting the Key Steps of the DNA Double-Strand Break Repair In vitro             Matthew J. Rossi, Dmitry V. Bugreev, Olga M. Mazina, and Alexander V. Mazin   24. Biochemical Studies on Human Rad51-Mediated Homologous Recombination             Youngho Kwon, Weixing Zhao, and Patrick Sung   ...