DNA Repair: Methods and Protocols

ISBN-13: 9781493995028 / Angielski / Miękka / 2020 / 352 str.

Lata Balakrishnan;Jason A. Stewart

Opis

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.

Spis treści

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 Replication

Emily 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 Response

Jae Jin Kim, Ramhari Kumbhar, Fade Gong, and Kyle M. Miller

4. Quantification of Double Strand Breaks in Mammalian Cells using Pulsed-Field Electrophoresis

Kelvin W. Pond and Nathan A. Ellis

5. Methods to Study Trinucleotide Repeat Instability Induced by DNA Damage and Repair

Yanhao Lai, Ruipeng Lei, Yaou Ren, and Yuan Liu

6. Extracting and Measuring dNTP Pools in Saccharomyces cerevisiae

Radha 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 Donors

Yinan 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 Extracts

Yunfeng Lin, Anh Ha, and Shan Yan

10. Chromatin Immunoprecipitation (ChIP) of Plasmid-Bound Proteins in Xenopus Egg Extracts

Kelly B. Wolfe and David T. Long 

11. Cellular Assays to Study the Functional Importance of Human DNA Repair Helicases

Sanket Awate, Srijita Dhar, Joshua A. Sommers, and Robert M. Brosh, Jr.

12. A Mammalian Genetic Complementation Assay for Assessing Cellular Resistance to Genotoxic Compounds

Nicole M. Reilly and Douglas L. Pittman

13. Small Molecule Inhibitor Screen for DNA Repair Proteins

John 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 Curtains

Micheal M. Soniat, Logan R. Myler, and Ilya J. Finkelstein

15. Thin-Layer Chromatography and Real-Time Coupled Assays to Measure ATP Hydrolysis

Christopher W. Sausen, Cody M. Rogers, and Mathew L. Bochman 

16. Gel-Based Assays for Measuring DNA Unwinding, Annealing, and Strand Exchange

Cody M. Rogers, Christopher W. Sausen, and Matthew L. Bochman 

17. In Vitro Assay for Plasmid Length DNA Strand Exchange by Human DMC1

Steven D. Goodson, Russell B. Hawes, Sarah M. Waldvogel, and Michael G. Sehorn 

18. In Vitro Assays for DNA Branch Migration

Andrew A. Kelso, Steven D. Goodson, and Michael G. Sehorn

19. Stabilization of Human DMC1 Nucleoprotein Filament

Sarah 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 FISH

Himabindu 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 Chromosomes

P. Logan Schuck, Jason A. Stewart