Skip to main content
SpringerLink
Log in

Affinity-Based Assays for the Identification and Quantitative Evaluation of Noncovalent Poly(ADP-Ribose)-Binding Proteins

  • Protocol
  • First Online:
Poly(ADP-ribose) Polymerase

Part of the book series: Methods in Molecular Biology ((MIMB,volume 780))

Abstract

Poly(ADP-ribose) polymerases have been linked to several cellular functions, most of which being mediated through the dynamics of poly(ADP-ribose) (pADPr). In several pathways, pADPr is the effector molecule that regulates cellular signaling and dictates biological outcomes. pAPDr is a central molecule that is capable of promoting both cell survival through the maintenance of genome integrity and cell death that occurs by way of a signal-mediated apoptotic-like process. Thus, interactions with pADPr are extremely important in bringing about the balanced regulation that controls cell fate. Further clues regarding these functions are emerging from a growing list of proteins with which pADPr interacts. Here, we describe the current approaches for investigating noncovalent protein interactions with pADPr.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution

Subscribe and save

Springer+ Basic
$34.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or eBook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 89.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 119.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Similar content being viewed by others

References

  1. Hassa PO, Haenni SS, Elser M, Hottiger MO (2006) Nuclear ADP-ribosylation reactions in mammalian cells: where are we today and where are we going? Microbiol Mol Biol Rev 70:789–829

    Article  PubMed  CAS  Google Scholar 

  2. Schreiber V, Dantzer F, Ame JC, de Murcia G (2006) Poly(ADP-ribose): novel functions for an old molecule. Nat Rev Mol Cell Biol 7:517–528

    Article  PubMed  CAS  Google Scholar 

  3. Malanga M, Althaus F (2006) DNA damage signaling through poly(ADP-Ribose). In: Burkle A (ed) Poly(ADP-Ribosyl)ation. Landes Bioscience and Springer Science  +  Business Media, New York, NY, pp 41–50

    Chapter  Google Scholar 

  4. Haince JF, McDonald D, Rodrigue A, Dery U, Masson JY, Hendzel MJ, Poirier GG (2008) PARP1-dependent kinetics of recruitment of MRE11 and NBS1 proteins to multiple DNA damage sites. J Biol Chem 283:1197–1208

    Article  PubMed  CAS  Google Scholar 

  5. Gottschalk AJ, Timinszky G, Kong SE, Jin J, Cai Y, Swanson SK, Washburn MP, Florens L, Ladurner AG, Conaway JW, Conaway RC (2009) Poly(ADP-ribosyl)ation directs recruitment and activation of an ATP-dependent chromatin remodeler. Proc Natl Acad Sci USA 106:13770–13774

    Article  PubMed  CAS  Google Scholar 

  6. Beneke S, Burkle A (2007) Poly(ADP-ribosyl)ation in mammalian ageing. Nucleic Acids Res 35:7456–7465

    Article  PubMed  CAS  Google Scholar 

  7. Chang P, Jacobson MK, Mitchison TJ (2004) Poly(ADP-ribose) is required for spindle assembly and structure. Nature 432:645–649

    Article  PubMed  CAS  Google Scholar 

  8. d’Adda di Fagagna F, Hande MP, Tong WM, Lansdorp PM, Wang ZQ, Jackson SP (1999) Functions of poly(ADP-ribose) polymerase in controlling telomere length and chromosomal stability. Nat Genet 23:76–80

    PubMed  Google Scholar 

  9. Kraus WL (2008) Transcriptional control by PARP-1: chromatin modulation, enhancer-binding, coregulation, and insulation. Curr Opin Cell Biol 20:294–302

    Article  PubMed  CAS  Google Scholar 

  10. Hassa PO (2009) The molecular “Jekyll and Hyde” duality of PARP1 in cell death and cell survival. Front Biosci 14:72–111

