mass spectrometry; DNA; photodetachment; electron; radical; fragmentation
Abstract :
[en] We hereby explore the effects of irradiating DNA polyanions stored in a quadrupole ion trap mass spectrometer with an optical parametric oscillator laser between 250 and 285 nm. We studied DNA 6-20-mer single strands and 12-base pair double strands. In all cases, laser irradiation causes electron detachment from the multiply charged DNA anions. Electron photodetachment efficiency directly depends on the number of guanines in the strand, and maximum efficiency is observed between 260 and 275 nm. Subsequent collision-induced dissociation (CID) of the radical anions produced by electron photodetachment results in extensive fragmentation. In addition to neutral losses, a large number of fragments from the w, d, a*, and z* ion series are obtained, contrasting with the w and (a-base) ion series observed in regular CID. The major advantage of this technique, coined electron photodetachment dissociation (EPD) is the absence of internal fragments, combined with good sequence coverage. EPD is therefore a highly promising approach for de novo sequencing of oligonucleotides. EPD of nucleic acids is also expected to give specific radical-induced strand cleavages, with conservation of other fragile bonds, including noncovalent bonds. In effect, preliminary results on a DNA hairpin and on double strands suggest that EPD could also be used to probe intra- and intermolecular interactions in nucleic acids.
Disciplines :
Chemistry
Author, co-author :
Gabelica, Valérie ; Université de Liège - ULiège > Département de Chimie (Sciences) > Chimie physique, spectrométrie de masse
Tabarin, Thibault; Université Lyon 1 et CNRS > Laboratoire de Spectrométrie Ionique et Moléculaire - LASIM
Antoine, Rodolphe; Université Lyon 1 et CNRS > Laboratoire de Spectrométrie Ionique et Moléculaire - LASIM
Rosu, Frédéric ; Université de Liège - ULiège > Département de Chimie (Sciences) > Chimie physique, spectrométrie de masse
Compagnon, Isabelle; Université Lyon 1 et CNRS > Laboratoire de Spectrométrie Ionique et Moléculaire - LASIM
Broyer, Michel; Université Lyon 1 et CNRS > Laboratoire de Spectrométrie Ionique et Moléculaire - LASIM
De Pauw, Edwin ; Université de Liège - ULiège > Département de chimie (sciences) > Chimie physique, spectrométrie de masse
Dugourd, Philippe; Université Lyon 1 et CNRS > Laboratoire de Spectrométrie Ionique et Moléculaire - LASIM
Language :
English
Title :
Electron photodetachment dissociation of DNA polyanions in a quadrupole ion trap mass spectrometer
Publication date :
2006
Journal title :
Analytical Chemistry
ISSN :
0003-2700
eISSN :
1520-6882
Publisher :
American Chemical Society, Washington, United States - District of Columbia
Rosu, F.; Gabelica, V.; Houssier, C.; Colson, P.; De Pauw, E. Rapid Commun. Mass Spectrom. 2002, 16, 1729-1736.
Goodlett, D. R.; Camp, D. G., II; Hardin, C. C.; Corregan, M.; Smith, R. D. Biol. Mass Spectrom. 1993, 22, 181-183.
David, W. M.; Brodbelt, J.; Kerwin, S. M.; Thomas, P. W. Anal. Chem. 2002, 74, 2029-2033.
Hofstadler, S. A; Griffey, R. H. Chem. Rev. 2001, 101, 377-390.
Schnier, P. D.; Klassen, J. S.; Strittmatter, E. F.; Williams, E. R. J. Am. Chem. Soc. 1998, 120, 9605-9613.
Gabelica, V.; De Pauw, E. J. Mass Spectrom. 2001, 36, 397-402.
Gabelica, V.; De Pauw, E. Int. J. Mass Spectrom. 2002, 219, 151-159.
Rueda, M.; Kalko, S. G.; Luque, F. J.; Orozco, M. J. Am. Chem. Soc. 2003, 125, 8007-8014.
Gidden, J.; Baker, E. S.; Ferzoco, A.; Bowers, M. T. Int. J. Mass Spectrom. 2004, 240, 200-210.
Gidden, J.; Ferzoco, A.; Shammer Baker, E.; Bowers, M. T. J. Am. Chem. Soc. 2004, 126, 15132-15140.
