Functional insights gained from structural analyses of DNA duplexes that contain UV-damaged photoproducts

Photochemistry and Photobiology

Volumn 83, Issue 1, 2007, Pages 187-195

  Park, Chin Ju ^a   Lee, Joon Hwa ^b   Choi, Byong Seok ^a  

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

^b Gyeongsang National University   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; DNA BINDING PROTEIN; DNA DIRECTED RNA POLYMERASE;

CHEMICAL STRUCTURE; CHEMISTRY; CONFERENCE PAPER; DNA DAMAGE; DNA REPAIR; ENZYMOLOGY; ESCHERICHIA COLI; GENETICS; METABOLISM; MUTAGENESIS; RADIATION EXPOSURE; ULTRAVIOLET RADIATION; X RAY CRYSTALLOGRAPHY;

CRYSTALLOGRAPHY, X-RAY; DNA; DNA DAMAGE; DNA REPAIR; DNA-BINDING PROTEINS; DNA-DIRECTED RNA POLYMERASES; ESCHERICHIA COLI; MODELS, MOLECULAR; MUTAGENESIS; ULTRAVIOLET RAYS;

EID: 34247853457     PISSN: 00318655     EISSN: None     Source Type: Journal    
DOI: 10.1562/2006-02-28-IR-820     Document Type: Conference Paper

References (46)

