Crosslinking of the NER damage recognition proteins XPC-HR23B, XPA and RPA to photoreactive probes that mimic DNA damages

Biochimica et Biophysica Acta - General Subjects

Volumn 1770, Issue 5, 2007, Pages 781-789

  Maltseva, Ekaterina A ^a   Rechkunova, Nadejda I ^a   Gillet, Ludovic C ^b   Petruseva, Irina O ^a   Schärer, Orlando D ^b,c   Lavrik, Olga I ^a  

^a INSTITUTE OF CHEMICAL BIOLOGY AND FUNDAMENTAL MEDICINE   (Russian Federation)

^b UNIVERSITY OF ZURICH   (Switzerland)

^c STONY BROOK UNIVERSITY   (United States)

Author keywords

Nucleotide excision repair; Photoaffinity modification; RPA; XPA; XPC HR23B

Indexed keywords

DEOXYCYTIDINE TRIPHOSPHATE; DEOXYRIBONUCLEOTIDE; DEOXYURIDINE TRIPHOSPHATE PYROPHOSPHATASE; DNA DIRECTED DNA POLYMERASE BETA; DOUBLE STRANDED DNA; MAGNESIUM ION; PLASMID DNA; PROTEIN SUBUNIT; PROTEIN XPC HR23B; SINGLE STRANDED DNA; UNCLASSIFIED DRUG; XERODERMA PIGMENTOSUM GROUP A PROTEIN; XERODERMA PIGMENTOSUM GROUP C PROTEIN;

ARTICLE; COMPLEX FORMATION; CONTROLLED STUDY; DNA CROSS LINKING; DNA DAMAGE; DNA PROBE; EXCISION REPAIR; HELA CELL; HUMAN; HUMAN CELL; MOLECULAR MIMICRY; NONHUMAN; PHOTOAFFINITY LABELING; PHOTOREACTIVITY; PLASMID; PRIORITY JOURNAL; PROTEIN CROSS LINKING; PROTEIN DNA INTERACTION; PROTEIN MODIFICATION;

ANIMALS; BIOLOGICAL ASSAY; CROSS-LINKING REAGENTS; DNA ADDUCTS; DNA DAMAGE; DNA PROBES; DNA-BINDING PROTEINS; ESCHERICHIA COLI; HELA CELLS; HISTIDINE; HUMANS; RECOMBINANT PROTEINS; REPLICATION PROTEIN A; SPODOPTERA; ULTRAVIOLET RAYS; XERODERMA PIGMENTOSUM GROUP A PROTEIN;

MAMMALIA;

EID: 33947113402     PISSN: 03044165     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bbagen.2007.01.007     Document Type: Article

References (52)

