Skip to main content
SpringerLink
Log in

Purification and Characterization of Poly(ADP-Ribosyl)ated DNA Replication/Repair Complexes

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

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

Abstract

PARP-1, the best studied isoform and most abundantly expressed member of the PARP family of 18 proteins, catalyzes the poly(ADP-ribosyl)ation (PARylation) of various nuclear proteins and play key roles in DNA repair, genome maintenance, DNA replication, recombination, apoptosis, gene expression, and regulation of chromatin function. PARylation modulates the functions of target proteins, mainly PARP-1 itself. A multifunctional enzyme, PARP-1 has been localized within DNA replication, repair, recombination, and transcription complexes, and modifies and regulates the functions of specific components of these complexes. PARylation can regulate the activities of replicative enzymes, such as DNA polymerases α, δ, and ε, topo I and II, primase, RPA, and PCNA in isolated enzymes or within DNA replication complexes (DNA synthesome). PARP-1 and PARylation may (1) play dual roles in nuclear processes, depending on the levels of the substrate NAD and the presence of PARP-activating DNA breaks, (2) recruit acceptor proteins to certain sites or complexes through direct association or through binding to PAR and PAR-binding proteins, and (3) alters the nucleosomal structure of DNA by PARylation of nucleosomal proteins, such as histone H1 to destabilize higher order chromatin structures and promote access of DNA repair and replication enzymes as well as transcription factors to these sites. Here, we describe biochemical approaches that have been utilized in our laboratory for the purification and characterization of PARylated DNA replicative complexes. These methods can be modified for the purification of complexes involved in other nuclear processes. This chapter also briefly discusses current methods by which new PARylated complexes are being identified and studied. Identification, evaluation, and characterization of new complexes could aid in the elucidation of the molecular mechanisms by which PARylation and PARP mediates its pleiotropic roles in various nuclear processes.

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

Access this chapter

Log in via an institution
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

References

  1. Rouleau M, Patel A, Hendzel M, Kaufmann S, Poirier G (2010) PARP inhibition: PARP1 and beyond. Nat Rev Cancer 10:293–301

    Article  PubMed  CAS  Google Scholar 

  2. Cherney BW, McBride OW, Chen DF, Alkhatib H, Bhatia K, Hensley P, Smulson ME (1987) cDNA sequence, protein structure, and chromosomal location of the human gene for poly(ADP-ribose) polymerase. Proc Natl Acad Sci 84:8370–8374

    Article  PubMed  CAS  Google Scholar 

  3. Menissier-de Murcia J, Molinete M, Gradwohl G, de Murcia G (1989) Zinc-binding domain of poly(ADP-ribose)polymerase participates in the recognition of single strand breaks on DNA. J Mol Biol 210:229–233

    Article  PubMed  CAS  Google Scholar 

  4. Langelier M, Ruhl D, Planck J, Kraus W, Pascal J (2010) The Zn3 domain of human poly(ADP-ribose) polymerase-1 (PARP-1) functions in both DNA-dependent poly(ADP-ribose) ­synthesis activity and chromatin compaction. J Biol Chem 285:18877–18887

    Article  PubMed  CAS  Google Scholar 

  5. Satoh MS, Lindahl T (1992) Role of poly(ADP-ribose) formation in DNA repair. Nature 356:356–358

    Article  PubMed  CAS  Google Scholar 

  6. Smulson M, Istock N, Ding R, Cherney B (1994) Deletion mutants of poly(ADP-ribose) polymerase support a model of cyclic association and dissociation of enzyme from DNA ends during DNA repair. Biochemistry 33:6186–6191

    Article  PubMed  CAS  Google Scholar 

  7. Smulson M, Pang D, Jung M, Dimtchev A, Chasovskikh S, Spoonde A, Simbulan-Rosenthal C, Rosenthal D, Yakovlev A, Dritschilo A (1998) Irreversible binding of poly(ADP-ribose) polymerase cleavage product to DNA ends revealed by atomic force microscopy: possible role in apoptosis. Cancer Res 58:3495–3498

    PubMed  CAS  Google Scholar 

  8. Simbulan-Rosenthal C, Rosenthal D, Hilz H, Hickey R, Malkas L, Applegren N, Wu Y, Bers G, Smulson M (1996) The expression of poly(ADP-ribose) polymerase during differentiation-linked DNA replication reveals that this enzyme is a component of the multiprotein DNA replication complex. Biochemistry 35:11622–11633

