Application of Molecular Mass Spectrometry for The Structural Characterization of a DNA-Protein Cross-Links
Keywords:DNA-Protein Crosslink, ICP-MS/MS, LC-MS
To date, many different analytical methods have been used to investigate the cross-linking reaction mechanism and to obtain the chemical structure of DNA-Protein Cross-links (DPCs). Direct MS analysis of DPCs is challenging because of the ionization properties of DNA and the protein. However, peptide sequencing and mass spectrometry (MS) as analytical techniques are playing increasingly important roles for the structure determination of DPCs model. In our previous study, a novel approach was presented for purification, detection and quantification of DPCs by newly developed inductively coupled plasma mass spectrometry (ICPMS/MS), which allows sub-ppb detection of S and P, key heteroelements in DNA and proteins.
In this study, we enhanced our previously developed method and it was complemented by the use of molecular MS to allow complete characterization of a DNA-protein cross-link. First, a small molecule model is utilized to identify the adduct structure that will likely occur in an intact DNA-protein cross-link. We investigate the thermal stability of DNA-protein cross-links, both in an intact DPC and a small molecule adduct to determine feasibility of digestion/thermal degradationof DNA without the cross-link information being lost. Thermal degradation was conducted to reduce the cross-linked DNA into a single nucleoside. The remaining protein-nucleoside adduct then was proteolytically digested, generating a peptide-nucleoside adduct. The absence of the phosphate moiety allows for facile structural characterization via electrospray ionization mass spectrometry (ESI-MS). Additional calculations were done for peptide matching allowing us to determine the cross-link location in the protein, made possible via MS/MS analysis. Additionally, we show that steric effects play an important role in DPC formation.
Beckman, K. B.; Ames, B. N. The Journal of biological chemistry 1997, 272 (32), 19633-6.
Cooke, M. S.; Olinski, R.; Evans, M. D. Clinica chimica acta; international journal of clinical chemistry 2006, 365 (1-2), 30-49.
Winterbourn, C. C. Nature chemical biology 2008, 4 (5), 278-86.
Nathan, C.; Cunningham-Bussel, A. Nature reviews. Immunology 2013, 13 (5), 349-61.
Steenken, S.; Jovanovic, S. V. J Am Chem Soc 1997, 119 (3), 617-618.
Salem, A. M.; Nakano, T.; Takuwa, M.; Matoba, N.; Tsuboi, T.; Terato, H.; Yamamoto, K.; Yamada, M.; Nohmi, T.; Ide, H. Journal of bacteriology 2009, 191 (18), 5657-68.
Ide, H.; Shoulkamy, M. I.; Nakano, T.; Miyamoto-Matsubara, M.; Salem, A. M. Mutation research 2011, 711 (1-2), 113-22.
Voitkun, V.; Zhitkovich, A. Mutation research 1999, 424 (1-2), 97-106.
Patierno, S. R.; Costa, M. Chem-Biol Interact 1985, 55 (1-2), 75-91.
Patierno, S. R.; Sugiyama, M.; Basilion, J. P.; Costa, M. Cancer Res 1985, 45 (11), 5787-5794.
Misra, M.; Olinski, R.; Dizdaroglu, M.; Kasprzak, K. S. Chem Res Toxicol 1993, 6 (1), 33-37.
Zhitkovich, A.; Voitkun, V.; Kluz, T.; Costa, M. Environ Health Persp 1998, 106, 969-974.
Macfie, A.; Hagan, E.; Zhitkovich, A. Chem Res Toxicol 2010, 23 (2), 341-347.
Bau, D. T.; Wang, T. S.; Chung, C. H.; Wang, A. S. S.; Jan, K. Y. Environ Health Persp 2002, 110, 753-756.
Kurbanyan, K.; Nguyen, K. L.; To, P.; Rivas, E. V.; Lueras, A. M.; Kosinski, C.; Steryo, M.; Gonzalez, A.; Mah, D. A.; Stemp, E. D. Biochemistry 2003, 42 (34), 10269-81.
Johansen, M. E.; Muller, J. G.; Xu, X.; Burrows, C. J. Biochemistry 2005, 44 (15), 5660-71.
Xu, X.; Muller, J. G.; Ye, Y.; Burrows, C. J. J Am Chem Soc 2008, 130 (2), 703-9.
Solivio, M. J.; Joy, T. J.; Sallans, L.; Merino, E. J. J Inorg Biochem 2010.
Solivio, M. J.; Nemera, D. B.; Sallans, L.; Merino, E. J. Chem Res Toxicol 2012, 25 (2), 326-36.
Zhou, C.; Greenberg, M. M. J Am Chem Soc 2012, 134 (19), 8090-3.
Zhou, C.; Sczepanski, J. T.; Greenberg, M. M. J Am Chem Soc 2012, 134 (40), 16734-41.
Sczepanski, J. T.; Zhou, C.; Greenberg, M. M. Biochemistry 2013.
Zhou, C.; Sczepanski, J. T.; Greenberg, M. M. J Am Chem Soc 2013, 135 (14), 5274-7.
Rhee, H. S.; Pugh, B. F.Cell 2011, 147 (6), 1408-1419.
Geyer, H.; Geyer, R.; Pingoud, V. Nucleic Acids Res 2004, 32 (16).
Doneanu, C. E.; Gafken, P. R.; Bennett, S. E.; Barofsky, D. F. A. Anal Chem 2004, 76 (19), 5667-5676.
Gong, J. W.; Solivio, M. J.; Merino, E. J.; Caruso, J. A.; Landero-Figueroa, J. A.,. Anal Bioanal Chem 2015, 407 (9), 2433-2437.
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