DNA-binding properties of the antibody specific for the Dewar photoproduct of thymidylyl-(3′-5′)-thymidine

Nucleosides, Nucleotides and Nucleic Acids

Volumn 25, Issue 4-6, 2006, Pages 667-679

  Morioka, Hiroshi ^a   Kurihara, Mikiko ^a   Kobayashi, Hiroyuki ^a   Satou, Kousuke ^a   Komatsu, Yasuo ^a   Uchida, Makiyo ^a   Ohtsuka, Eiko ^a   Torizawa, Takuya ^b   Kato, Koichi ^b   Shimada, Ichio ^b   Matsunaga, Tsukasa ^c   Nikaido, Osamu ^c  

^a HOKKAIDO UNIVERSITY   (Japan)

^b UNIVERSITY OF TOKYO   (Japan)

^c KANAZAWA UNIVERSITY   (Japan)

Author keywords

Dewar photoproduct; Monoclonal antibody; UV damaged DNA

Indexed keywords

DEWAR PHOTOPRODUCT; EPITOPE; IMMUNOGLOBULIN F(AB) FRAGMENT; MONOCLONAL ANTIBODY; MONOCLONAL ANTIBODY DEM 1; NUCLEOTIDE DERIVATIVE; OLIGONUCLEOTIDE; PYRIMIDINE DERIVATIVE; TETRANUCLEOTIDE; THYMIDINE DERIVATIVE; THYMIDYLYL (3',5') THYMIDINE; UNCLASSIFIED DRUG;

ANTIGEN BINDING; ARTICLE; BINDING AFFINITY; BIOTINYLATION; CHEMICAL STRUCTURE; DNA BINDING; DNA DAMAGE; MOLECULAR CLONING; MOLECULAR RECOGNITION; MOLECULAR SIZE; NUCLEOTIDE METABOLISM; PHOTOREACTIVITY; QUANTITATIVE ANALYSIS; STRUCTURE ANALYSIS; SURFACE PLASMON RESONANCE;

AMINO ACID SEQUENCE; ANTIBODIES; ANTIBODY SPECIFICITY; DNA; IMMUNOGLOBULIN FAB FRAGMENTS; MOLECULAR SEQUENCE DATA; MOLECULAR STRUCTURE; PHOTOCHEMISTRY; THYMIDINE;

EID: 33747627106     PISSN: 15257770     EISSN: 15322335     Source Type: Journal    
DOI: 10.1080/15257770600686469     Document Type: Article

References (38)

