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Poly(ADP-Ribose) Polymerase

Methods and Protocols

  • Book
  • © 2017

Overview

Editors:
  1. Alexei V. Tulin

    1. Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, USA

    View editor publications

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  • Includes updated, cutting-edge methods and protocols for the study of PARP research
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts
  • Includes supplementary material: sn.pub/extras

Part of the book series: Methods in Molecular Biology (MIMB, volume 1608)

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Table of contents (30 protocols)

  1. Front Matter

    Pages i-xv
    Download chapter PDF

  2. Detection and Quantification of pADPr

    1. Front Matter

      Pages 1-1
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    2. Quantitation of Poly(ADP-Ribose) by Isotope Dilution Mass Spectrometry

      • Tabea Zubel, Rita Martello, Alexander Bürkle, Aswin Mangerich
      Pages 3-18

    3. Quantification of PARP Activity in Human Tissues: Ex Vivo Assays in Blood Cells and Immunohistochemistry in Human Biopsies

      • Eszter M. Horvath, Zsuzsanna K. Zsengellér, Csaba Szabo
      Pages 19-26

    4. Detecting and Quantifying pADPr In Vivo

      • Yi-Chen Lai, Rajesh K. Aneja, Margaret A. Satchell, Robert S. B. Clark
      Pages 27-43

    5. Compartment-Specific Poly-ADP-Ribose Formation as a Biosensor for Subcellular NAD Pools

      • Magali R. VanLinden, Marc Niere, Andrey A. Nikiforov, Mathias Ziegler, Christian Dölle
      Pages 45-56

    6. Cell Cycle Resolved Measurements of Poly(ADP-Ribose) Formation and DNA Damage Signaling by Quantitative Image-Based Cytometry

      • Jone Michelena, Matthias Altmeyer
      Pages 57-68

  3. Identification of Protein Targets

    1. Front Matter

      Pages 69-69
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    2. Detecting Protein ADP-Ribosylation Using a Clickable Aminooxy Probe

      • Rory K. Morgan, Michael S. Cohen
      Pages 71-77

    3. ADP-Ribosylated Peptide Enrichment and Site Identification: The Phosphodiesterase-Based Method

      • Casey M. Daniels, Shao-En Ong, Anthony K. L. Leung
      Pages 79-93

    4. Using Clickable NAD+ Analogs to Label Substrate Proteins of PARPs

      • Lu Zhang, Hening Lin
      Pages 95-109

    5. Identification of Protein Substrates of Specific PARP Enzymes Using Analog-Sensitive PARP Mutants and a “Clickable” NAD+ Analog

      • Bryan A. Gibson, W. Lee Kraus
      Pages 111-135

    6. Identification of ADP-Ribose Acceptor Sites on In Vitro Modified Proteins by Liquid Chromatography–Tandem Mass Spectrometry

      • Mario Leutert, Vera Bilan, Peter Gehrig, Michael O. Hottiger
      Pages 137-148

    7. Proteome-Wide Identification of In Vivo ADP-Ribose Acceptor Sites by Liquid Chromatography–Tandem Mass Spectrometry

      • Sara C. Larsen, Mario Leutert, Vera Bilan, Rita Martello, Stephanie Jungmichel, Clifford Young et al.
      Pages 149-162

  4. Functional Analysis

    1. Front Matter

      Pages 163-163
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    2. Poly(ADP-Ribose)-Dependent Chromatin Remodeling in DNA Repair

      • Théo Lebeaupin, Rebecca Smith, Sébastien Huet, Gyula Timinszky
      Pages 165-183

    3. Methods to Assess the Role of Poly(ADP-Ribose) Polymerases in Regulating Mitochondrial Oxidation

      • Edit Mikó, Tünde Kovács, Tamás Fodor, Péter Bai
      Pages 185-200

    4. Approaches for Investigating Translational Regulation Controlled by PARP1: Biotin-Based UV Cross-Linking and Luciferase Reporter Assay

      • Yingbiao Ji
      Pages 201-210

    5. Methodology to Identify Poly-ADP-Ribose Polymerase 1 (PARP1)–mRNA Targets by PAR-CLiP

      • Manana Melikishvili, Elena Matveeva, Yvonne Fondufe-Mittendorf
      Pages 211-228

  5. Regulation of PARP-1 and Its Partners

    1. Front Matter

      Pages 229-229
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Keywords

About this book

This book presents multiple new and classical methods for studying the vital poly-ADP-ribose (pADPr) pathway. Beginning with techniques for the detection and quantification of the product of poly(ADP-ribose) polymerase (PARP) enzymatic activity and detection of variation in pADPr production during the cell cycle, the volume continues with sections on the identification of pADPr protein acceptors, methods focusing on studying molecular mechanisms of PARP functions in eukaryotic cells, particularly those involved in control of DNA repair and oxidative stress, as well as in expression regulation, approaches to the in vitro reconstitution of PARP-1 interaction with chromatin, the development and testing of small molecule PARP inhibitors, and the functions of understudied members of PARP family.  Written for the highly successful Methods in Molecular Biology series, 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 practical, Poly(ADP-Ribose) Polymerase: Methods and Protocols, Second Edition serves as an ideal companion to the first edition for scientists whose investigations involve this important pathway.


The chapter 'Identifying and Validating Tankyrase Binders and Substrates: A Candidate Approach' is published open access under a CC BY 4.0 license.

Editors and Affiliations

  • Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, USA

    Alexei V. Tulin

Bibliographic Information

  • Book Title: Poly(ADP-Ribose) Polymerase

  • Book Subtitle: Methods and Protocols

  • Editors: Alexei V. Tulin

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4939-6993-7

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media LLC 2017

  • Hardcover ISBN: 978-1-4939-6992-0Published: 11 July 2017

  • Softcover ISBN: 978-1-4939-8361-2Published: 12 June 2018

  • eBook ISBN: 978-1-4939-6993-7Published: 09 July 2017

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 2

  • Number of Pages: XV, 528

  • Number of Illustrations: 35 b/w illustrations, 47 illustrations in colour

  • Topics: Protein Science

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