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DNA Damage Responses

Methods and Protocols

  • Book
  • © 2022

Overview

Editors:
  1. Nima Mosammaparast

    1. Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, USA

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  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 2444)

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About this book

This volume provides detailed methods and key approaches used to mechanistically study DNA damage, as well as the factors involved in the damage response. Chapters guide readers through proteomics and biophysical approaches, analyzing protein function, quantifying DNA replication dynamics and nucleic acid base damage, as well as biochemical reconstitution of key pathways involved in DNA repair. 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.

 Authoritative and cutting-edge, DNA Damage Responses: Methods and Protocols aims to be a useful practical guide to researches to help further their study in this field.

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Table of contents (17 protocols)

  1. Front Matter

    Pages i-xi
    Download chapter PDF

  2. Robust Computational Approaches to Defining Insights on the Interface of DNA Repair with Replication and Transcription in Cancer

    • Albino Bacolla, John A. Tainer
    Pages 1-13

  3. A Whole Genome CRISPR/Cas9 Screening Approach for Identifying Genes Encoding DNA End-Processing Proteins

    • Bo-Ruei Chen, Barry P. Sleckman
    Pages 15-27

  4. Immunoaffinity Purification of Epitope-Tagged DNA Repair Complexes from Human Cells

    • Brittany A. Townley, Jennifer M. Soll, Nima Mosammaparast
    Pages 29-41

  5. Universally Accessible Structural Data on Macromolecular Conformation, Assembly, and Dynamics by Small Angle X-Ray Scattering for DNA Repair Insights

    • Naga Babu Chinnam, Aleem Syed, Kathryn H. Burnett, Greg L. Hura, John A. Tainer, Susan E. Tsutakawa
    Pages 43-68

  6. Assessing DNA Damage Responses Using B Lymphocyte Cultures

    • Rachel Johnston, Lynn S. White, Jeffrey J. Bednarski
    Pages 69-80

  7. Studying Single-Stranded DNA Gaps at Replication Intermediates by Electron Microscopy

    • Jessica Jackson, Alessandro Vindigni
    Pages 81-103

  8. Approaches to Monitor Termination of DNA Replication Using Xenopus Egg Extracts

    • Tamar Kavlashvili, James M. Dewar
    Pages 105-123

  9. Use of High-Performance Liquid Chromatography-Mass Spectrometry (HPLC-MS) to Quantify Modified Nucleosides

    • Rebecca Rodell, Ning Tsao, Adit Ganguly, Nima Mosammaparast
    Pages 125-140

  10. Targeted Formation of 8-Oxoguanine in Telomeres

    • Ryan P. Barnes, Sanjana A. Thosar, Elise Fouquerel, Patricia L. Opresko
    Pages 141-159

  11. Qualitative and Quantitative Analysis of DNA Cytidine Deaminase Activity

    • Rachel DeWeerd, Abby M. Green
    Pages 161-169

  12. Characterization of DNA-PK-Bound End Fragments Using GLASS-ChIP

    • Rajashree A. Deshpande, Tanya T. Paull
    Pages 171-182

  13. Monitoring Nuclease Activity by X-Ray Scattering Interferometry Using Gold Nanoparticle-Conjugated DNA

    • Daniel J. Rosenberg, Aleem Syed, John A. Tainer, Greg L. Hura
    Pages 183-205

  14. In Vitro Reconstitution of BRCA1-BARD1/RAD51-Mediated Homologous DNA Pairing

    • Meiling Wang, Cody M. Rogers, Dauren Alimbetov, Weixing Zhao
    Pages 207-225

  15. Purification of DNA-Dependent Protein Kinase Catalytic Subunit (DNA-PKcs) from HeLa Cells

    • Linda Lee, Yaping Yu, Susan P. Lees-Miller
    Pages 227-241

  16. Purification and Characterization of Human DNA Ligase IIIα Complexes After Expression in Insect Cells

    • Ishtiaque Rashid, Miaw-Sheue Tsai, Aleksandr Sverzhinsky, Aye Su Hlaing, Brian Shih, Aye C. Thwin et al.
    Pages 243-269

  17. Generation of Monoubiquitin and K63-Linked Polyubiquitin Chains for Protein Interaction Studies

    • Rita Anoh, Kate A. Burke, Dhane P. Schmelyun, Patrick M. Lombardi
    Pages 271-282

  18. Correction to: Approaches to Monitor Termination of DNA Replication Using Xenopus Egg Extracts

    • Tamar Kavlashvili, James M. Dewar
    Pages C1-C1

  19. Back Matter

    Pages 283-284
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Editors and Affiliations

  • Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, USA

    Nima Mosammaparast

Bibliographic Information

  • Book Title: DNA Damage Responses

  • Book Subtitle: Methods and Protocols

  • Editors: Nima Mosammaparast

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-0716-2063-2

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: The Editor(s) (if applicable) and The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature 2022

  • Hardcover ISBN: 978-1-0716-2062-5Published: 16 March 2022

  • Softcover ISBN: 978-1-0716-2065-6Published: 16 March 2023

  • eBook ISBN: 978-1-0716-2063-2Published: 15 March 2022

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XI, 284

  • Number of Illustrations: 16 b/w illustrations, 59 illustrations in colour

  • Topics: Genetics and Genomics

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