    Article  PubMed  CAS  Google Scholar 

  11. Andrabi SA, Kim NS, Yu SW, Wang H, Koh DW, Sasaki M, Klaus JA, Otsuka T, Zhang Z, Koehler RC, Hurn PD, Poirier GG, Dawson VL, Dawson TM (2006) Poly(ADP-ribose) (PAR) polymer is a death signal. Proc Natl Acad Sci USA 103:18308–18313

    Article  PubMed  CAS  Google Scholar 

  12. D’Amours D, Desnoyers S, D’Silva I, Poirier GG (1999) Poly(ADP-ribosyl)ation reactions in the regulation of nuclear functions. Biochem J 342(Pt 2):249–268

    Article  PubMed  Google Scholar 

  13. Minaga T, Kun E (1983) Probable helical conformation of poly(ADP-ribose). The effect of cations on spectral properties. J Biol Chem 258:5726–5730

    PubMed  CAS  Google Scholar 

  14. Minaga T, Kun E (1983) Spectral analysis of the conformation of polyadenosine diphosphoribose. Evidence indicating secondary structure. J Biol Chem 258:725–730

    PubMed  CAS  Google Scholar 

  15. Kleine H, Poreba E, Lesniewicz K, Hassa PO, Hottiger MO, Litchfield DW, Shilton BH, Luscher B (2008) Substrate-assisted catalysis by PARP10 limits its activity to mono-ADP-ribosylation. Mol Cell 32:57–69

    Article  PubMed  CAS  Google Scholar 

  16. Chang P, Coughlin M, Mitchison TJ (2005) Tankyrase-1 polymerization of poly(ADP-ribose) is required for spindle structure and function. Nat Cell Biol 7:1133–1139

    Article  PubMed  CAS  Google Scholar 

  17. Rippmann JF, Damm K, Schnapp A (2002) Functional characterization of the poly(ADP-ribose) polymerase activity of tankyrase 1, a potential regulator of telomere length. J Mol Biol 323:217–224

    Article  PubMed  CAS  Google Scholar 

  18. Loseva O, Jemth AS, Bryant HE, Schuler H, Lehtio L, Karlberg T, Helleday T (2010) PARP-3 is a mono-ADP-ribosylase that activates PARP-1 in the absence of DNA. J Biol Chem 285:8054–8060

    Article  PubMed  CAS  Google Scholar 

  19. Gagné JP, Hendzel MJ, Droit A, Poirier GG (2006) The expanding role of poly(ADP-ribose) metabolism: current challenges and new perspectives. Curr Opin Cell Biol 18:145–151

    Article  PubMed  Google Scholar 

  20. Andrabi SA, Dawson TM, Dawson VL (2008) Mitochondrial and nuclear cross talk in cell death: parthanatos. Ann NY Acad Sci 1147:233–241

    Article  PubMed  CAS  Google Scholar 

  21. de Murcia G, Huletsky A, Lamarre D, Gaudreau A, Pouyet J, Daune M, Poirier GG (1986) Modulation of chromatin superstructure induced by poly(ADP-ribose) synthesis and degradation. J Biol Chem 261:7011–7017

    PubMed  Google Scholar 

  22. de Murcia G, Huletsky A, Poirier GG (1988) Modulation of chromatin structure by poly(ADP-ribosyl)ation. Biochem Cell Biol 66:626–635

    Article  PubMed  Google Scholar 

  23. Egloff MP, Malet H, Putics A, Heinonen M, Dutartre H, Frangeul A, Gruez A, Campanacci V, Cambillau C, Ziebuhr J, Ahola T, Canard B (2006) Structural and functional basis for ADP-ribose and poly(ADP-ribose) binding by viral macro domains. J Virol 80:8493–8502

    Article  PubMed  CAS  Google Scholar 

  24. Karras GI, Kustatscher G, Buhecha HR, Allen MD, Pugieux C, Sait F, Bycroft M, Ladurner AG (2005) The macro domain is an ADP-ribose binding module. EMBO J 24:1911–1920