    Article  PubMed  CAS  Google Scholar 

  9. Simbulan-Rosenthal C, Rosenthal D, Iyer S, Boulares AH, Smulson M (1998) Transient poly(ADP-ribosyl)ation of nuclear proteins and role for poly(ADP-ribose) polymerase in the early stages of apoptosis. J Biol Chem 273:13703–13712

    Article  PubMed  CAS  Google Scholar 

  10. Hassa P, Hottiger M (2008) The diverse biological roles of mammalian PARPS, a small but powerful family of poly-ADP-ribose polymerases. Front Biosci 13:3046–3082

    Article  PubMed  CAS  Google Scholar 

  11. Lautier D, Lagueux J, Thibodeau J, Menard L, Poirier G (1993) Molecular and biochemical features of poly(ADP-ribose)metabolism. Mol Cell Biochem 122:171–193

    Article  PubMed  CAS  Google Scholar 

  12. Althaus FR (1987) Poly-ADP-ribosylation reactions. In: Althaus FR, Richter C (eds) ADP-ribosylation of proteins, enzymology and biological significance. Springer, Berlin, pp 1–126

    Chapter  Google Scholar 

  13. Altmeyer M, Messner S, Hassa P, Fey M, Hottiger M (2009) Molecular mechanism of poly(ADP-ribosyl)ation by PARP1 and identification of lysine residues as ADP-ribose acceptor sites. Nucleic Acids Res 37:3723–3738

    Article  PubMed  CAS  Google Scholar 

  14. Miwa M, Saikawa N, Yamaizumi Z, Nishimura S, Sugimura T (1979) Structure of poly(adenosine diphosphate ribose): identification of 2–-[1"-ribosyl-2"-(or 3"-)(1"–-ribosyl)]adenosine-5–,5",5"–-tris(phosphate) as a branch linkage. Proc Natl Acad Sci USA 76:595–599

    Article  PubMed  CAS  Google Scholar 

  15. Amé J, Jacobson E, Jacobson M (1999) Molecular heterogeneity and regulation of poly(ADP-ribose) glycohydrolase. Mol Cell Biochem 193:75–81

    Article  PubMed  Google Scholar 

  16. Bonicalzi M, Haince J, Droit A, Poirier G (2005) Regulation of poly(ADP-ribose) metabolism by poly(ADP-ribose) glycohydrolase: where and when? Cell Mol Life Sci 62:739–750

    Article  PubMed  CAS  Google Scholar 

  17. Gagné J, Hendzel M, Droit A, Poirier G (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 

  18. Oka S, Kato J, Moss J (2006) Identification and characterization of a mammalian 39-kDa poly(ADP- ribose) glycohydrolase. J Biol Chem 281:705–713

    Article  PubMed  CAS  Google Scholar 

  19. Kupper JH, Muller M, Jacobson MK, Tatsumi-Miyajima J, Coyle DL, Jacobson EL, Burkle A (1995) Trans-dominant inhibition of poly(ADP-ribosyl)ation sensitizes cells against gamma-irradiation and N-methyl-N–-nitro-N-nitrosoguanidine but does not limit DNA replication of a polyomavirus replicon. Mol Cell Biol 15:3154–3163

    PubMed  CAS  Google Scholar 

  20. Molinete M, Vermeulen W, Burkle A, de Murcia JM, Kupper JH, Hoeijmakers JHJ, de Murcia G (1993) Overproduction of the poly(ADP-ribose) polymerase DNA-binding domain blocks alkylation-induced DNA repair synthesis in mammalian cells. EMBO J 12:2109–2117

    PubMed  CAS  Google Scholar 

  21. Schreiber V, Hunting D, Trucco C, Gowans B, Grunwald D, De Murcia G, De Murcia JM (1995) A dominant-negative mutant of human poly(ADP-ribose) polymerase affects cell recovery, apoptosis, and sister chromatid exchange following DNA damage. Proc Natl Acad Sci USA 92:4753–4757

    Article  PubMed  CAS  Google Scholar 

  22. Ding R, Pommier Y, Kang V, Smulson M (1992) Depletion of poly(ADP-ribose) polymerase by antisense RNA expression results in a delay in DNA strand break rejoining. J Biol Chem 267:2804–2812

    Google Scholar 

  23. Ding R, Smulson M (1994) Depletion of nuclear poly(ADP-ribose) polymerase by antisense RNA expression: influences on genomic stability, chromatin organization and carcinogen cytotoxicity. Cancer Res 54:4627–4634

    PubMed  CAS  Google Scholar 

  24. Rosenthal D, Simbulan C, Smulson M (1995) Model systems for the study of the role of PADPRP in essential biological processes. Biochimie 77:439–443

    Article  PubMed  CAS  Google Scholar 

  25. Smulson ME, Kang VH, Ntambi JM, Rosenthal DS, Ding R, Simbulan C (1995) Requirement for the expression of poly(ADP-ribose) polymerase during the early stages of differentiation of 3T3-L1 preadipocytes, as studied by antisense RNA induction. J Biol Chem 270:119–127

    Article  PubMed  CAS  Google Scholar 

  26. Simbulan-Rosenthal C, Rosenthal D, Ding R, Jackman J, Smulson M (1996) Depletion of nuclear poly(ADP-ribose) polymerase by antisense RNA expression: influence on genomic stability, chromatin organization, and DNA repair/replication. Prog Nucleic Acids Res Mol Biol 55:135–156

    Article  CAS  Google Scholar 

  27. Simbulan-Rosenthal C, Rosenthal DS, Iyer S, Yoshihara K, Smulson ME (1999) Requirement for PARP and poly(ADP-ribosyl)ation in apoptosis and DNA replication. Mol Cell Biochem 193:137–148

    Article  PubMed  CAS  Google Scholar 

  28. Wang ZQ, Auer B, Stingl L, Berghammer H, Haidacher D, Schweiger M, Wagner EF (1995) Mice lacking ADPRT and poly(ADP-ribosyl)ation develop normally but are susceptible to skin disease. Genes Dev 9:509–520

    Article  PubMed  CAS  Google Scholar 

  29. de Murcia J, Niedergang C, Trucco C, Ricoul M, Dutrillaux B, Mark M, Oliver FJ, Masson M, Dierich A, Le Meur M, Walztinger C, Chambon P, de Murcia G (1997) Requirement of poly(ADP-ribose)polymerase in recovery from DNA damage in mice and in cells. Proc Natl Acad Sci USA 94:7303–7307

    Article  PubMed  Google Scholar 

  30. Masutani M, Suzuki H, Kamada N, Watanabe M, Ueda O, Nozaki T, Jishage K, Watanabe T, Sugimoto T, Nakagama H, Ochiya T, Sugimura T (1999) Poly(ADP-ribose)polymerase gene disruption conferred mice resistant to streptozotocin-induced diabetes. Proc Natl Acad Sci USA 96:2301–2304

    Article  PubMed  CAS  Google Scholar 

  31. Trucco C, Oliver FJ, de Murcia G, Menissier-de Murcia J (1998) DNA repair defect in poly(ADP-ribose)polymerase-deficient cell lines. Nucleic Acids Res 26:2644–2649

    Article  PubMed  CAS  Google Scholar 

  32. Simbulan-Rosenthal CM, Ly DH, Rosenthal DS, Konopka G, Luo R, Wang ZQ, Schultz PG, Smulson ME (2000) Misregulation of gene expression in primary fibroblasts lacking poly(ADP-ribose) polymerase. Proc Natl Acad Sci USA 97:11274–11279

    Article  PubMed  CAS  Google Scholar 

  33. Ménissier-de Murcia J, Ricoul M, Tartier L, Niedergang C, Huber A, Dantzer F, Schreiber V, Amé J, Dierich A, LeMeur M, Sabatier L, Chambon P, de Murcia G (2003) Functional interaction between PARP-1 and PARP-2 in chromosome stability and embryonic development in mouse. EMBO J 22:2255–2263

    Article  PubMed  Google Scholar 

  34. Hassa P, Hottiger M (2002) The functional role of poly(ADP-ribose)polymerase 1 as novel coactivator of NF-kappaB in inflammatory disorders. Cell Mol Life Sci 59:1534–1553