1. de Laat, W. L., N. G. Jaspers J. H. Hoeijmakers (1999) Molecular mechanism of nucleotide excision repair. Genes Dev. 13, 768 785.
2. Van Houten, B., D. L. Croteau, M. J. Dellavecchia, H. Wang C. Kisker (2005) "Close-fitting sleeves": DNA damage recognition by the UvrABC nuclease system. Mutat. Res. 577, 92 117.
3. Sancar, A. (2003) Structure and function of DNA photolyase and cryptochrome blue-light photoreceptors. Chem. Rev. 103, 2203 2237.
4. Woodgate, R. A. S. Levine (1996) Damage inducible mutagenesis: Recent insights into the activities of the Umu family of mutagenesis proteins. Cancer Surv. 28, 117 140.
5. Pfeifer, G. P. (1997) Formation and processing of UV photoproducts: Effects of DNA sequence and chromatin environment. Photochem. Photobiol. 65, 270 283.
6. Pfeifer, G. P., Y. H. You A. Besaratinia (2005) Mutations induced by ultraviolet light. Mutat. Res. 571, 19 31.
7. Taylor, J. S., H. F. Lu J. J. Kotyk (1990) Quantitative conversion of the (6-4) photoproduct of TpdC to its Dewar valence isomer upon exposure to simulated sunlight. Photochem. Photobiol. 51, 161 167.
8. Yoon, J. H., C. S. Lee, T. R. O'Connor, A. Yasui G. P. Pfeifer (2000) The DNA damage spectrum produced by simulated sunlight. J. Mol. Biol. 299, 681 693.
9. Svoboda, D. L., C. A. Smith, J. S. Taylor A. Sancar (1993) Effect of sequence, adduct type, and opposing lesions on the binding and repair of ultraviolet photodamage by DNA photolyase and (A)BC excinuclease. J. Biol. Chem. 268, 10694 10700.
10. Cordonnier, A. M. R. P. Fuchs (1999) Replication of damaged DNA: Molecular defect in xeroderma pigmentosum variant cells. Mutat. Res. 435, 111 119.
11. Smith, C. A., M. Wang, N. Jiang, L. Che, X. Zhao J. S. Taylor (1996) Mutation spectra of M13 vectors containing site-specific cis-syn, Trans-Syn-I, (6-4), and Dewar pyrimidone photoproducts of thymidylyl-(3′→5′) -thymidine in Escherichia coli under SOS conditions. Biochemistry 35, 4146 4154.
12. Banerjee, S. K., R. B. Christensen, C. W. Lawrence J. E. LeClerc (1988) Frequency and spectrum of mutations produced by a single cis-syn thymine-thymine cyclobutane dimer in a single-stranded vector. Proc. Natl Acad. Sci. USA 85, 8141 8145.
13. Banerjee, S. K., A. Borden, R. B. Christensen, J. E. LeClerc C. W. Lawrence (1990) SOS-dependent replication past a single trans-syn T-T cyclobutane dimer gives a different mutation spectrum and increased error rate compared with replication past this lesion in uninduced cells. J. Bacteriol. 172, 2105 2112.
14. Gibbs, P. E., B. J. Kilbey, S. K. Banerjee C. W. Lawrence (1993) The frequency and accuracy of replication past a thymine-thymine cyclobutane dimer are very different in Saccharomyces cerevisiae and Escherichia coli. J. Bacteriol. 175, 2607 2612.
15. LeClerc, J. E., A. Borden C. W. Lawrence (1991) The thymine-thymine pyrimidine-pyrimidone (6-4) ultraviolet light photoproduct is highly mutagenic and specifically induces 3′ thymine-to-cytosine transitions in Escherichia coli. Proc. Natl Acad. Sci. USA 88, 9685 9689.
16. Tang, M., P. Pham, X. Shen, J. S. Taylor, M. O'Donnell, R. Woodgate M. F. Goodman (2000) Roles of E. coli DNA polymerases IV and V in lesion-targeted and untargeted SOS mutagenesis. Nature 404, 1014 1018.
17. Lawrence, C. W., S. K. Banerjee, A. Borden J. E. LeClerc (1990) T-T cyclobutane dimers are misinstructive, rather than non-instructive, mutagenic lesions. Mol. Gen. Genet. 222, 166 168.
18. Kim, J. K., D. Patel B. S. Choi (1995) Contrasting structural impacts induced by cis-syn cyclobutane dimer and (6-4) adduct in DNA duplex decamers: Implication in mutagenesis and repair activity. Photochem. Photobiol. 62, 44 50.
19. McAteer, K., Y. Jing, J. Kao, J. S. Taylor M. A. Kennedy (1998) Solution-state structure of a DNA dodecamer duplex containing a cis-syn thymine cyclobutane dimer, the major UV photoproduct of DNA. J. Mol. Biol. 282, 1013 1032.
20. Park, H., K. Zhang, Y. Ren, S. Nadji, N. Sinha, J. S. Taylor C. Kang (2002) Crystal structure of a DNA decamer containing a cis-syn thymine dimer. Proc. Natl Acad. Sci. USA 99, 15965 15970.
21. Lee, J. H., Y. J. Choi B. S. Choi (2000a) Solution structure of the DNA decamer duplex containing a 3′-T × T basepair of the cis-syn cyclobutane pyrimidine dimer: Implication for the mutagenic property of the cis-syn dimer. Nucleic Acids Res. 28, 1794 1801.
22. Lee, J. H., C. J. Park, J. S. Shin, T. Ikegami, H. Akutsu B. S. Choi (2004) 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, 2474 2481.
23. Echols, H. M. F. Goodman (1991) Fidelity mechanisms in DNA replication. Annu. Rev. Biochem. 60, 477 511.