    Article  PubMed  CAS  Google Scholar 

  25. Till S, Ladurner AG (2009) Sensing NAD metabolites through macro domains. Front Biosci 14:3246–3258

    Article  PubMed  CAS  Google Scholar 

  26. Ahel I, Ahel D, Matsusaka T, Clark AJ, Pines J, Boulton SJ, West SC (2008) Poly(ADP-ribose)-binding zinc finger motifs in DNA repair/checkpoint proteins. Nature 451:81–85

    Article  PubMed  CAS  Google Scholar 

  27. Li GY, McCulloch RD, Fenton AL, Cheung M, Meng L, Ikura M, Koch CA (2010) Structure and identification of ADP-ribose recognition motifs of APLF and role in the DNA damage response. Proc Natl Acad Sci USA 107(20):9129–9134

    Article  PubMed  CAS  Google Scholar 

  28. Timinszky G, Till S, Hassa PO, Hothorn M, Kustatscher G, Nijmeijer B, Colombelli J, Altmeyer M, Stelzer EH, Scheffzek K, Hottiger MO, Ladurner AG (2009) A macrodomain-containing histone rearranges chromatin upon sensing PARP1 activation. Nat Struct Mol Biol 16:923–929

    Article  PubMed  CAS  Google Scholar 

  29. Pleschke JM, Kleczkowska HE, Strohm M, Althaus FR (2000) Poly(ADP-ribose) binds to specific domains in DNA damage checkpoint proteins. J Biol Chem 275:40974–40980

    Article  PubMed  CAS  Google Scholar 

  30. Gagné JP, Isabelle M, Lo KS, Bourassa S, Hendzel MJ, Dawson VL, Dawson TM, Poirier GG (2008) Proteome-wide identification of poly(ADP-ribose) binding proteins and poly(ADP-ribose)-associated protein complexes. Nucleic Acids Res 36:6959–6976

    Article  PubMed  Google Scholar 

  31. Malanga M, Pleschke JM, Kleczkowska HE, Althaus FR (1998) Poly(ADP-ribose) binds to specific domains of p53 and alters its DNA binding functions. J Biol Chem 273:11839–11843

    Article  PubMed  CAS  Google Scholar 

  32. Dani N, Stilla A, Marchegiani A, Tamburro A, Till S, Ladurner AG, Corda D, Di Girolamo M (2009) Combining affinity purification by ADP-ribose-binding macro domains with mass spectrometry to define the mammalian ADP-ribosyl proteome. Proc Natl Acad Sci USA 106:4243–4248

    Article  PubMed  CAS  Google Scholar 

  33. Riggs AD, Bourgeois S, Newby RF, Cohn M (1968) DNA binding of the lac repressor. J Mol Biol 34:365–368

    Article  PubMed  CAS  Google Scholar 

  34. Fahrer J, Kranaster R, Altmeyer M, Marx A, Burkle A (2007) Quantitative analysis of the binding affinity of poly(ADP-ribose) to specific binding proteins as a function of chain length. Nucleic Acids Res 35:e143

    Article  PubMed  Google Scholar 

  35. Slama JT, Aboul-Ela N, Goli DM, Cheesman BV, Simmons AM, Jacobson MK (1995) Specific inhibition of poly(ADP-ribose) glycohydrolase by adenosine diphosphate (hydroxymethyl)pyrrolidinediol. J Med Chem 38:389–393

    Article  PubMed  CAS  Google Scholar 

  36. Slama JT, Aboul-Ela N, Jacobson MK (1995) Mechanism of inhibition of poly(ADP-ribose) glycohydrolase by adenosine diphosphate (hydroxymethyl)pyrrolidinediol. J Med Chem 38:4332–4336

    Article  PubMed  CAS  Google Scholar 

  37. Kawamitsu H, Hoshino H, Okada H, Miwa M, Momoi H, Sugimura T (1984) Monoclonal antibodies to poly(adenosine diphosphate ribose) recognize different structures. Biochemistry 23:3771–3777

    Article  PubMed  CAS  Google Scholar 

  38. Kawamitsu H, Hoshino H, Miwa M, Sugimura T (1983) Monoclonal antibodies against poly(ADP-ribose) recognize different structures of poly(ADP-ribose). Princess Takamatsu Symp 13:41–47