Rueda, M.; Luque, F. J.; Orozco, M. J. Am. Chem. Soc. 2006, 128, 3608-3619.
Huber, C. G.; Oberacher, H. Mass Spectrom. Rev. 2001, 20, 310-343.
Crain, P. F.; McCloskey, J. A Curr. Opin. Biotechnol. 1998, 9, 25-34.
Nordhoff, E.; Kirpekar, F.; Roepstorff, P. Mass Spectrom. Rev. 1996, 15, 67-138.
Beck, J.; Colgrave, M. L.; Ralph, S. F.; Sheil, M. M. Mass Spectrom. Rev. 2001, 20, 61-87.
Wu, J.; McLuckey, S. A. Int. J. Mass Spectrom. 2004, 237, 197-241.
McLuckey, S. A.; Van Berkel, G. J.; Glish, G. L. J. Am. Soc. Mass Spectrom. 1992, 3, 60-70.
McLuckey, S. A.; Habibi-Goudarzi, S. J. Am. Chem. Soc. 1993, 115, 12085-12095.
Hakansson, K.; Hudgins, R. R.; Marshall, A. G.; O'Hair, R. A. J. Am. Soc. Mass Spectrom. 2003, 14, 23-41.
Schultz, K. N.; Hakansson, K. Int. J. Mass Spectrom. 2004, 234, 123-130.
Budnik, B. A.; Haselmann, K. F.; Zubarev, R. A. Chem. Phys. Lett. 2001, 342, 299-302.
Yang, J.; Mo, J. J.; Adamson, J. T.; Hakansson, K. Anal. Chem. 2005, 77, 1876-1882.
Cooper, H. J.; Hakansson, K.; Marshall, A. G. Mass Spectrom. Rev. 2005, 24, 201-222.
Horn, D. M.; Ge, Y.; McLafferty, F. W. Anal. Chem. 2000, 72, 4778-4784.
Kjeldsen, F.; Haselmann, K. F.; Budnik, B. A.; Sorensen, E. S.; Zubarev, R. A. Anal. Chem. 2004.
Pesavento, J. J.; Kim, Y.-B.; Taylor, G. K.; Kelleher, N. L. J. Am. Chem. Soc. 2004, 126, 3386-3387.
Shi, S. D.; Hemling, M. E.; Carr, S. A.; Horn, D. M.; Lindh, I.; McLafferty, F. W. Anal. Chem. 2001, 73, 19-22.
Migorodskaya, E.; Roepstorff, P.; Zubarev, R. A. Anal. Chem. 1999, 71, 4431-4436.
McLuckey, S. A.; Stephenson, J. L. Mass Spectrom. Rev. 1998, 17, 369-407.
Syka, J. E.; Coon, J. J.; Schroeder, M. J.; Shabanowitz, J.; Hunt, D. F. Proc. Natl. Acad. Sci. U. S. A 2004, 101, 9528-9533.
Coon, J. J.; Shabanowitz, J.; Hunt, D. F.; Syka, J. E. J. Am. Soc. Mass Spectrom. 2005, 16, 880-882.
Chu, I. K.; Rodriguez, C. F.; Rodriguez, F.; Hopkinson, A. C.; Siu, K. W. M. J. Am. Soc. Mass Spectrom. 2001, 12, 1114-1119.
Hodyss, R.; Cox, H. A.; Beauchamp, J. L. J. Am. Chem. Soc. 2005, 127, 12436-12437.
Barlow, C. K.; McFadyen, W. D.; O'Hair, R. A. J. J. Am. Chem. Soc. 2005, 127, 6109-6115.
Misharin, A. S.; Silivra, O. A.; Kjeldsen, F.; Zubarev, R. A. Rapid Commun. Mass Spectrum. 2005, 19, 2163-2171.
Thompson, M. S.; Cui, W. D.; Reilly, J. P. Angew. Chem., Int. Ed. 2004, 43, 4791-4794.
Kim, T. Y.; Thompson, M. S.; Reilly, J. P. Rapid Commun. Mass Spectrom. 2005, 19, 1657-1665.
Cui, W. D.; Thompson, M. S.; Reilly, J. P. J. Am. Soc. Mass Spectrom. 2005, 16, 1384-1398.
Williams, E. R.; Furlong, J. J. P.; McLafferty, F. W. J. Am. Soc. Mass Spectrom. 1990, 1, 288-294.
