Scanning confocal fluorescence microscopy for single molecule analysis of nucleotide excision repair complexes

Nucleic Acids Research

Volumn 30, Issue 21, 2002, Pages 4720-4727

  Segers Nolten, G M J ^a   Wyman, C ^b   Wijgers, N ^b   Vermeulen, W ^b   Lenferink, A T M ^a   Hoeijmakers, J H J ^b   Greve, J ^a   Otto, C ^a  

^a UNIVERSITY OF TWENTE   (Netherlands)

^b ERASMUS MEDICAL CENTER   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

DOUBLE STRANDED DNA; GENE PRODUCT; GREEN FLUORESCENT PROTEIN; UNCLASSIFIED DRUG; XERODERMA PIGMENTOSUM GROUP A PROTEIN;

ARTICLE; COMPLEX FORMATION; CONFOCAL MICROSCOPY; CONTROLLED STUDY; DNA PROTEIN COMPLEX; EXCISION REPAIR; FLUORESCENCE MICROSCOPY; HUMAN; PRIORITY JOURNAL; PROTEIN DNA BINDING; PROTEIN DNA INTERACTION; PROTEIN LOCALIZATION; PROTEIN PURIFICATION; QUANTITATIVE ANALYSIS; VALIDATION PROCESS;

EID: 0036849355     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkf599     Document Type: Article

References (42)