    PubMed  CAS  Google Scholar 

  39. Affar EB, Duriez PJ, Shah RG, Winstall E, Germain M, Boucher C, Bourassa S, Kirkland JB, Poirier GG (1999) Immunological determination and size characterization of poly(ADP-ribose) synthesized in vitro and in vivo. Biochim Biophys Acta 1428:137–146

    Article  PubMed  CAS  Google Scholar 

  40. Panzeter PL, Realini CA, Althaus FR (1992) Noncovalent interactions of poly(adenosine diphosphate ribose) with histones. Biochemistry 31:1379–1385

    Article  PubMed  CAS  Google Scholar 

  41. Gagné JP, Hunter JM, Labrecque B, Chabot B, Poirier GG (2003) A proteomic approach to the identification of heterogeneous nuclear ribonucleoproteins as a new family of poly(ADP-ribose)-binding proteins. Biochem J 371:331–340

    Article  PubMed  Google Scholar 

  42. Shah GM, Poirier D, Duchaine C, Brochu G, Desnoyers S, Lagueux J, Verreault A, Hoflack JC, Kirkland JB, Poirier GG (1995) Methods for biochemical study of poly(ADP-ribose) metabolism in vitro and in vivo. Anal Biochem 227:1–13

    Article  PubMed  CAS  Google Scholar 

  43. Fried MG (1989) Measurement of protein-DNA interaction parameters by electrophoresis mobility shift assay. Electrophoresis 10:366–376

    Article  PubMed  CAS  Google Scholar 

  44. Willander M, Al-Hilli S (2009) Analysis of biomolecules using surface plasmons. Methods Mol Biol 544:201–229

    Article  PubMed  CAS  Google Scholar 

  45. Panzeter PL, Zweifel B, Althaus FR (1992) Synthesis of poly(ADP-ribose)-agarose beads: an affinity resin for studying (ADP-ribose)n-protein interactions. Anal Biochem 207:157–162

    Article  PubMed  CAS  Google Scholar 

  46. Combet C, Blanchet C, Geourjon C, Deleage G (2000) NPS@: network protein sequence analysis. Trends Biochem Sci 25:147–150

    Article  PubMed  CAS  Google Scholar 

  47. Ménard L, Poirier GG (1987) Rapid assay of poly(ADP-ribose) glycohydrolase. Biochem Cell Biol 65:668–673

    Article  PubMed  Google Scholar 

  48. Cardenas-Corona ME, Jacobson EL, Jacobson MK (1987) Endogenous polymers of ADP-ribose are associated with the nuclear matrix. J Biol Chem 262:14863–14866

    PubMed  CAS  Google Scholar 

  49. Alvarez-Gonzalez R, Jacobson MK (1987) Characterization of polymers of adenosine diphosphate ribose generated in vitro and in vivo. Biochemistry 26:3218–3224

    Article  PubMed  CAS  Google Scholar 

  50. Wielckens K, Schmidt A, George E, Bredehorst R, Hilz H (1982) DNA fragmentation and NAD depletion. Their relation to the turnover of endogenous mono(ADP-ribosyl) and poly(ADP-ribosyl) proteins. J Biol Chem 257:12872–12877

    PubMed  CAS  Google Scholar 

  51. Juarez-Salinas H, Sims JL, Jacobson MK (1979) Poly(ADP-ribose) levels in carcinogen-treated cells. Nature 282:740–741

    Article  PubMed  CAS  Google Scholar 

  52. Hall RA (2004) Studying protein-protein interactions via blot overlay or Far Western blot. Methods Mol Biol 261:167–174

    PubMed  CAS  Google Scholar 

  53. Kiehlbauch CC, Aboul-Ela N, Jacobson EL, Ringer DP, Jacobson MK (1993) High resolution fractionation and characterization of ADP-ribose polymers. Anal Biochem 208:26–34