Guan, Z.; Kelleher, N. L.; O'Connor, P. B.; Aaserud, D. J.; Little, D. P.; McLafferty, F. W. Int. J. Mass Spectrom. Ion Processes 1996, 157-158, 357-364.
Moon, J. H.; Yoon, S. H.; Kim, M. S. Rapid Commun. Mass Spectrom. 2005, 19, 3248-3252.
Oh, J. Y.; Moon, J. H.; Kim, M. S. Rapid Commun. Mass Spectrom. 2004, 18, 2706-2712.
Oh, J. Y.; Moon, J. H.; Lee, Y. H.; Hyung, S. W.; Lee, S. W.; Kim, M. S. Rapid Commun. Mass Spectrom. 2005, 19, 1283-1288.
Tabarin, T.; Antoine, R.; Broyer, M.; Dugourd, P. Rapid Commun. Mass Spectrom. 2005, 19, 2883-2892.
Lemoine, J.; Tabarin, T.; Antoine, R.; Broyer, M.; Dugourd, P. Rapid Commun. Mass Spectrom. 2006, 20, 507-511.
Markham, N. R.; Zuker, M. Nucleic Acids Res. 2005, 33, W577-W581.
Talbot, F. O.; Tabarin, T.; Antoine, R.; Broyer, M.; Dugourd, P. J. Chem. Phys. 2005, 122.
Gabelica, V.; De Pauw, E. J. Am. Soc. Mass Spectrom. 2002, 13, 91-98.
Yang, X.; Wang, X. B.; Vorpagel, E. R.; Wang, L. S. Proc. Natl. Acad. Sci. U. S. A. 2004, 101, 17588-17592.
Danell, A. S.; Parks, J. H. J. Am. Soc. Mass Spectrom. 2003, 14, 1330-1339.
Wetmore, S. D.; Boyd, R. J.; Eriksson, L. A. Chem. Phys. Lett. 2000, 322, 129-135.
Kim, N. S.; LeBreton, P. R. J. Am. Chem. Soc. 1996, 118, 3694-3707.
Starikov, E. B.; Lewis, J. P.; Sankey, O. F. Int. J. Mod. Phys. B 2005, 19, 4331-4357.
Hush, N. S.; Cheung, A. S. Chem. Phys. Lett. 1975, 34, 11-13.
Herron, W. J.; Goeringer, D. E.; McLuckey, S. A. J. Am. Chem. Soc. 1995, 117, 11555-11562.
McLuckey, S. A.; Stephenson, J. L.; Ohair, R. A. J. J. Am. Soc. Mass Spectrom. 1997, 8, 148-154.
Wu, J.; McLuckey, S. A. Int. J. Mass Spectrom. 2003, 228, 577-597.
Liu, B.; Hvelplund, P.; Nielsen, S. B.; Tomita, S. Int. J. Mass Spectrom. 2003, 230, 19-24.
Patterson, S. D.; Katta, V. Anal. Chem. 1994, 66, 3727-3732.
Takayama, M. J. Am. Soc. Mass Spectrom. 2001, 12, 1044-1049.
Kocher, T.; Engstrom, A.; Zubarev, R. A. Anal. Chem. 2005, 77, 172-177.
Wang, B. H.; Hopkins, C. E.; Belenky, A. B.; Cohen, A. S. Int. J. Mass Spectrom. 1997, 169, 331-350.
Juhasz, P.; Roskey, M. T.; Smirnov, I. P.; Haff, L. A.; Vestal, M. L.; Martin, S. A. Anal. Chem. 1996, 68, 941-946.
Rozenski, J.; McCloskey, J. A. J. Am. Soc. Mass Spectrom. 2002, 13, 200-203.
Weber, J. M.; Ioffe, I. N.; Berndt, K. M.; Loffler, D.; Friedrich, J.; Ehrler, O. T.; Danell, A. S.; Parks, J. H.; Kappes, M. M. J. Am. Chem. Soc. 2004, 126, 8585-8589.
Horn, D. M.; Breuker, K.; Frank, A. J.; McLafferty, F. W. J. Am. Chem. Soc. 2001, 123, 9792-9799.
Breuker, K.; Oh, H.; Horn, D. M.; Cerda, B. A.; McLafferty, F. W. J. Am. Chem. Soc. 2002, 124, 6407-6420.