1. Weiss, S. (1999) Fluorescence spectroscopy of single biomolecules. Science, 283, 1676-1683.
2. Ishijima, A. and Yanagida, T. (2001) Single molecule nanobioscience. Trends Biochem. Sci., 26, 438-444.
3. Ishii, Y. and Yanagida, T. (2000) Single molecule detection in life sciences. Single Mol., 1, 5-16.
4. Ha, T. (2001) Single-molecule fluorescence methods for the study of nucleic acids. Curr. Opin. Struct. Biol., 11, 287-292.
5. Weiss, S. (2000) Measuring conformational dynamics of biomolecules by single molecule fluorescence spectroscopy. Nature Struct. Biol., 7, 724-729.
6. Ha, T. (2001) Single-molecule fluorescence resonance energy transfer. Methods, 25, 78-86.
7. Weber, M.A., Stracke, F. and Meixner, A.J. (1999) Dynamics of single molecules observed by confocal imaging and spectroscopy. Cytometry, 36, 217-223.
8. Hansma, H.G., Kim, K.J., Laney, D.E., Garcia, R.A., Argaman, M., Allen, M.J. and Parsons, S.M. (1997) Properties of biomolecules measured from atomic force microscope images: a review. J. Struct. Biol., 119, 99-108.
9. Hansma, H.G. (2001) Surface biology of DNA by atomic force microscopy. Annu. Rev. Phys. Chem., 52, 71-92.
10. Engel, A., Lyubchenko, Y. and Müller, D. (1999) Atomic force microscopy: a powerful tool to observe biomolecules at work. Trends Cell Biol., 9, 77-80.
11. Betzig, E. and Chichester, R.J. (1993) Single molecules observed by near-field scanning optical microscopy. Science, 262, 1422-1425.
12. Meixner, A.J. and Kneppe, H. (1998) Scanning near-field optical microscopy in cell biology and microbiology. Cell. Mol. Biol., 44, 673-688.
13. Peterman, E.J.G., Brasselet, S. and Moerner, W.E. (1999) The fluorescence dynamics of single molecules of green fluorescent protein. J. Phys. Chem., 103A, 10553-10556.
14. Brasselet, S., Peterman, E.J.G., Miyawaki, A. and Moerner, W.E. (2000) Single-molecule fluorescence resonant energy transfer in calcium concentration dependent cameleon. J. Phys. Chem., 104B, 3676-3682.
15. Kubitscheck, U., Kückmann, O., Kues, T. and Peters, R. (2000) Imaging and tracking of single GFP molecules in solution. Biophys. J., 78, 2170-2179.
16. Moerner, W.E., Peterman, E.J.G., Brasselet, S., Kummer, S. and Dickson, R.M. (1999) Optical methods for exploring dynamics of single copies of green fluorescent protein. Cytometry, 36, 232-238.
17. Sugasawa, K., Ng, J., Masutani, C., van der Spek, P.J., Eker, A.P.M., Hanaoka, F., Bootsma, D. and Hoeijmakers, J.H.J. (1998) Xeroderma pigmentosum group C protein complex is the initiator of global genome nucleotide excision repair. Mol. Cell, 2, 223-232.
18. Houtsmuller, A.B., Rademakers, S., Nigg, A.L., Hoogstraten, D., Hoeijmakers, J.H. and Vermeulen, W. (1999) Action of DNA repair endonuclease ERCC1/XPF in living cells. Science, 284, 958-961.
19. de Laat, W.L., Jaspers, N.G.J. and Hoeijmakers, J.H.J. (1999) Molecular mechanism of nucleotide excision repair. Genes Dev., 13, 768-785.
20. Araujo, S.J. and Wood, R.D. (1999) Protein complexes in nucleotide excision repair. Mutat. Res., 435, 23-33.
21. Matsunaga, T., Park, C.H., Bessho, T., Mu, D. and Sancar, A. (1996) Replication protein A confers structure-specific endonuclease activities to the XPF-ERCC1 and XPG subunits of human DNA repair excision nuclease. J. Biol. Chem., 271, 11047-11050.
22. Hey, T., Lipps, G. and Krauss, G. (2001) Binding of XPA and RPA to damaged DNA investigated by fluorescence anisotropy. Biochemistry, 40, 2901-2910.
23. Buschta-Hedayat, N., Buterin, T., Hess, M.T., Missura, M. and Naegeli, H. (1999) Recognition of nonhybridizing base pairs during nucleotide excision repair of DNA. Proc. Natl Acad. Sci. USA, 96, 6090-6095.
24. Li, L., Peterson, C.A., Lu, X. and Legerski, R.J. (1995) Mutations in XPA that prevent association with ERCC1 are defective in nucleotide excision repair. Mol. Cell. Biol., 15, 1993-1998.
25. Mu, D., Wakasugi, M., Hsu, D.S. and Sancar, A. (1997) Characterization of reaction intermediates of human excision repair nuclease. J. Biol. Chem., 272, 28971-28979.
26. Stigger, E., Drissi, R. and Lee, S.-H. (1998) Functional analysis of human replication protein A in nucleotide excision repair. J. Biol. Chem., 273, 9337-9343.
27. Jones, C.J. and Wood, R.D. (1993) Preferential binding of the xeroderma. pigmentosum group A complementing protein to damaged DNA. Biochemistry, 32, 12096-12104.
28. Wang, M., Mahrenholz, A. and Lee, S.-H. (2000) RPA stabilizes the XPA-damaged DNA complex through protein-protein interaction. Biochemistry, 39, 6433-6439.
29. Wakasugi, M. and Sancar, A. (1999) Order of assembly of human DNA repair excision nuclease. J. Biol. Chem., 274, 18759-18768.
30. Hoeijmakers, J.H.J. (2001) Genome maintenance mechanisms for preventing cancer. Nature, 411, 366-374.
31. Henricksen, L.A., Umbricht, C.B. and Wold, M.S. (1994) Recombinant replication protein A: expression, complex formation and functional characterization. J. Biol. Chem., 269, 11121-11132.
32. de Laat, W.L., Appeldoorn, E., Sugasawa, K., Weterings, E., Jaspers, N.G. and Hoeijmakers, J.H. (1998) DNA-binding polarity of human replication protein A positions nucleases in nucleotide excision repair. Genes Dev., 12, 2598-2609.
33. Vermeulen, W., van Vuuren, A.J., Chipoulet, M., Schaeffer, L., Appeldoorn, E., Weeda, G., Jaspers, N.G., Priestley, A., Arlett, C.F., Lehmann, A.R. et al. (1994) Three unusual repair deficiencies associated with transcription factor BTF2(TFIIH): evidence for the existence of a transcription syndrome. Cold Spring Harbor Symp. Quant. Biol., 59, 317-329.
34. Eker, A.P., Vermeulen, W., Miura, N., Tanaka, K., Jaspers, N.G., Hoeijmakers, J.H. and Bootsma, D. (1992) Xeroderma pigmentosum group A correcting protein from calf thymus. Mutat. Res. 274, 211-24.
35. Garcia-Parajo, M.F., Veerman, J.-A., Segers-Nolten, G.M.J., de Grooth, B.G., Greve, J. and van Hulst, N.F. (1999) Visualising individual green fluorescent proteins with a near field optical microscope. Cytometry, 36, 239-246.
36. Garcia-Parajo, M.F., Segers-Nolten, G.M.J., Veerman, J.-A., Greve, J. and van Hulst, N.F. (2000) Real-time light-driven dynamics of the fluorescence emission in single green fluorescent protein molecules. Proc. Natl Acad. Sci. USA, 97, 7237-7242.
37. Dickson, R.M., Cubitt, A.B., Tsien, R.Y. and Moerner, W.E. (1997) On/off blinking and switching behaviour of single molecules of green fluorescent protein. Nature, 388, 355-358.
38. He, Z., Henricksen, L.A., Wold, M.S. and Ingles, C.J. (1995) RPA involvement in the damage-recognition and incision steps of nucleotide excision repair. Nature, 374, 566-569.
39. Patrick, S.M. and Turchi, J.J. (2002) Xeroderma pigmentosum complementation group A protein (XPA) modulates RPA-DNA interactions via enhanced complex stability and inhibition of strand separation activity. J. Biol. Chem., 277, 16096-16101.
40. Iakoucheva, L.M., Walker, R.K., van Houten, B. and Ackerman, E.J. (2002) Equilibrium and stop-flow kinetic studies of fluorescently labeled DNA substrates with DNA repair proteins XPA and replication protein A. Biochemistry, 41, 131-143.
41. Kim, C., Paulus, B.F. and Wold, M.S. (1994) Interactions of human replication protein A with oligonucleotides. Biochemistry, 33, 14197-14206.
42. Lu, H.P., Iakoucheva, L.M. and Ackerman, E.J. (2001) Single-molecule conformational dynamics of fluctuating noncovalent DNA-protein interactions in DNA damage recognition. J. Am. Chem. Soc., 123, 9184-9185.