Main description:

The volume outlines techniques used to study the primary mechanisms of important DNA repair pathways. The chapters in this book are organized into five sections, each discussing a specific aspect of repair biology. Part I reviews the role of post-translational modifications of HDR, and DNA damage caused by defective telomere replication. Part II describes methods to detect and measure DNA breaks and proteins involved in DNA damage response. Part III talks about methods designed to measure DNA repair efficiency and characterize factors involved in the repair process. Part IV discusses various in vitro assays used to purify recombinant proteins that are used to study DNA repair enzyme mechanisms. Lastly, Part V focuses on methods to study the damage arising during DNA replication. Written in the highly 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 laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

Cutting-edge and authoritative, DNA Repair: Methods and Protocols is an essential resource for novice and experienced researchers, and provides easily adaptable techniques to help them advance in their specific protein or repair pathway of interest.

Contents:

Preface...Table of Contents...Contributing Authors...
Part I Reviews
1. Homologous Recombination-Mediated DNA Repair and Implications for Clinical Treatment of Repair Defective Cancers Nicole M. Reilly, Brian D. Yard, and Douglas L. Pittman
2. Resolving Roadblocks to Telomere ReplicationEmily Mason-Osann, Himabindu Gali, and Rachel L. Flynn
Part II Cellular Assays to Detect and Measure DNA Damage and Damage Response
3. In Time and Space: Laser Micro-Irradiation and the DNA Damage ResponseJae Jin Kim, Ramhari Kumbhar, Fade Gong, and Kyle M. Miller
4. Quantification of Double Strand Breaks in Mammalian Cells using Pulsed-Field ElectrophoresisKelvin W. Pond and Nathan A. Ellis
5. Methods to Study Trinucleotide Repeat Instability Induced by DNA Damage and RepairYanhao Lai, Ruipeng Lei, Yaou Ren, and Yuan Liu
6. Extracting and Measuring dNTP Pools in Saccharomyces cerevisiaeRadha Subramaniam, Natalie A. Lamb, Yoonchan Hwang, Lauren Johengen, and Jennifer A. Surtees
Part III Cellular and Cell Extract-Based Assays to Measure DNA Repair
7. Conversion Tract Analysis of Homology-Directed Genome Editing using Oligonucleotide DonorsYinan Kan and Eric A. Hendrickson
8. Reporter Assays for BER Pathways Dorota Piekna-Przybylska
9. Methods for Studying DNA Single-Strand Break Repair and Signaling in Xenopus laevis Egg ExtractsYunfeng Lin, Anh Ha, and Shan Yan
10. Chromatin Immunoprecipitation (ChIP) of Plasmid-Bound Proteins in Xenopus Egg ExtractsKelly B. Wolfe and David T. Long
11. Cellular Assays to Study the Functional Importance of Human DNA Repair HelicasesSanket Awate, Srijita Dhar, Joshua A. Sommers, and Robert M. Brosh, Jr.
12. A Mammalian Genetic Complementation Assay for Assessing Cellular Resistance to Genotoxic CompoundsNicole M. Reilly and Douglas L. Pittman
13. Small Molecule Inhibitor Screen for DNA Repair ProteinsJohn J. Turchi and Pamela S. VanderVere-Carozza
Part IV In Vitro Biochemical and Biophysical Methods to Study DNA Repair
14. Assembling the Human Resectosome on DNA CurtainsMicheal M. Soniat, Logan R. Myler, and Ilya J. Finkelstein
15. Thin-Layer Chromatography and Real-Time Coupled Assays to Measure ATP HydrolysisChristopher W. Sausen, Cody M. Rogers, and Mathew L. Bochman
16. Gel-Based Assays for Measuring DNA Unwinding, Annealing, and Strand ExchangeCody M. Rogers, Christopher W. Sausen, and Matthew L. Bochman
17. In Vitro Assay for Plasmid Length DNA Strand Exchange by Human DMC1Steven D. Goodson, Russell B. Hawes, Sarah M. Waldvogel, and Michael G. Sehorn
18. In Vitro Assays for DNA Branch MigrationAndrew A. Kelso, Steven D. Goodson, and Michael G. Sehorn
19. Stabilization of Human DMC1 Nucleoprotein FilamentSarah M. Waldvogel, Steven D. Goodson, and Michael G. Sehorn
Part V Methods to Assess Telomeric and Replication-Induced DNA Damage and Repair
20. Measuring UV Photoproduct Repair in Isolated Telomeres and Bulk Genomic DNA Elise Fouquerel, Ryan P. Barnes, Hong Wang, and Patricia L. Opresko
21. Single-Molecule DNA Fiber Analyses to Characterize Replication Fork Dynamics in Living Cells Srijita Dhar, Arindam Datta, Taraswi Banerjee, and Robert M. Brosh Jr.
22. Direct Visualization of DNA Replication at Telomeres using DNA Fiber Combing Combined with Telomere FISHHimabindu Gali, Emily Mason-Osann, Rachel Litman Flynn
23. Telomere and G-Quadruplex Co-Localization Analysis by Immunofluorescence-Fluorescence In Situ Hybridization (IF-FISH)Miaomiao Zhang, Rui Lui, and Feng Wang
24. FISHing for Damage on Metaphase ChromosomesP. Logan Schuck, Jason A. Stewart