3174 Nucleic Acids Research, 2011, Vol. 39, No. 8 Figure 7. Model for BER and the inﬂuence of PARP. The MPG glycosylase is recognizing N-methylated purines, likely through scanning the DNA for base lesions. Once a lesion is recognized, MPG excises the damaged base and the APE1 endonuclease cleaves the newly formed AP-site into a SSB intermediate. If this intermediate is uncoupled from the repair process before repair is ﬁnished, PARP1 may recognize and bind to the SSB intermediate, which overall might slow down the BER process. In the event that PARP1 is inhibited it will be trapped on the SSB and prevent ligation. However, PARP1 is not required for accurate repair if the repair pathway remains intact. In the event of the BER complex being unable to accurately ligate, long patch repair is thought to take over. Our model does not exclude an active role for PARP1 in BER by inﬂuencing DNA damage-induced chromatin remodelling. aqueous solutions with a half life of 17 min at 37 C (29), so only 0.3% of the original DMS would remain in the cells, even if no DMS was removed by the washing step. Our conclusion is that it takes time for the BER machin- ery to identify a fraction of the damaged bases to make the incisions. ACKNOWLEDGEMENTS We wish to thank Prof. Keith Caldecott for providing the EM9-V and EM9-XH cell lines, Dr Grigory Dianov and Dr Jason Parsons for discussions and the anonymous re- viewers for their suggestions. FUNDING The Swedish Cancer Society; the Swedish Children’s Cancer Foundation the Swedish Research Council; the Swedish Pain Relief Foundation and the Medical Research Council. Funding for open access charge: The Swedish Research Council. Conﬂict of interest statement. None declared. REFERENCES 1. Lindahl,T. (1993) Instability and decay of the primary structure of DNA. Nature, 362, 709–715. 2. Satoh,M.S. and Lindahl,T. (1992) Role of poly(ADP-ribose) formation in DNA repair. Nature, 356, 356–358. 3. El-Khamisy,S.F., Masutani,M., Suzuki,H. and Caldecott,K.W. (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. 4. Dantzer,F., de La Rubia,G., Menissier-De Murcia,J., Hostomsky,Z., de Murcia,G. and Schreiber,V. (2000) Base excision repair is impaired in mammalian cells lacking Poly(ADP-ribose) polymerase-1. Biochemistry, 39, 7559–7569. 5. Leppard,J.B., Dong,Z., Mackey,Z.B. and Tomkinson,A.E. (2003) Physical and functional interaction between DNA ligase IIIalpha and poly(ADP-Ribose) polymerase 1 in DNA single-strand break repair. Mol. Cell. Biol., 23, 5919–5927. 6. Prasad,R., Lavrik,O.I., Kim,S.J., Kedar,P., Yang,X.P., Vande Berg,B.J. and Wilson,S.H. (2001) DNA polymerase beta-mediated long patch base excision repair. Poly(ADP-ribose)polymerase-1 stimulates strand displacement DNA synthesis. J. Biol. Chem., 276, 32411–32414. 7. Frouin,I., Maga,G., Denegri,M., Riva,F., Savio,M., Spadari,S., Prosperi,E. and Scovassi,A.I. (2003) Human proliferating cell nuclear antigen, poly(ADP-ribose) polymerase-1, and p21waf1/ cip1. A dynamic exchange of partners. J. Biol. Chem., 278, 39265–39268. 8. Godon,C., Cordelieres,F.P., Biard,D., Giocanti,N., Megnin- Chanet,F., Hall,J. and Favaudon,V. (2008) PARP inhibition versus PARP-1 silencing: different outcomes in terms of single-strand break repair and radiation susceptibility. Nucleic Acids Res., 36, 4454–4464. 9. Loizou,J.I., El-Khamisy,S.F., Zlatanou,A., Moore,D.J., Chan,D.W., Qin,J., Sarno,S., Meggio,F., Pinna,L.A. and Caldecott,K.W. (2004) The protein kinase CK2 facilitates repair of chromosomal DNA single-strand breaks. Cell, 117, 17–28. 10. Hjertvik,M., Erixon,K. and Ahnstrom,G. (1998) Repair of DNA damage in mammalian cells after treatment with UV and dimethyl sulphate: discrimination between nucleotide and base excision repair by their temperature dependence. Mutat. Res., 407, 87–96. 11. Loseva,O., Jemth,A.S., Bryant,H.E., Schuler,H., Lehtio,L., Karlberg,T. and Helleday,T. PARP-3 is a mono-ADP-ribosylase that activates PARP-1 in the absence of DNA. J. Biol. Chem., 285, 8054–8060. 12. Erixon,K. and Ahnstrom,G. (1979) Single-strand breaks in DNA during repair of UV-induced damage in normal human and xeroderma pigmentosum cells as determined by alkaline DNA unwinding and hydroxylapatite chromatography: effects of hydroxyurea, 5-ﬂuorodeoxyuridine and 1-beta-D-arabinofuranosylcytosine on the kinetics of repair. Mutat. Res., 59, 257–271. 13. Ahnstro¨ m,G. and Erixon,K. (1981) Measurement of Strand Breaks by Alkaline Denaturation and Hydroxylapatite Chromatography. Marcel Dekker, New York and Basel. 14. Rydberg,B. (1975) The rate of strand separation in alkali of DNA of irradiated mammalian cells. Radiat. Res., 61, 274–287. 15. Fisher,A.E., Hochegger,H., Takeda,S. and Caldecott,K.W. (2007) Poly(ADP-ribose) polymerase 1 accelerates single-strand break repair in concert with poly(ADP-ribose) glycohydrolase. Mol. Cell. Biol., 27, 5597–5605. 16. Whitehouse,C.J., Taylor,R.M., Thistlethwaite,A., Zhang,H., Karimi-Busheri,F., Lasko,D.D., Weinfeld,M. and Caldecott,K.W. (2001) XRCC1 stimulates human polynucleotide kinase activity at damaged DNA termini and accelerates DNA single-strand break repair. Cell, 104, 107–117. 17. Johansson,F., Lagerqvist,A., Erixon,K. and Jenssen,D. (2004) A method to monitor replication fork progression in mammalian cells: nucleotide excision repair enhances and homologous recombination delays elongation along damaged DNA. Nucleic Acids Res., 32, e157.