Toxicity inspired cross-linking for probing DNA-peptide interactions

Bioconjugate Chemistry

Volumn 24, Issue 12, 2013, Pages 2008-2014

  Carrette, Lieselot L G ^a   Morii, Takashi ^b   Madder, Annemieke ^a  

^a GHENT UNIVERSITY   (Belgium)

^b KYOTO UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; AROMATIC COMPOUNDS; DNA; ORGANIC POLLUTANTS; PROTEINS;

CROSS LINKING; DNA DAMAGES; DNA-PROTEIN INTERACTION; DNA-PROTEINS; FURAN MOIETY; LYSINE SIDE CHAINS; METABOLIC ACTIVATION; ON DEMANDS; PROTEIN CROSS-LINK; SITE SELECTIVE;

OLIGONUCLEOTIDES;

ALDEHYDE; DNA; FURAN DERIVATIVE; LYSINE; OLIGONUCLEOTIDE;

ARTICLE; DNA DAMAGE; DNA PROBE; ELECTROSPRAY; MELTING POINT; METABOLIC ACTIVATION; NUCLEOPHILICITY; OXIDATION; PROTEIN CROSS LINKING; PROTEIN DNA BINDING; TOXICITY;

AMINO ACID SEQUENCE; BASE SEQUENCE; CROSS-LINKING REAGENTS; DNA; DNA DAMAGE; FURANS; MODELS, MOLECULAR; MOLECULAR PROBES; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; PEPTIDES; PROTEIN BINDING; PROTEIN CONFORMATION;

EID: 84890821853     PISSN: 10431802     EISSN: 15204812     Source Type: Journal    
DOI: 10.1021/bc400327q     Document Type: Article

References (49)