    Article  PubMed  CAS  Google Scholar 

  35. Koh D, Dawson T, Dawson V (2005) Mediation of cell death by poly(ADP-ribose) polymerase-1. Pharmacol Res 52:5–14

    Article  PubMed  CAS  Google Scholar 

  36. Strosznajder R, Czubowicz K, Jesko H, Strosznajder J (2010) Poly(ADP-ribose) metabolism in brain and its role in ischemia pathology. Mol Neurobiol 41:187–196

    Article  PubMed  CAS  Google Scholar 

  37. Li X, Klaus J, Zhang J, Xu Z, Kibler K, Andrabi S, Rao K, Yang Z, Dawson T, Dawson V, Koehler R (2010) Contributions of poly(ADP-ribose) polymerase-1 and -2 to nuclear translocation of apoptosis-inducing factor and injury from focal cerebral ischemia. J Neurochem 113:1012–1022

    Article  PubMed  CAS  Google Scholar 

  38. Farmer H, McCabe N, Lord C, Tutt A, Johnson D, Richardson T, Santarosa M, Dillon K, Hickson I, Knights C, Martin N, Jackson S, Smith G, Ashworth A (2005) Targeting the DNA repair defect in BRCA mutant cells as a therapeutic strategy. Nature 434:917–921

    Article  PubMed  CAS  Google Scholar 

  39. Bryant HE, Schultz N, Thomas HD, Parker KM, Flower D, Lopez E, Kyle S, Meuth M, Curtin NJ, Helleday T (2007) Specific killing of BRCA2-deficient tumours with inhibitors of poly(ADP-ribose) polymerase. Nature 447:346

    Article  CAS  Google Scholar 

  40. Fong P, Boss D, Yap T, Tutt A, Wu P, Mergui-Roelvink M, Mortimer P, Swaisland H, Lau A, O’Connor M, Ashworth A, Carmichael J, Kaye S, Schellens J, de Bono J (2009) Inhibition of poly(ADP-ribose) polymerase in tumors from BRCA mutation carriers. N Engl J Med 361:123–134

    Article  PubMed  CAS  Google Scholar 

  41. Mandir AS, Przedborski S, Jackson-Lewis V, Wang ZQ, Simbulan-Rosenthal CM, Smulson ME, Hoffman BE, Guastella DB, Dawson VL, Dawson TM (1999) Poly(ADP-ribose) polymerase activation mediates 1-methyl-4-phenyl-1, 2,3,6-tetrahydropyridine (MPTP)-induced parkinsonism. Proc Natl Acad Sci USA 96:5774–5779

    Article  PubMed  CAS  Google Scholar 

  42. Mendes-Pereira AM, Martin SA, Brough R, McCarthy A, Taylor JR, Kim JS, Waldman T, Lord CJ, Ashworth A (2009) Synthetic lethal targeting of PTEN mutant cells with PARP inhibitors. EMBO Mol Med 1:315–322

    Article  PubMed  CAS  Google Scholar 

  43. Drew Y, Plummer R (2010) The emerging potential of poly(ADP-ribose) polymerase inhibitors in the treatment of breast cancer. Curr Opin Obstet Gynecol 22:67–71

    Article  PubMed  Google Scholar 

  44. Wong M, Kanai Y, Miwa M, Bustin M, Smulson M (1983) Immunological evidence for the in vivo occurrence of a crosslinked complex of poly(ADP-ribosylated) histone H1. Proc Natl Acad Sci USA 80:205–209

    Article  PubMed  CAS  Google Scholar 

  45. Malik N, Smulson ME (1984) A Relationship between nuclear poly(ADP-rib) and acetylation post-translational modifications: I Nucleosome studies. Biochemistry 23:3721–3725

    Article  PubMed  CAS  Google Scholar 

  46. Althaus FR, Hofferer L, Kleckzkowska HE, Malanga M, Naegeli H, Penzeter PL, Realini CA (1994) Histone shuttling by poly ADP-ribosylation. Mol Cell Biochem 138:53–60

    Article  PubMed  CAS  Google Scholar 

  47. Kasid UN, Halligan B, Liu LF, Dritschilo A, Smulson M (1989) Poly(ADP-ribose)-mediated post-translational modification of chromatin-associated human topoisomerase I. Inhibitory effects on catalytic activity. J Biol Chem 264:18687–18692