    Article  PubMed  CAS  Google Scholar 

  54. Isogai S, Kanno S, Ariyoshi M, Tochio H, Ito Y, Yasui A, Shirakawa M (2010) Solution structure of a zinc-finger domain that binds to poly-ADP-ribose. Genes Cells 15:101–110

    Article  PubMed  CAS  Google Scholar 

  55. Shuman S (2001) Analysis of topoisomerase-DNA interactions by electrophoretic mobility shift assay. Methods Mol Biol 95:65–74

    PubMed  CAS  Google Scholar 

  56. Affar EB, Duriez PJ, Shah RG, Sallmann FR, Bourassa S, Kupper JH, Burkle A, Poirier GG (1998) Immunodot blot method for the detection of poly(ADP-ribose) synthesized in vitro and in vivo. Anal Biochem 259:280–283

    Article  PubMed  CAS  Google Scholar 

  57. Eustermann S, Brockmann C, Mehrotra PV, Yang JC, Loakes D, West SC, Ahel I, Neuhaus D (2010) Solution structures of the two PBZ domains from human APLF and their interaction with poly(ADP-ribose). Nat Struct Mol Biol 17:241–243

    Article  PubMed  CAS  Google Scholar 

  58. Ahel D, Horejsi Z, Wiechens N, Polo SE, Garcia-Wilson E, Ahel I, Flynn H, Skehel M, West SC, Jackson SP, Owen-Hughes T, Boulton SJ (2009) Poly(ADP-ribose)-dependent regulation of DNA repair by the chromatin remodeling enzyme ALC1. Science 325:1240–1243

    Article  PubMed  CAS  Google Scholar 

  59. Malanga M, Althaus FR (2005) The role of poly(ADP-ribose) in the DNA damage signaling network. Biochem Cell Biol 83:354–364

    Article  PubMed  CAS  Google Scholar 

  60. Althaus FR, Kleczkowska HE, Malanga M, Muntener CR, Pleschke JM, Ebner M, Auer B (1999) Poly ADP-ribosylation: a DNA break signal mechanism. Mol Cell Biochem 193:5–11

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

The authors are supported by research funds from a Canada research chair in proteomics, the Canadian Institutes of Health Research (CIHR grants MOP-74648 and IG1-14052), the Cancer Research Society, the Alberta Cancer Board, the National Institutes of Health (NIH grant P50 CA136393-01), Fonds de la Recherche en Santé du Québec (scholarship to JPG); Strategic Training Program grant in genomics, proteomics and bioinformatics (CIHR STP-53894 to JPG). The authors thank Michèle Rouleau for critical review of the manuscript and their colleagues who contributed to the methods described in this chapter.

Author information

Authors and Affiliations

  1. CHUQ Research Center (CHUL), Laval University, Quebec City, QC, Canada

    Jean-Philippe Gagné (Faculty of Medicine), Jean-François Haince (Faculty of Medicine), Émilie Pic (Faculty of Medicine) & Guy G. Poirier (Faculty of Medicine)

Authors
  1. Jean-Philippe Gagné
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Jean-François Haince
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Émilie Pic
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Guy G. Poirier
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Keystone Program in Epigenetics &, Progenitor Cells, Fox Chase Cancer Center, Cottman Avenue 333, Philadelphia, 19111, Pennsylvania, USA

    Alexei V. Tulin

Rights and permissions

Reprints and permissions

Copyright information

© 2011 Springer Science+Business Media, LLC

About this protocol

Cite this protocol

Gagné, JP., Haince, JF., Pic, É., Poirier, G.G. (2011). Affinity-Based Assays for the Identification and Quantitative Evaluation of Noncovalent Poly(ADP-Ribose)-Binding Proteins. In: Tulin, A. (eds) Poly(ADP-ribose) Polymerase. Methods in Molecular Biology, vol 780. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-61779-270-0_7

Download citation

  • DOI: https://doi.org/10.1007/978-1-61779-270-0_7

  • Published:

  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-61779-269-4

  • Online ISBN: 978-1-61779-270-0

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation