DNA Recombination: Methods and Protocols

ISBN-13: 9781617791284 / Angielski / Twarda / 2011 / 580 str.

Hideo Tsubouchi

Opis

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(t) 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.

Spis treści

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

            Belén Gómez-González, José F. Ruiz, and Andrés 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 Mézard

 

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

 

25. Studying DNA Replication Fork Stability in Xenopus Egg Extract

            Yoshitami Hashimoto and Vincenzo Costanzo

 

26. Supported Lipid-Bilayers and DNA Curtains for High-Throughput Single Molecule Studies

            Ilya J. Finkelstein and Eric C. Greene

 

27. FRET-Based Assays to Monitor DNA Binding and Annealing by Rad52 Recombination Mediator Protein

            Jill M. Grimme and Maria Spies

 

28. Visualization of Human Dmc1 Presynaptic Filaments

            Michael G. Sehorn and Hilarie A. Sehorn

 

Part IV.  Cell Biological Approaches to Study the In Vivo Behavior of Homologous Recombination

 

29. Tracking of Single and Multiple Genomic Loci in Living Yeast Cells

            Imen Lassadi and Kerstin Bystricky

 

30. Cell Biology of Homologous Recombination in Yeast

            Nadine Eckert-Boulet, Rodney Rothstein, and Michael Lisby

 

31. Live Cell Imaging of Meiotic Chromosome Dynamics in Yeast

            Harry Scherthan and Caroline Adelfalk

 

32. Chromosome Structure and Homologous Chromosome Association during Meiotic Prophase in C. elegans

            Kentaro Nabeshima

Blurb

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.