    PubMed  CAS  Google Scholar 

  48. Darby M, Schmitt B, Jongstra B, Vosberg H (1985) Inhibition of calf thy-mus type II DNA topoisomerase by poly(ADP-ribosylation). EMBO J 4:2129–2134

    PubMed  CAS  Google Scholar 

  49. Park S, Leung C, Cheng Y (2008) ATP modulates poly(ADP-ribose) polymerase-1-facilitated topoisomerase I-linked DNA religation in the presence of camptothecin. Mol Pharmacol 73:1829–1837

    Article  PubMed  CAS  Google Scholar 

  50. Eki T, Hurwitz J (1991) Influence of poly(ADP-ribose) polymerase on the enzymatic synthesis of SV40 DNA. J Biol Chem 266:3087–3100

    PubMed  CAS  Google Scholar 

  51. Hassa P, Hottiger M (1999) A role of poly (ADP-ribose) polymerase in NF-kappaB transcriptional activation. Biol Chem 380:953–959

    Article  PubMed  CAS  Google Scholar 

  52. Simbulan-Rosenthal C, Rosenthal D, Luo RB, Samara R, Jung M, Dritschilo A, Spoonde A, Smulson M (2001) Poly(ADP-ribosyl)ation of p53 in vitro and in vivo modulates binding to its DNA consensus sequence. Neoplasia 3:179–188

    Article  PubMed  CAS  Google Scholar 

  53. Malanga M, Pleschke J, Kleczkowska H, Althaus F (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 

  54. Ghosh U, Das N, Bhattacharyya N (2007) Inhibition of telomerase activity by reduction of poly(ADP-ribosyl)ation of TERT and TEP1/TP1 expression in HeLa cells with knocked down PARP-1 gene. Mutat Res 615:66–74

    Article  PubMed  CAS  Google Scholar 

  55. Wollmann Y, Schmidt U, Wieland G, Zipfel P, Saluz H, Hänel F (2007) The DNA topoisomerase IIbeta binding protein 1 (TopBP1) interacts with poly (ADP-ribose) polymerase (PARP-1). J Cell Biochem 102:171–182

    Article  PubMed  CAS  Google Scholar 

  56. Caiafa P, Guastafierro T, Zampieri M (2009) Epigenetics: poly(ADP-ribosyl)ation of PARP-1 regulates genomic methylation patterns. FASEB J 23:672–678

    Article  PubMed  CAS  Google Scholar 

  57. Monaco L, Kolthur-Seetharam U, Loury R, Murcia J, de Murcia G, Sassone-Corsi P (2005) Inhibition of Aurora-B kinase activity by poly(ADP-ribosyl)ation in response to DNA damage. Proc Natl Acad Sci USA 102:14244–14248

    Article  PubMed  CAS  Google Scholar 

  58. Huang D, Yang C, Wang Y, Liao Y, Huang K (2009) PARP-1 suppresses adiponectin expression through poly(ADP-ribsosyl)ation of PPAR gamma in cardiac fibroblasts. Cardiovasc Res 81:98–107

    Article  PubMed  CAS  Google Scholar 

  59. Valdor R, Schreiber V, Saenz L, Martinez T, Munoz-Suano A, Dominguez-Villar M, Ramirez R, Parilla P, Aguado E, Garcia-Cozar F, Yelamos J (2008) Reguation of NFAT by PARP activity in T cells. Mol Immunol 45:1863–1871

    Article  PubMed  CAS  Google Scholar 

  60. Poirier GG, de Murcia G, Jongstra-Bilen J, Niedergang C, Mandel P (1982) Poly(ADP-ribosyl)ation of polynucleosomes causes relaxation of chromatin structure. Proc Natl Acad Sci USA 79:3423–3427

    Article  PubMed  CAS  Google Scholar 

  61. Butt TR, Smulson ME (1980) The relationship between NAD concentration and in vitro synthesis of poly (adenosine dephosphate-ribose) on purified nucleosomes. Biochemistry 19:5235–5243

    Article  PubMed  CAS  Google Scholar 

  62. Kim M, Mauro S, Gévry N, Lis J, Kraus W (2004) NAD+−dependent modulation of chromatin structure and transcription by nucleosome binding properties of PARP-1. Cell 119:735–736