1. Verzele, D., Carrette, L. L. G., and Madder, A. (2010) Peptide scalpels for site-specific dissection of the DNA-protein interface Drug Discovery Today: Technol. 7, e115-e123 (and references therein)
2. Tate, J. J., Persinger, J., and Bartholomew, B. (1998) Survey of four different photoreactive moieties for DNA photoaffinity labeling of yeast RNA polymerase III transcription complexes Nucleic Acids Res. 26, 1421-1426
3. Winnacker, M., Breeger, S., Strasser, R., and Carell, T. (2009) Novel diazirine-containing DNA photoaffinity probes for the investigation of DNA-protein-interactions ChemBioChem 10, 109-118
4. Shigdel, U. K., Zhang, J., and He, C. (2008) Diazirine-based DNA photo-cross-linking probes for the study of protein-DNA interactions Angew. Chem., Int. Ed. 47, 90-93
5. Zhu, G. Y. and Lippard, S. J. (2009) Photoaffinity labeling reveals nuclear proteins that uniquely recognize Cisplatin-DNA interstrand cross-links Biochemistry 48, 4916-4925
6. Dolinnaya, N. G., Zubin, E. M., Kubareva, E. A., Zatsepin, T. S., and Oretskaya, T. S. (2009) Design and synthesis of 2′-functionalised oligonucleotides. their application for covalent trapping the protein-DNA complexes Curr. Org. Chem. 13, 1029-1049
7. Joenje, H. (2011) Metabolism: alcohol, DNA and disease Nature 475, 45-46
8. O'Brien, P. J., Siraki, A. G., and Shangari, N. (2005) Aldehyde sources, metabolism, molecular toxicity mechanisms, and possible effects on human health Crit. Rev. Toxicol. 35, 609-662
9. Ide, H., Shoulkamy, M. I., Nakano, T., Miyamoto-Matsubara, M., and Salem, A. M. H. (2011) Repair and biochemical effects of DNA-protein crosslinks Mutat. Res. 711, 113-122
10. Barker, S., Weinfeld, M., and Murray, D. (2005) DNA-protein crosslinks: their induction, repair, and biological consequences Mutat. Res. 589, 111-135
11. Szekely, J., Rizzo, C. J., and Marnett, L. J. (2008) Chemical properties of oxopropenyl adducts of purine and pyrimidine nucleosides and their reactivity toward amino acid cross-link formation J. Am. Chem. Soc. 130, 2195-2201
12. Voitkun, V. and Zhitkovich, A. (1999) Analysis of DNA-protein Crosslinking activity of malondialdehyde in vitro Mutat. Res. 424, 97-106
13. Nelson, J. D., Denisenko, O., and Bomsztyk, K. (2006) Protocol for the fast chromatin immunoprecipitation (ChIP) method Nat. Protoc. 1, 179-185
14. 17O NMR J. Am. Chem. Soc. 111, 1894-1896
15. Sczepanski, J. T., Wong, R. S., McKnight, J. N., Bowman, G. D., and Greenberg, M. M. (2010) Rapid DNA-protein cross-linking and strand scission by an abasic site in a nucleosome core particle Proc. Nat. Acad. Sci. U.S.A. 107, 22475-22480
16. Guan, L. and Greenberg, M. M. (2010) Irreversible inhibition of DNA polymerase β by an oxidised abasic lesion J. Am. Chem. Soc. 132, 5004-5005
17. Brevnov, M. G., Gritsenko, O. M., Mikhailov, S. N., Efimtseva, E. V., Ermolinsky, B. S., Van Aerschot, A., Herdewijn, P., Repyk, A. V., and Gromova, E. S. (1997) DNA duplexes with reactive dialdehyde groups as novel reagents for cross-linking to restriction-modification enzymes Nucleic Acids Res. 25, 3302-3309
18. Romanenkov, A. S., Ustyugov, A. A., Zatsepin, T. S., Nikulova, A. A., Kolesnikov, I. V., Metelev, V. G., Oretskaya, T. S., and Kubareva, E. A. (2005) Analysis of DNA-Protein interactions in complexes of transcription factor NF-κB with DNA Biochemistry (Moscow) 70, 1212-1222
19. Tunitskaya, V. L., Rusakova, E. E., Memelova, L. V., Kochetkov, S. N., Van Aerschot, A., Herdewijn, P., Efimtseva, E. V., Ermolinsky, B. S., and Mikhailov, S. N. (1999) Mapping of T7 RNA polymerase active site with novel reagents-oligonucleotides with reactive dialdehyde groups FEBS Lett. 442, 20-24
20. Sugiyama, T., Kittaka, A., Takayama, H., Tomioka, M., Ida, Y., and Kuroda, R. (2003) Aggregation of RecA-derived peptides on single-stranded oligonucleotides triggered by Schiff base-mediated crosslinking Bioorg. Med. Chem. Lett. 13, 2847-2851
21. Klungland, A., Paulsen, R., Yamada, Y., Ueno, Y., Wiik, P., Matsuda, A., Seeberg, E., and Bjelland, S. (2001) 5-Formyluracil and its nucleoside derivatives confer toxicity and mutagenicity to mammalian cells by interfering with normal RNA and DNA metabolism Toxicol. Lett. 119, 71-78
22. Kellinger, M. W., Song, C. X., Chong, J., Lu, X. Y., He, C., and Wang, D. (2012) 5-formylcytosine and 5-carboxylcytosine reduce the rate and substrate specificity of RNA polymerase II transcription Nat. Struct. Chem. Biol. 19, 831-834
23. Mee, L. K. and Adelstein, S. J. (1981) Predominance of core histones in formation of DNA-protein crosslinks in γ-irradiated chromatin Proc. Nat. Acad. Sci. U.S.A. 78, 2194-2198
