Poly (ADP-ribose) polymerase : methods and protocols / edited by Alexei V. Tulin.

Online resource; title from PDF title page (SpringerProtocol, viewed July 11, 2017).

Includes bibliographical references and index.

Quantitation of poly(ADP-ribose) by isotope dilution mass spectrometry / Tabea Zubel, Rita Martello, Alexander Bürkle, and Aswin Mangerich -- Quantification of PARP activity in human tissues : ex vivo assays in blood cells and immunohistochemistry in human biopsies / Eszter M. Horvath, Zsuzsanna K. Zsengellér, and Csaba Szabo -- Detecting and quantifying pADPr in vivo / Yi-Chen Lai, Rajesh K. Aneja, Margaret A. Satchell, and Robert S.B. Clark -- Compartment-specific poly-ADP-ribose formation as a biosensor for subcellular NAD pools / Magali R. VanLinden, Marc Niere, Andrey A. Nikiforov, Mathias Ziegler, and Christian Dölle -- Cell cycle resolved measurements of poly(ADP-ribose) formation and DNA damage signaling by quantitative image-based cytometry / Jone Michelena and Matthias Altmeyer -- Detecting protein ADP-ribosylation using a clickable aminooxy probe / Rory K. Morgan and Michael S. Cohen -- ADP-ribosylated peptide enrichment and site identification : the phosphodiesterase-based method / Casey M. Daniels, Shao-En Ong, and Anthony K.L. Leung -- Using clickable NAD+ analogs to label substrate proteins of PARPs / Lu Zhang and Hening Lin -- Identification of protein substrates of specific PARP enzymes using analog- sensitive PARP mutants and a "Clickable" NAD+ analog / Bryan A. Gibson and W. Lee Kraus -- Identification of ADP-ribose acceptor sites on in vitro modified proteins by liquid chromatography-tandem mass spectrometry / Mario Leutert, Vera Bilan, Peter Gehrig, and Michael O. Hottiger -- 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, Michael O. Hottiger, and Michael L. Nielsen -- Poly(ADP-ribose)-dependent chromatin remodeling in DNA repair / Théo Lebeaupin, Rebecca Smith, Sébastien Huet, and Gyula Timinszky -- Methods to assess the role of poly(ADP-ribose) polymerases in regulating mitochondrial oxidation / Edit Mikó, Tünde Kovács, Tamás Fodor, and Péter Bai -- Approaches for investigating translational regulation controlled by PARP1 : biotin-based UV cross-linking and Luciferase reporter assay / Yingbiao Ji -- Methodology to identify poly-ADP-ribose polymerase 1 (PARP1)-mRNA targets by PAR-CLiP / Manana Mekishvili, Elena Matveeva, and Yvonne Fondufe-Mittendorf -- Biochemical and biophysical methods for analysis of poly(ADP-ribose) polymerase 1 and its interactions with chromatin / Maggie H. Chassé, Uma M. Muthurajan, Nicholas J. Clark, Michael A. Kramer, Srinivas Chakravarthy, Thomas Irving, and Karolin Luger -- PARP-1 interaction with and activation by histones and nucleosomes / Colin Thomas, Elena Kotova, and Alexei V. Tulin -- Strategies employed for the development of PARP inhibitors / Stacie Canan, Karen Maegley, and Nicola J. Curtin -- High-throughput colorimetric assay for identifying PARP-1 inhibitors using a large small-molecule collection / Elena Kotova and Alexei V. Tulin -- Testing PARP inhibitors using a murine xenograft model / Peter Makhov, Sei Naito, and Vladimir M. Kolenko -- In vitro long-term proliferation assays to study antiproliferative effects of PARP inhibitors on cancer cells / Heike Keilhack and Paul Chang -- Use of inosine monophosphate dehydrogenase activity assay to determine the specificity of PARP-1 inhibitors / Sajitha Anthony, Jeffrey R. Peterson, and Yingbiao Ji -- Use of PARP inhibitors in cancer therapy : use as adjuvant with chemotherapy or radiotherapy, use as a single agent in susceptible patients, and techniques used to identify susceptible patients / Sydney Shall, Terry Gaymes, Farzin Farzaneh, Nicola J. Curtin, and Ghulam J. Mufti -- Purification of recombinant human PARP-3 / Jean-Christophe Amé, Barbara Camuzeaux, Françoise Dantzer, and Valérie Schreiber -- Purification of recombinant human PARG and activity assays / Jean-Christophe Amé, Éléa Héberlé, Barbara Camuzeaux, Françoise Dantzer, and Valérie Schreiber -- Studying catabolism of protein ADP-ribosylation / Luca Palazzo, Dominic I. James, Ian D. Waddell, and Ivan Ahel -- Purification of DNA damage-dependent PARPs from E. coli for structural and biochemical analysis / Marie-France Langelier, Jamin D. Steffen, Amanda A. Riccio, Michael McCauley, and John M. Pascal -- Identifying and validating tankyrase binders and substrates : a candidate approach / Katie Pollock, Michael Ranes, Ian Collins, and Sebastian Guettler -- Computational and experimental studies of ADP-ribosylation / Robert G. Hammond, Xuan Tan, Matthew Chan, Anupam Goel, and Margaret A. Johnson.

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.