    Article  Google Scholar 

  63. Wacker D, Ruhl D, Balagamwala E, Hope K, Zhang T, Kraus W (2007) The DNA binding and catalytic domains of poly(ADP-ribose) polymerase 1 cooperate in the regulation of chromatin structure and transcription. Mol Cell Biol 27:7475–7485

    Article  PubMed  CAS  Google Scholar 

  64. Tulin A, Spradling A (2003) Chromatin loosening by poly(ADP)-ribose polymerase (PARP) at Drosophila puff loci. Science 299:560–562

    Article  PubMed  CAS  Google Scholar 

  65. Kraus W, Lis J (2003) PARP goes transcription. Cell 113:677–683

    Article  PubMed  CAS  Google Scholar 

  66. Rouleau M, Aubin R, Poirier G (2004) Poly(ADP-ribosyl)ated chromatin domains: access granted. J Cell Sci 117:815–825

    Article  PubMed  CAS  Google Scholar 

  67. Dantzer F, Nasheuer HP, Vonesch JL, de Murcia G, Menissier-de Murcia J (1998) Functional association of poly(ADP-ribose) polymerase with DNA polymerase alpha-primase complex: a link between DNA strand break detection and DNA replication. Nucleic Acids Res 26:1891–1898

    Article  PubMed  CAS  Google Scholar 

  68. Masson M, Niedergang C, Schreiber V, Muller S, Menissier-de Murcia J, de Murcia G (1998) XRCC1 is specifically associated with poly(ADP-ribose) polymerase and negatively regulates its activity following DNA damage. Mol Cell Biol 18:3563–3571

    PubMed  CAS  Google Scholar 

  69. El-Khamisy S, Masutani M, Suzuki H, Caldecott K (2003) A requirement for PARP-1 for the assembly or stability of XRCC1 nuclear foci at sites of oxidative DNA damage. Nucleic Acids Res 31:5526–5533

    Article  PubMed  CAS  Google Scholar 

  70. Kraus W (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 

  71. Haince J, McDonald D, Rodrigue A, Déry U, Masson J, Hendzel M, Poirier G (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 

  72. Simbulan C, Suzuki M, Izuta S, Sakurai T, Savoysky E, Kojima K, Miyahara K, Shizuta Y, Yoshida S (1993) Poly (ADP-ribose) polymerase stimulates DNA polymerase alpha. J Biol Chem 268:93–99

    PubMed  CAS  Google Scholar 

  73. Ferro AM, Higgins NP, Olivera BM (1983) Poly (ADP-ribosylation) of a DNA topoisomerase. J Biol Chem 258:6000–6003

    PubMed  CAS  Google Scholar 

  74. Simbulan-Rosenthal C, Rosenthal D, Boulares AH, Hickey R, Malkas L, Coll JM, Smulson M (1998) Regulation of the expression or recruitment of components of the DNA synthesome by poly(ADP-ribose) polymerase. Biochemistry 37:9363–9370

    Article  PubMed  CAS  Google Scholar 

  75. Cazzalini O, Donà F, Savio M, Tillhon M, Maccario C, Perucca P, Stivala L, Scovass IA, Prosperi E (2010) p21(CDKN1A) participates in base excision repair by regulating the activity of poly(ADP-ribose) polymerase-1. DNA Repair (Amst) 9:627–635

    Article  CAS  Google Scholar 

  76. Althaus F, Kleczkowska H, Malanga M, Müntener C, Pleschke J, Ebner M, Auer B (1999) Poly ADP-ribosylation: a DNA break signal mechanism. Mol Cell Biochem 193:5–11

    Article  PubMed  CAS  Google Scholar 

  77. Lévy N, Oehlmann M, Delalande F, Nasheuer H, Van Dorsselaer A, Schreiber V, de Murcia G, Ménissier-de Murcia J, Maiorano D, Bresson A (2009) XRCC1 interacts with the p58 subunit of DNA Pol alpha-primase and may coordinate DNA repair and replication during S phase. Nucleic Acids Res 37:3177–3188

    Article  PubMed  Google Scholar 

  78. Yan S, Michael W (2009) TopBP1 and DNA polymerase alpha-mediated recruitment of the 9-1-1 complex to stalled replication forks: implications for a replication restart-based mechanism for ATR checkpoint activation. Cell Cycle 8:2877–2884