24. Kasai, H., Iida, A., Yamaizumi, Z., Nishimura, S., and Tanooka, H. (1990) 5-Formyldeoxyuridine: aa new type of DNA damage induced by ionizing radiation and its mutagenicity to Salmonella strain TA102 Mutat. Res. Lett. 243, 249-253
25. Okamoto, A., Tainaka, K., and Saito, I. (2002) A facile incorporation of the aldehyde function into DNA: 3-formylindole nucleoside as an aldehyde-containing universal nucleoside Tetrahedron Lett. 43, 4581-4583
26. Raindlová, V., Pohl, R., and Hocek, M. (2012) Synthesis of aldehyde-linked nucleotides and DNA and their bioconjugations with lysine and peptides through reductive amination Chem.-Eur. J. 18, 4080-4087
27. Peterson, L. A. (2006) Electrophilic intermediates produced by bioactivation of furan Drug Metabol. Rev. 38, 615-626
28. Stevens, K. and Madder, A. (2009) Furan-modified oligonucleotides for fast, high-yielding and site-selective DNA inter-strand cross-linking with non-modified complements Nucleic Acids Res. 37, 1555-1565
29. Halila, S., Velasco, T., De Clercq, P., and Madder, A. (2005) Fine-tuning furan toxicity: fast and quantitative DNA interchain crosslink formation upon selective oxidation of a furan containing oligonucleotide Chem. Commun. 7, 936-938
30. Op de Beeck, M. and Madder, A. (2011) Unprecedented C-selective interstrand cross-linking through in situ oxidation of furan-modified oligodeoxynucleotides J. Am. Chem. Soc. 133, 796-807
31. Op de Beeck, M. and Madder, A. (2012) Sequence specific DNA cross-linking triggered by visible light J. Am. Chem. Soc. 134, 10737-10740
32. Carrette, L. L. G., Gyssels, E., and Madder, A. DNA interstrand cross-link formation by using furan as a masked reactive aldehyde. Curr. Prot. Nucl. Acid Chem. 2013, in press
33. Schmidt, M. J. and Summerer, D. (2013) Red-light-controlled protein-RNA crosslinking with a genetically encoded furan Angew. Chem. 52, 4690-4693
34. Spande, T. F. and Witkop, B. (1967) Determination of the tryptophan content of proteins with N-bromosuccinimide Method. Enzymol 11, 498-506
35. Williams, M. N. (1975) Effect of N-bromosuccinimide modification on dihydrofolate reductase from a methotrexate-resistant strain of Escherichia coli J. Biol. Chem. 250, 322-330
36. Pace, N. C. and Scholtz, M. J. (1998) A helix propensity scale based on experimental studies of peptides and proteins Biophys. J. 75, 422-427
37. Kondo, J. and Westhof, E. (2011) Classification of pseudo pairs between nucleotide bases and amino acids by analysis of nucleotide-protein complexes Nucleic Acids Res. 39, 8628-8637
38. Suzuki, M. (1993) Common features in DNA recognition helices of eukaryotic transcription factors EMBO J, 12, 3221-3226
39. Luscombe, N. M. and Thornton, J. M. (2002) Protein-DNA interactions: amino acid conservation and the effects of mutations on binding specificity J. Mol. Biol. 320, 991-1009
40. Ueno, M., Murakami, K., Makino, K., and Morii, T. (1993) Arranging quaternary structure of peptides by cyclodextrin-guest inclusion complex: sequence specific DNA binding by a peptide dimer with artificial dimerization module J. Am. Chem. Soc. 115, 12575-12576
41. Hurst, H. C. (1995) Transcription Factors 1: bZIP proteins Protein Profile 2, 101-168
42. Greco, N. J. and Tor, Y. (2005) Simple fluorescent pyrimidine analogues detect the presence of DNA abasic sites J. Am. Chem. Soc. 127, 10784-10785
43. Wicke, L. and Engels, J. W. (2012) Postsynthetic on column RNA labeling via stille coupling Bioconjugate Chem. 23, 627-642
44. Srivatsan, S. G. and Tor, Y. (2007) Fluorescent pyrimidine ribonucleotide: synthesis, enzymatic incorporation, and utilization J. Am. Chem. Soc. 129, 2044-2053
45. Keller, W., König, P., and Richmond, T. J. (1995) Crystal structure of a bZIP/DNA complex at 2.2 Å: determinants of DNA specific recognition J. Mol. Biol. 254, 657-667
46. Zatsepin, T. S., Stetsenko, D. A., Gait, M. J., and Oretskaya, T. S. (2005) Use of carbonyl group addition-elimination reactions for synthesis of nucleic acids conjugates Bioconjugate Chem. 16, 471-489
47. Blatter, E. E., Ebright, Y. W., and Ebright, R. H. (1992) Identification of an amino acid-base contact in the GCN4-DNA complex by bromouracil-mediated photocross-linking Nature 359, 650-652
48. Doktycz, M. J. (1997) Nucleic acids: thermal stability and denaturation. In Encyclopedia of Life Science, pp 3123-3140, John Wiley & Sons, Chichester.
49. Misra, V. K., Hecht, J. L., Sharp, K. A., Friedman, R. A., and Honig, B. (1994) Salt Effects on Protein-DNA Interactions: The λcI Repressor and EcoRI Endonuclease J. Mol. Biol. 238, 264-280