1. Setlow, R.B. Repair deficient human disorders and cancer. Nature 1978, 271, 713-717.
2. Friedberg, E.C.; Walker, G.C.; Siede, W. DNA Repair and Mutagenesis. ASM Press, Washington, DC 1995.
3. Taylor, J.S.; Cohrs, M.P. DNA, light, and Dewar pyrimidinones: the structure and biological significance to TpT3. Journal of the American Chemical Society 1987, 109, 2834-2835.
4. LeClerc, J.E.; Borden, A.; Lawrence, C.W. The thymine-thymine pyrimidine-pyrimidone(6-4) ultraviolet light photoproduct is highly mutagenic and specifically induces 3′ thymine-to-cytosine transitions in Escherichia coli. Proceedings of the National Academy of Sciences USA 1991, 88, 9685-9689.
5. Smith, C.A.; Wang, M.; Jiang, N.; Che, L.; Zhao, X.; Taylor, J.S. 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 1996, 35, 4146-4154.
6. Sancar, A. DNA excision repair. Annual Review of Biochemistry 1996, 65, 43-81.
7. Wood, R.D. DNA repair in eukaryotes. Annual Review of Biochemistry 1996, 65, 135-167.
8. Mitchell, D.L.; Clarkson, J.M. The development of a radioimmunoassay for the detection of photoproducts in mammalian cell DNA. Biochimica et Biophysica Acta 1981, 655, 54-60.
9. Eggset, G.; Volden, G.; Krokan, H. U.V.-induced DNA damage and its repair in human skin in vivo studied by sensitive immunohistochemical methods. Carcinogenesis 1983, 4, 745-750.
10. Wani, A.A.; Gibson-D'Ambrosio, R.E.; D'Ambrosio, S.M. Antibodies to UV irradiated DNA: the monitoring of DNA damage by ELISA and indirect immunofluorescence. Photochemistry and Photobiology 1984, 40, 465-471.
11. Mori, T.; Matsunaga, T.; Hirose, T.; Nikaido, O. Establishment of a monoclonal antibody recognizing ultraviolet light-induced (6-4)photoproducts. Mutation Research 1988, 194, 263-270.
12. Roza, L.; von der Wlup, K.J.M.; MacFarlane, S.J.; Lohman, P.H.M.; Baan, R.A. Detection of cyclobutane thymine dimers in DNA of human cells with monoclonal antibodies raised against a thymine dimer-containing tetranucleotide. Photochemistry and Photobiology 1988, 48, 627-633.
13. Mori, T.; Nakane, M.; Hattori, T.; Matsunaga, T.; Ihara, M.; Nikaido, O. Simultaneous establishment of monoclonal antibodies specific for either cyclobutane pyrimidine dimer or (6-4)photoproduct from the same mouse immunized with ultraviolet-irradiated DNA. Photochemistry and Photobiology 1991, 54, 225-232.
14. Mizuno, T.; Matsunaga, T.; Ihara, M.; Nikaido, O. Establishment of a monoclonal antibody recognizing cyclobutane-type thymine dimers in DNA: a comparative study with 64M-1 antibody specific for (6-4)photoproducts. Mutation Research 1991, 254, 175-184.
15. Matsunaga, T.; Hakakeyama, Y.; Ohta, M.; Mori, T.; Nikaido, O. Establishment and characterization of a monoclonal antibody recognizing the Dewar isomers of (6-4)photoproducts. Photochemistry and Photobiology 1993, 57, 934-940.
16. Morioka, H.; Miura, H.; Kobayashi, H.; Koizumi, T.; Fujii, K.; Asano, K.; Matsunaga, T.; Nikaido, O.; Stewart, J.D.; Ohtsuka, E. Antibodies specific for (6-4) DNA photoproducts: cloning, antibody modeling and construction of a single-chain Fv derivative. Biochimica et Biophysica Acta 1998, 1385, 17-32.
17. Kobayashi, H.; Morioka, H.; Torizawa, T.; Kato, K.; Shimada, I.; Nikaido, O.; Ohtsuka, E. Specificities and rates of binding of anti-(6-4) photoproduct antibody fragments to synthetic thymine photoproducts. Journal of Biochemistry (Tokyo) 1998, 123, 182-188.
18. 31P NMR study of the interaction between oligonucleotides containing (6-4) photoproduct and Fab fragment of monoclonal antibodies specific for (6-4) photoproduct. FEBS Letters 1998, 429, 157-161.
19. Kobayashi, H.; Morioka, H.; Tobisawa, K.; Torizawa, T.; Kato, K.; Shimada, I.; Nikaido, O.; Stewart, J.D.; Ohtsuka, E. Probing the interaction between a high-affinity single-chain Fv and a pyrimidine (6-4) pyrimidone photodimer by site-directed mutagenesis. Biochemistry 1999, 38, 532-539.
20. Torizawa, T.; Kato, K.; Kato, J.; Kobayashi, H.; Komatsu, Y.; Morioka, H.; Nikaido, O.; Ohtsuka, E.; Shimada, I. Conformational multiplicity of the antibody combining site of a monoclonal antibody specific for a (6-4) photoproduct. Journal of Molecular Biology 1999, 290, 731-740.