24. Jing, Y., J. F. Kao J. S. Taylor (1998) Thermodynamic and base-pairing studies of matched and mismatched DNA dodecamer duplexes containing cis-syn, (6-4) and Dewar photoproducts of TT. Nucleic Acids Res. 26, 3845 3853.
25. Kim, J. K. B. S. Choi (1995) The solution structure of DNA duplex-decamer containing the (6-4) photoproduct of thymidylyl(3′→5′) thymidine by NMR and relaxation matrix refinement. Eur. J. Biochem. 228, 849 854.
26. Lee, J. H., G. S. Hwang B. S. Choi (1999) Solution structure of a DNA decamer duplex containing the stable 3′-T-G base pair of the pyrimidine(6-4)pyrimidone photoproduct ([6-4] adduct): implications for the highly specific 3′-T→C transition of the (6-4) adduct. Proc. Natl Acad. Sci. USA 96, 6632 6636.
27. Lee, J. H., S. H. Bae B. S. Choi (2000b) The Dewar photoproduct of thymidylyl(3′→5′)-thymidine (Dewar product) exhibits mutagenic behavior in accordance with the ''A rule''. Proc. Natl. Acad. Sci. USA 97, 4591 4596.
28. Lee, J. H., G. S. Hwang, J. K. Kim B. S. Choi (1998) The solution structure of DNA decamer duplex containing the Dewar product of thymidylyl(3′→5′)thymidine by NMR and full relaxation matrix refinement. FEBS Lett. 428, 269 274.
29. Taylor, J. S. (2002) New structural and mechanistic insight into the A-rule and the instructional and non-instructional behavior of DNA photoproducts and other lesions. Mutat. Res. 510, 55 70.
30. Prakash, S. L. Prakash (2002) Translesion DNA synthesis in eukaryotes: A one- or two-polymerase affair. Genes Dev. 16, 1872 1883.
31. Trincao, J., R. E. Johnson, C. R. Escalante, S. Prakash, L. Prakash A. K. Aggarwal (2001) Structure of the catalytic core of S. cerevisiae DNA polymerase η: implications for translesion DNA synthesis. Mol. Cell 8, 417 426.
32. Ling, H., F. Boudsocq, R. Woodgate W. Yang (2001) Crystal structure of a Y-family DNA polymerase in action: A mechanism for error-prone and lesion-bypass replication. Cell 107, 91 102.
33. Ling, H., F. Boudsocq, B. S. Plosky, R. Woodgate W. Yang (2003) Replication of a cis-syn thymine dimer at atomic resolution. Nature 424, 1083 1087.
34. Li, Y., S. Dutta, S. Doublie, H. M. Bdour, J. S. Taylor T. Ellenberger (2004) Nucleotide insertion opposite a cis-syn thymine dimer by a replicative DNA polymerase from bacteriophage T7. Nat. Struct. Mol. Biol. 11, 784 790.
35. Mees, A., T. Klar, P. Gnau, U. Hennecke, A. P. Eker, T. Carell L. O. Essen (2004) Crystal structure of a photolyase bound to a CPD-like DNA lesion after in situ repair. Science 306, 1789 1793.
36. Vassylyev, D. G., T. Kashiwagi, Y. Mikami, M. Ariyoshi, S. Iwai, E. Ohtsuka K. Morikawa (1995) Atomic model of a pyrimidine dimer excision repair enzyme complexed with a DNA substrate: Structural basis for damaged DNA recognition. Cell 83, 773 782.
37. Reardon, J. T., A. F. Nichols, S. Keeney, C. A. Smith, J. S. Taylor, S. Linn A. Sancar (1993) Comparative analysis of binding of human damaged DNA-binding protein (XPE) and Escherichia coli damage recognition protein (UvrA) to the major ultraviolet photoproducts: T[c,s]T, T[t,s]T, T[6-4]T, and T[Dewar]T. J. Biol. Chem. 268, 21301 21308.
38. Mizukoshi, T., T. S. Kodama, Y. Fujiwara, T. Furuno, M. Nakanishi S. Iwai (2001) Structural study of DNA duplexes containing the (6-4) photoproduct by fluorescence resonance energy transfer. Nucleic Acids Res. 29, 4948 4954.
39. Van Houten, B. (1990) Nucleotide excision repair in Escherichia coli. Microbiol. Rev. 54, 18 51.
40. Skorvaga, M., K. Theis, B. S. Mandavilli, C. Kisker B. Van Houten (2002) The beta-hairpin motif of UvrB is essential for DNA binding, damage processing, and UvrC-mediated incisions. J. Biol. Chem. 277, 1553 1559.
41. Isaacs, R. J. H. P. Spielmann (2004) A model for initial DNA lesion recognition by NER and MMR based on local conformational flexibility. DNA Repair (Amst). 3, 455 464.
42. Sugasawa, K., T. Okamoto, Y. Shimizu, C. Masutani, S. Iwai F. Hanaoka (2001) A multistep damage recognition mechanism for global genomic nucleotide excision repair. Genes Dev. 15, 507 521.
43. Buterin, T., C. Meyer, B. Giese H. Naegeli (2005) DNA quality control by conformational readout on the undamaged strand of the double helix. Chem. Biol. 12, 913 922.
44. Hermanson-Miller, I. L. J. J. Turchi (2002) Strand-specific binding of RPA and XPA to damaged duplex DNA. Biochemistry 41, 2402 2408.
45. Lee, J. H., C. J. Park, A. I. Arunkumar, W. J. Chazin B. S. Choi (2003) 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 Res. 31, 4747 4754.
46. Eryilmaz, J., S. Ceschini, J. Ryan, S. Geddes, T. L. Waters T. E. Barrett (2006) Structural insights into the cryptic DNA-dependent ATPase activity of UvrB. J. Mol. Biol. 357, 62 72.