NMR study on the interaction between RPA and DNA decamer containing cis-syn cyclobutane pyrimidine dimer in the presence of XPA: Implication for damage verification and strand-specific dual incision in nucleotide excision repair

Nucleic Acids Research

Volumn 31, Issue 16, 2003, Pages 4747-4754

  Lee, Joon Hwa ^b   Park, Chin Ju ^b   Arunkumar, Alphonse I ^a   Chazin, Walter J ^a   Choi, Byong Seok ^b  

^a VANDERBILT UNIVERSITY   (United States)

^b Korea Advanced Institute of Science and Technology (KAIST)   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

CYCLOBUTANE; DNA; DNA BINDING PROTEIN; DOUBLE STRANDED DNA; NUCLEASE; PYRIMIDINE; REPLICATION PROTEIN A; SINGLE STRANDED DNA BINDING PROTEIN;

ARTICLE; BINDING AFFINITY; COMPLEX FORMATION; CONTROLLED STUDY; DNA ADDUCT; DNA CLEAVAGE; DNA DAMAGE; DNA STRAND; EXCISION REPAIR; GENETIC ASSOCIATION; HUMAN; HUMAN CELL; MAMMAL CELL; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL; PROTEIN DNA BINDING; PROTEIN DOMAIN; PROTEIN FAMILY; PROTEIN INTERACTION; XERODERMA PIGMENTOSUM;

DNA; DNA DAMAGE; DNA REPAIR; DNA, SINGLE-STRANDED; DNA-BINDING PROTEINS; HUMANS; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, MOLECULAR; PROTEIN BINDING; PROTEIN CONFORMATION; PYRIMIDINE DIMERS; XERODERMA PIGMENTOSUM GROUP A PROTEIN;

MAMMALIA;

EID: 0344443704     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkg683     Document Type: Article

References (28)

1. Wood,R.D. (1999) DNA damage recognition during nucleotide excision repair in mammalian cells. Biochimie, 81, 39-44.
2. deLaat,W.L., Jaspers,N.G.J. and Hoeijmakers,J.H. (1999) Molecular mechanism of nucleotide excision repair. Genes Dev., 13, 768-785.
3. Batty,D.P. and Wood,R.D. (2000) Damage recognition in nucleotide excision repair of DNA. Gene, 241, 193-204.
4. 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.
5. 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.
6. Burns,J.L., Huzder,S.N., Sung,P., Prakash,S. and Prakash,L. (1996) An affinity of human replication protein A for ultraviolet-damaged DNA. J. Biol. Chem., 271, 11607-11610.
7. Gomes,X.V. and Wold,M.S. (1996) Functional domains of the 70-kilodalton subunit of human replication protein A. Biochemistry, 35, 10558-10568.
8. Pfuetzner,R.A., Bochkarev,A., Frappier,L. and Edwards,A.M. (1997) Replication protein A. Characterization and crystallization of the DNA binding domain. J. Biol. Chem., 272, 430-434.
9. Bochkarev,A., Pfuetzner,R.A., Edwards,A.M. and Frappier,L. (1997) Structure of the single-stranded-DNA-binding domain of replication protein A bound to DNA. Nature, 385, 176-181.
10. Matusa,T., Saijo,M., Kuraoka,I., Kobayashi,T., Nakatsu,Y., Nagai,A., Enjosi,T., Masutani,C., Sugasawa,K. and Hanaoka,F. (1995) DNA repair protein XPA binds replication protein A (RPA). J. Biol. Chem., 270, 4152-4157.
11. 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.
12. Li,L., Lu,X., Peterson,C.A. and Legerski,R.J. (1995) An interaction between the DNA repair factor XPA and replication protein A appears essential for nucleotide excision repair. Mol. Cell. Biol., 15, 5396-5402.
13. 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.
14. Ikegami,T., Kuraoka,I., Saijo,M., Kodo,N., Kyogoku,Y., Morikawa,K., Tanaka,K. and Shirakawa,M. (1998) Solution structure of the DNA- and RPA-binding domain of the human repair factor XPA. Nature Struct. Biol., 5, 701-706.
15. Buchko,G.W., Ni,S., Thrall,B.D. and Kennedy,M.A. (1998) Structural features of the minimal DNA binding domain (M98-F219) of human nucleotide excision repair protein XPA. Nucleic Acids Res., 26, 2779-2788.
16. Sugasawa,K., Ng,J.M.Y., Masutani,C., Iwai,S., van der Spek,P.J., Eker,A.P.M., Hanaoka,F., Bootsma,D. and Hoeijmakers,J.H. (1998) Xeroderma pigmentosum group C protein complex is the initiator of global genome nucleotide excision repair. Mol. Cell, 2, 223-232.
17. Lindahl,T. and Wood,R.D. (1999) Quality control by DNA repair. Science, 286, 1897-1905.
18. Sugasawa,K., Okamoto,T., Shimizu,Y., Masutani,C., Iwai,S. and Hanaoka,F. (2001) A multistep damage recognition mechanism for global genomic nucleotide excision repair. Genes Dev., 15, 507-521.
19. deLaat,W.L., Appeldoorn,E., Sugasawa,K., Weterings,E., Jaspers,N.G.J. and Hoeijmakers,J.H.J. (1998) DNA-binding polarity of human replication protein A positions nucleases in nucleotide excision repair. Genes Dev., 12, 2598-2609.
20. Lee,J.-H., Choi,Y.-J. and Choi,B.-S. (2000) Solution structure of the DNA decamer duplex containing a 3′-T·T base pair of the cis-syn cyclobutane pyrimidine dimer: implication for the mutagenic property of the cis-syn dimer. Nucleic Acids Res., 28, 1794-1801.
21. Bhattacharya,S., Botuyan,M.-V., Hsu,F., Shan,X., Arunkumar,A.I., Arrowsmith,C.H., Edwards,A.M. and Chazin,W.J. (2002) Characterization of binding-induced changes in dynamics suggests a model for sequence-nonspecific binding of ssDNA by replication protein A. Protein Sci., 11, 2316-2325.
22. Bhattacharya,S., Arunkumar,A.I., Sullivan,S.L., Botuyan,M.-V., Arrowsmith,C.H. and Chazin,W.J. (2003) Complete assignment of the 1H, 13C and 15N resonances of the tandem high affinity binding domains of replication protein A. J. Biomol. NMR, in press.
23. Bochkareva,E., Belegu,V., Korolev,S. and Bochkarev A. (2001) Structure of the major single-stranded DNA-binding domain of replication protein A suggests a dynamic mechanism for DNA binding. EMBO J., 20, 612-618.
24. Arunkumar,A.I., Stauffer,M.E., Bochkareva,E., Bochkarev,A. and Chazin,W.J. (2003) Independent and coordinated functions of the replication protein A tandem high affinity ssDNA binding domains. J. Biol. Chem., in press.
25. Lao,Y., Gomes,X.V., Ren,Y., Taylor,J.-S. and Wold,M.S. (2000) Replication protein A interactions with DNA. III. Molecular basis of recognition of damaged DNA. Biochemistry, 39, 850-859.
26. Kim C., Snyder,R.O. and Wold,M.S. (1992) Binding properties of replication protein A from human and yeast cells. Mol. Cell. Biol., 12, 3050-3059.
27. Hermanson-Miller,I.L. and Turchi,J.J. (2002) Strand-specific binding of RPA and XPA to damaged duplex DNA. Biochemistry, 41, 2402-2408.
28. Yokoi,M., Masutani,C., Maekawa,T., Sugasawa,K., Ohkuma,Y. and Hanaoka,F. (2000) 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, 9870-9875.