1. Wood R.D. DNA repair in eukaryotes. Annu. Rev. Biochem. 65 (1996) 135-167
2. Sancar A. DNA excision repair. Annu. Rev. Biochem. 65 (1996) 43-81
3. Schärer O.D. Chemistry and biology of DNA repair. Angew. Chem., Int. Ed. Engl. 42 (2003) 2946-2974
4. Gillet L.C.J., and Schärer O.D. Molecular mechanisms of mammalian global genome nucleotide excision repair. Chem. Rev. 106 (2006) 253-276
5. Bohr V.A., Smith C.A., Okumoto D.S., and Hanawalt P.C. DNA repair in an active gene: removal of pyrimidine dimers from the DHFR gene of CHO cells is much more efficient than in the genome overall. Cell 40 (1985) 359-369
6. Buschta-Hedayat N., Buterin T., Hess M.T., Missura M., and Naegeli H. Recognition of nonhybridizing base pairs during nucleotide excision repair of DNA. Proc. Natl. Acad. Sci. U. S. A. 96 (1999) 6090-6095
7. Sugasawa K., Okamoto T., Shimizu Y., Masutani C., Iwai S., and Hanaoka F. A multistep damage recognition mechanism for global genomic nucleotide excision repair. Genes Dev. 15 (2001) 507-521
8. Sugasawa K., Ng J.M., Masutani C., Iwai S., van der Spek P.J., Eker A.P., Hanaoka F., Bootsma D., and Hoeijmakers J.H. Xeroderma pigmentosum group C protein complex is the initiator of global genome nucleotide excision repair. Mol. Cell 2 (1998) 223-232
9. Volker M., Mone M.J., Karmakar P., van Hoffen A., Schul W., Vermeulen W., Hoeijmakers J.H., van Driel R., van Zeeland A.A., and Mullenders L.H. Sequential assembly of the nucleotide excision repair factors in vivo. Mol. Cell 8 (2001) 213-224
10. Nishi R., Okuda Y., Watanabe E., Mori T., Iwai S., Masutani C., Sugasawa K., and Hanaoka F. Centrin 2 stimulates nucleotide excision repair by interacting with xeroderma pigmentosum group C protein. Mol. Cell. Biol. 25 (2005) 5664
11. Gong F., Kwon Y., and Smerdon M.J. Nucleotide excision repair in chromatin and the right of entry. DNA Rep. 4 (2005) 884-896
12. Reed S.H. Nucleotide excision repair in chromatin: the shape of things to come. DNA Rep. 4 (2005) 909-918
13. Yokoi M., Masutani C., Maekawa T., Sugasawa K., Ohkuma Y., and Hanaoka F. The xeroderma pigmentosum group C protein complex XPC-HR23B plays an important role in the recruitment of transcription factor IIH to damaged DNA. J. Biol. Chem. 275 (2000) 9870-9875
14. Evans E., Moggs J.G., Hwang J.R., Egly J.M., and Wood R.D. Mechanism of open complex and dual incision formation by human nucleotide excision repair factors. EMBO J. 16 (1997) 6559-6573
15. Tapias A., Auriol J., Forget D., Enzlin J.H., Scharer O.D., Coin F., Coulombe B., and Egly J.M. Ordered conformational changes in damaged DNA induced by nucleotide excision repair factors. J. Biol. Chem. 279 (2004) 19074-19083
16. Araujo S.J., Nigg E.A., and Wood R.D. Strong functional interactions of TFIIH with XPC and XPG in human DNA nucleotide excision repair, without a preassembled repairosome. Mol. Cell. Biol. 21 (2001) 2281-2291
17. Reardon J.T., and Sancar A. Recognition and repair of the cyclobutane thymine dimer, a major cause of skin cancers, by the human excision nuclease. Genes Dev. 17 (2003) 2539-2551
18. Dellavecchia M.J., Croteau D.L., Skorvaga M., Dezhurov S.V., Lavrik O.I., and Van Houten B. Analyzing the handoff of DNA from UvrA to UvrB utilizing DNA-protein photoaffinity labeling. J. Biol. Chem. 279 (2004) 45245-45256
19. Dezhurov S.V., Khodyreva S.N., Plekhanova E.S., and Lavrik O.I. A new highly efficient photoreactive analogue of dCTP. Synthesis, characterization, and application in photoaffinity modification of DNA binding proteins. Bioconjug. Chem. 16 (2005) 215-222
20. Kolpashchikov D.M., Zakharenko A.L., Dezhurov S.V., Rechkunova N.I., Khodyreva S.N., Degtiarev S.Kh., Litvak V.V., and Lavrik O.I. New reagents for affinity modification of biopolymers. Photoaffinity modification of Tte-DNA polymerase. Bioorg. Khim. 25 (1999) 129-136
21. Henricksen L.A., Umbricht C.B., and Wold M.S. Recombinant replication protein A: expression, complex formation, and functional characterization. J. Biol. Chem. 269 (1994) 11121-11132
22. Batty D., Rapic'-Otrin V., Levine A.S., and Wood R.D. Stable binding of human XPC complex to irradiated DNA confers strong discrimination for damaged sites. J. Mol. Biol. 300 (2000) 275-290
23. Beard W.A., and Wilson S.H. Purification and domain-mapping of mammalian DNA polymerase β. Methods Enzymol. 262 (1995) 98-107
24. Sambrook J., Fritsch E.F., and Maniatis T. Molecular Cloning: A Laboratory manual. 2nd Edn (1989)
25. Gillet L.C.J., Alzeer J., and Schärer O.D. Single-site specific incorporation of N-(deoxyguanosin-8-yl)-2-acetylaminofluorene (dG-AAF) into oligonucleotides using modified 'ultra-mild' DNA synthesis. Nucleic Acids Res. 33 (2005) 1961-1969
26. Shivji M.K., Moggs J.G., Kuraoka I., and Wood R.D. Dual-incision assays for nucleotide excision repair using DNA with a lesion at a specific site. Methods Mol. Biol. 113 (1999) 373-392