    Article  PubMed  CAS  Google Scholar 

  79. Coll J, Hickey R, Cronkey E, Jiang H, Schnaper L, Lee M, Uitto L, Syvaoja JE, Malkas L (1997) Mapping specific protein-protein interactions within the core component of the breast cell DNA synthesome. Oncol Res 9:629–639

    PubMed  CAS  Google Scholar 

  80. Vertino P, Sekowski J, Coll J, Applegren N, Han S, Hickey R, Malkas L (2002) DNMT1 is a component of a multiprotein DNA replication complex. Cell Cycle 1:416–423

    Article  PubMed  CAS  Google Scholar 

  81. Applegren N, Hickey R, Kleinschmidt A, Zhou Q, Coll J, Wills P, Swaby R, Wei Y, Quan J, Lee M, Malkas L (1995) Further characterization of the human cell multiprotein DNA replication complex. J Cell Biochem 59:91–107

    Article  PubMed  CAS  Google Scholar 

  82. Wu Y, Hickey R, Lawlor K, Wills P, Yu F, Ozer H, Starr R, Quan J, Lee M, Malkas L (1994) A 17S multiprotein form of murine cell DNA polymerase mediates polyomavirus DNA replication in vitro. J Cell Biochem 54:32–46

    Article  PubMed  CAS  Google Scholar 

  83. Tom T, Malkas L, Hickey R (1996) Identification of multiprotein compexes containing DNA replication factors by native immunoblotting of HeLa cell protein preparations with T-antigen-dependent SV40 DNA replication activity. J Cell Biochem 63:259

    Article  PubMed  CAS  Google Scholar 

  84. Yoshihara K, Itaya A, Tanaka Y, Ohashi Y, Ito K, Teraoka H, Tsukada K, Matsukage A, Kamiya T (1985) Inhibition of DNA polymerase a, DNA polymerase b, terminal nucleotidyltransferase and DNA ligase II by poly (ADP-ribosyl)ation reaction in vitro. Biochem Biophys Res Commun 128:61–67

    Article  PubMed  CAS  Google Scholar 

  85. Dantzer F, Nasheuer H, Vonesch J, de Murcia G, Ménissier-de Murcia J (1998) Functional association of poly(ADP-ribose) polymerase with DNA polymerase alpha-primase complex: a link between DNA strand break detection and DNA replication. Nucleic Acids Res 15:1891–1898

    Article  Google Scholar 

  86. Simbulan-Rosenthal C, Rosenthal D, Luo R, Samara R, Espinoza LA, Hassa P, Hottiger M, Smulson M (2003) PARP-1 binds E2F-1 independently of its DNA binding and catalytic domains, and acts as a novel coactivator of E2F-1-mediated transcription during re-entry of quiescent cells into S phase. Oncogene 22:8460–8471

    Article  PubMed  CAS  Google Scholar 

  87. Isabelle M, Moreel X, Gagné JP, Rouleau M, Ethier C, Gagné P, Hendzel M, Poirier G (2010) Research investigation of PARP-1, PARP-2, and PARG interactomes by affinity-purification mass spectrometry. Proteome Sci 8:22–33

    Article  PubMed  Google Scholar 

Download references

Acknowledgments

The authors would like to thank Drs. Linda Malkas and Bob Hickey and their lab for development of the purification protocols for the DNA synthesome and for their invaluable advice during the purification process and later characterization of the replicative complex.

Author information

Authors and Affiliations

  1. Department of Biochemistry and Molecular & Cellular Biology, Georgetown University School of Medicine, Washington, DC, USA

    Cynthia M. Simbulan-Rosenthal, Dean S. Rosenthal & Mark E. Smulson

Authors
  1. Cynthia M. Simbulan-Rosenthal
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Dean S. Rosenthal
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Mark E. Smulson
    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

Simbulan-Rosenthal, C.M., Rosenthal, D.S., Smulson, M.E. (2011). Purification and Characterization of Poly(ADP-Ribosyl)ated DNA Replication/Repair Complexes. 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_11

Download citation

  • DOI: https://doi.org/10.1007/978-1-61779-270-0_11

  • 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