21. Kobayashi, H.; Morioka, H.; Nikaido, O.; Stewart, J.D.; Ohtsuka, E. The role of surface lysines in pyrimidine (6-4) pyrimidone photoproduct binding by a high-affinity antibody. Protein Engineering 1998, 11, 1089-1092.
22. Kobayashi, H.; Kato, J.; Morioka, H.; Stewart, J.D.; Ohtsuka, E. Tryptophan H33 plays an important role in pyrimidine (6-4) pyrimidone photoproduct binding by a high-affinity antibody. Protein Engineering 1999, 12, 879-884.
23. Yokoyama, H.; Mizutani, R.; Satow, Y.; Komatsu, Y.; Ohtsuka, E.; Nikaido, O. Crystal structure of the 64M-2 antibody Fab fragment in complex with a DNA dT(6-4)T photoproduct formed by ultraviolet radiation. Journal of Molecular Biology 2000, 299, 711-723.
24. Komatsu, Y.; Tsujino, T.; Suzuki. T.; Nikaido, O.; Ohtsuka, E. Antigen structural requirements for recognition by a cyclobutane thymine dimer-specific monoclonal antibody. Nucleic Acids Research 1997, 25, 3889-3894.
25. Torizawa, T.; Yamamoto, N.; Suzuki, T.; Nobuoka, K.; Komatsu, Y.; Morioka, H.; Nikaido, O.; Ohtsuka, E.; Kato, K.; Shimada, I. DNA binding mode of the Fab fragment of a monoclonal antibody specific for cyclobutane pyrimidine dimer. Nucleic Acids Research 2000, 28, 944-951.
26. Sambrook, J.; Fritsch, E.F.; Maniatis, T. Molecular Cloning. A Laboratory Manual, 2nd ed.; Cold Spring Harbor, New York.
27. Smith, C.A.; Taylor, J.-S. Preparation and characterization of a set of deoxyoligonucleotide 49-mers containing site-specific cis-syn, trans-syn-I, (6-4), and Dewar photoproducts of thymidylyl(3′-5′)-thymidine. Journal of Biological Chemistry 1993, 268, 11143-11151.
28. Iwai, S.; Shimizu, M.; Kamiya, H.; Ohtsuka, E. Synthesis of a phosphoramidite coupling unit of the pyrimidine (6-4) pyrimidone photoproduct and its incorporation into oligonucleotides. Journal of the American Chemical Society 1996, 118, 7642-7643.
29. Fujiwara, Y.; Iwai, S. Thermodynamic studies of the hybridization properties of photolesions in DNA. Biochemistry 1997, 36, 1544-1550.
30. Satou, K.; Komatsu, Y.; Torizawa, T.; Kato, K.; Shimada, I.; Nikaido, O.; Ohtsuka, E. Efficient chemical synthesis of a pyrimidine (6-4) pyrimidone photoproduct analog and its properties. Tetrahedron Letters 2000, 41, 2175-2179.
31. Kabat, E.A.; Wu, T.T.; Perry, H.M.; Gottesman, K.S.; Foeller, C. Sequences of Proteins of Immunological Interest, 5th ed.; National Institutes of Health, Bethesda, MD 1991.
32. Huse, W.D.; Sastry, L.; Iverson, S.A.; Kang, A.S.; Alting-Mees, M.; Burton, D.R.; Benkovic, S.J.; Lerner, R.A. Generation of a large combinatorial library of the immunoglobulin repertoire in phage lambda. Science 1989, 246, 1275-1281.
33. Toyo'oka, T.; Imai, K. Isolation and characterization of cysteine-containing regions of proteins using 4-(aminosulfonyl)-7-fluoro-2,1,3- benzoxadiazole and high-performance liquid chromatography. Analytical Chemistry 1985, 57, 1931-1937.
34. Imai, K.; Uzu, S.; Kanda, S.; Baeyens, W.R.G. Availability of fluorogenic reagents having a benzofurazan structure in the biosciences. Analytica Chemica Acta 1994, 290, 3-20.
35. Yamaguchi, Y.; Kim, H.H.; Kato, K.; Matsuda, K.; Shimada, I.; Arata, Y. Proteolytic fragmentation with high specificity of mouse immunoglobulin G: mapping of proteolytic cleavage sites in the hinge region. Journal of Immunological Methods 1995, 181, 259-267.
36. Franklin, W.A.; Lo, K.M.; Haseltine, W.A. Alkaline lability of fluorescent photoproducts produced in ultraviolet light-irradiated DNA. Journal of Biological Chemistry 1982, 257, 13535-13543.
37. Shlomchik, M.; Mascelli, M.; Shan, H.; Radic, M.Z.; Pisetsky, D.; Marshak-Rothstein, A.; Weigert, M. Anti-DNA antibodies from autoimmune mice arise by clonal expansion and somatic mutation. The Journal of Experimental Medicine 1990, 171, 265-292.
38. Sims, M.J.; Krawinkel, U.; Taussig, M.J. Characterization of germ-line genes of the VGAM3.8 VH gene family from BALB/c mice. Journal of Immunology 1992, 149, 1642-1648.