27. Laemmli U.K. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227 (1970) 680-685
28. Heflich R.H., and Neft R.E. Genetic toxicity of 2-acetylaminofluorene, 2-aminofluorene and some of their metabolites and model metabolites. Mutat. Res. 318 (1994) 73-174
29. Buterin T., Meyer C., Giese B., and Naegeli H. DNA quality control by conformational readout on the undamaged strand of the double helix. Chem. Biol. 12 (2005) 913-922
30. Khodyreva S.N., and Lavrik O.I. Photoaffinity labeling technique for studying DNA replication and DNA repair. Curr. Med. Chem. 12 (2005) 641-655
31. Hey T., Lipps G., and Krauss G. Binding of XPA and RPA to damaged DNA investigated by fluorescence anisotropy. Biochemistry 40 (2001) 2901-2910
32. Lao Y., Lee C.G., and Wold M.S. Replication protein A interactions with DNA: 2. Characterization of double-stranded DNA-binding/helix-destabilization activities and the role of the zinc-finger domain in DNA interactions. Biochemistry 38 (1999) 3974-3984
33. Georgaki A., Strack B., Podust V., and Hubscher U. DNA unwinding activity of replication protein A. FEBS Lett. 308 (1992) 240-244
34. Wakasugi M., and Sancar A. Order of assembly of human DNA repair excision nuclease. J. Biol. Chem. 274 (1999) 18759-18768
35. Hey T., Lipps G., Sugasawa K., Iwai S., Hanaoka F., and Krauss G. The XPC-HR23B complex displays high affinity and specificity for damaged DNA in a true-equilibrium fluorescence assay. Biochemistry 41 (2002) 6583-6587
36. Rademakers S., Volker M., Hoogstraten D., Nigg A.L., Mone M.J., Van Zeeland A.A., Hoeijmakers J.H., Houtsmuller A.B., and Vermeulen W. Xeroderma pigmentosum group A protein loads as a separate factor onto DNA lesions. Mol. Cell. Biol. 23 (2003) 5755-5767
37. Camenisch U., Dip R., Schumacher S.B., Schuler B., and Naegeli H. Recognition of helical kinks by xeroderma pigmentosum group A protein triggers DNA excision repair. Nat. Struct. Mol. Biol. 13 (2006) 278-284
38. Gunz D., Hess M.T., and Naegeli H. Recognition of DNA adducts by human nucleotide excision repair. Evidence for a thermodynamic probing mechanism. J. Biol. Chem. 271 (1996) 25089-25098
39. Lee J.H., Park C.J., Shin J.S., Ikegami T., Akutsu H., and Choi B.S. NMR structure of the DNA decamer duplex containing double T*G mismatches of cis-syn cyclobutane pyrimidine dimer: implications for DNA damage recognition by the XPC-hHR23B complex. Nucleic Acids Res. 32 (2004) 2474-2481
40. Jones C.J., and Wood R.D. Preferential binding of the xeroderma pigmentosum group A complementing protein to damaged DNA. Biochemistry 32 (1993) 12096-12104
41. He Z., Henricksen L.A., Wold M.S., and Ingles C.J. RPA involvement in the damage-recognition and incision steps of nucleotide excision repair. Nature 374 (1995) 566-569
42. Maltseva E.A., Rechkunova N.I., Petruseva I.O., Silnikov V.N., Vermeulen W., and Lavrik O.I. Interaction of nucleotide excision repair factors RPA and XPA with DNA containing bulky photoreactive groups imitating damages. Biochemistry (Moscow) 71 (2006) 270-278
43. Mu D., Wakasugi M., Hsu D.S., and Sancar A. Characterization of reaction intermediates of human excision-repair nuclease. J. Biol. Chem. 272 (1997) 28971-28979
44. Satokata I., Iwai K., Matsuda T., Okada Y., and Tanaka K. Genomic characterization of the human DNA excision repair-controlling gene XPAC. Gene 136 (1993) 345-348
45. Koberle B., Roginskaya V., and Wood R.D. XPA protein as a limiting factor for nucleotide excision repair and UV sensitivity in human cells. DNA Rep. 5 (2006) 641-648
46. Park C.J., and Choi B.S. The protein shuffle. Sequential interactions among components of the human nucleotide excision repair pathway. FEBS J. 273 (2006) 1600-1608
47. Clugston C.K., McLaughlin K., Kenny M.K., and Brown R. Binding of human single-stranded DNA binding protein to DNA damaged by the anticancer drug cis-diamminedichloroplatinum (II). Cancer Res. 52 (1992) 6375-6379
48. Burns J.L., Guzder S.N., Sung P., Prakash S., and Prakash L. An affinity of human replication protein A for ultraviolet-damaged DNA. J. Biol. Chem. 271 (1996) 11607-11610
49. Reardon J.T., and Sancar A. Molecular anatomy of the human excision nuclease assembled at sites of DNA damage. Mol. Cell. Biol. 22 (2002) 5938-5945
50. Hermanson-Miller I.I., and Turchi J.J. Strand-specific binding of RPA and XPA to damaged duplex DNA. Biochemistry 41 (2002) 2402-2408
51. de Laat W.L., Appeldoorn E., Sugasawa K., Weterings E., Jaspers N.G., and Hoeijmakers J.H. DNA-binding polarity of human replication protein A positions nucleases in nucleotide excision repair. Genes Dev. 12 (1998) 2598-2609
52. Kolpashchikov D.M., Khodyreva S.N., Khlimankov D.Y., Wold M.S., Favre A., and Lavrik O.I. Polarity of human replication protein A binding to DNA. Nucleic Acids Res. 29 (2001) 373-379