New aspects of the fragmentation mechanisms of unmodified and methylphosphonate-modified oligonucleotides

  • Selina T. M. Monn
  • Stefan Schürch


A set of pentanucleotides was investigated by electrospray tandem mass spectrometry with the focus on the fragmentation mechanism. Results reveal new aspects of the fragmentation mechanism of modified and unmodified oligonucleotides and demonstrate the influence of the nucleobases on the decomposition of oligonucleotides. Adenine-rich oligonucleotides fragment easily resulting in abundant peaks corresponding to the DNA-typical a-B-and w-ions. On the other hand, thymine was found to have a stabilizing effect, which is reflected by the preferred formation of the w4-ions and the relatively low abundance of shorter w-ions upon dissociation of pentanucleotides. Data from investigation of the formation of w4-ions support a β-elimination mechanism. Results obtained by investigation of oligonucleotides with an abasic site confirm this mechanism, which is independent of nucleobase loss. Experiments with methylphosphonate oligonucleotides show a remarkable change in the fragmentation pattern due to the modification. It was found that charges are located on the nucleobases and initiate the fragmentation mechanism. The stability of the oligonucleotide is reduced and no a-B-fragment ions are formed wherever there is a methylphosphonate group within the backbone. This fact also demonstrates that fragmentation is locally controlled.


Phosphate Group Proton Affinity Collision Induce Dissociation Fragmentation Mechanism Abasic Site 
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  1. 1.
    Schulten, H.-R.; Schiebel, H. M. Sequence specific fragments in the field desorption mass spectra of dinucleoside phosphates. Nucleic Acids Res. 1976, 3, 2027–2031.CrossRefGoogle Scholar
  2. 2.
    Nordhoff, E.; Kirpekar, F.; Roepstorff, P. Mass Spectrometry of Nucleic Acids. Mass Spectrom. Rev. 1996, 15, 67–138.CrossRefGoogle Scholar
  3. 3.
    Wu, J.; McLuckey, S. A. Gas-Phase Fragmentation of Oligonucleotide Ions. Int. J. Mass Spectrom. 2004, 237, 197–241.CrossRefGoogle Scholar
  4. 4.
    Wang, Z.; Wan, K. X.; Ramanathan, R.; Taylor, J. S.; Gross, M. L. Structure and Fragmentation Mechanisms of Isomeric T-Rich Oligodeoxynucleotides: A Comparison of Four Tandem Mass Spectrometric Methods. J. Am. Soc. Mass. Spectrom. 1998, 9, 683–691.CrossRefGoogle Scholar
  5. 5.
    Wan, K. X.; Gross, J.; Hillenkamp, F.; Gross, M. L. Fragmentation Mechanisms of Oligodeoxynucleotides Studied by H/D Exchange and Electrospray Ionization Tandem Mass Spectrometry. J. Am. Soc. Mass Spectrom. 2001, 12, 193–205.CrossRefGoogle Scholar
  6. 6.
    Wan, K. X.; Gross, M. L. Fragmentation Mechanisms of Oligodeoxynucleotides: Effects of Replacing Phosphates with Methylphosphonates and Thymines with Other Bases in T-rich Sequences. J. Am. Soc. Mass Spectrom. 2001, 12, 580–589.CrossRefGoogle Scholar
  7. 7.
    Greco, F.; Liguori, A.; Sindona, G.; Uccella, N. Gas-Phase Proton Affinity of Deoxyribonucleotides and Related Nucleobases by Fast Atom Bombardment Tandem Mass Spectrometry. J. Am. Chem. Soc. 1990, 112, 9092–9096.CrossRefGoogle Scholar
  8. 8.
    Pan, S.; Verhoeven, K.; Lee, J. K. Investigation of the Initial Fragmentation of Oligodeoxynucleotides in a Quadrupole Ion Trap: Charge Level-Related Base Loss. J Am. Soc. Mass Spectrom. 2005, 16, 1853–1865.CrossRefGoogle Scholar
  9. 9.
    Cerny, R. L.; Gross, M. L.; Grotjahn, L. Fast Atom Bombardment Combined with Tandem Mass Spectrometry for the Study of Dinucleotides. Anal. Biochem. 1986, 156, 424–435.CrossRefGoogle Scholar
  10. 10.
    Sannes-Lowery, K. A.; Hofstadler, S. A. Sequence Confirmation of Modified Oligonucleotides Using IRMPD in the External Ion Reservoir of an Electrospray Ionization Fourier Transform Ion Cyclotron Mass Spectrometer. J Am. Soc. Mass Spectrom. 2003, 14, 825–833.CrossRefGoogle Scholar
  11. 11.
    Bartlett, M. G.; McCloskey, J. A.; Manalili, S.; Griffey, R. H. The Effect of Backbone Charge on the Collision-Induced Dissociation of Oligonucleotides. J. Mass Spectrom. 1996, 31, 1277–1283.CrossRefGoogle Scholar
  12. 12.
    Schürch, S.; Bernal-Mendez, E.; Leumann, C. J. Electrospray Tandem Mass Spectrometry of Mixed-Sequence RNA/DNA Oligonucleotides. J. Am. Soc. Mass Spectrom. 2002, 13, 936–945.CrossRefGoogle Scholar
  13. 13.
    De Nino, A.; Liguori, A.; Maiuolo, L.; Marino, T.; Procopio, A.; Sindona, G. Participation of the Nucleobases in the Regioselective Backbone Fragmentation of Nucleic Acids: A Molecular Dynamics and Tandem Mass Spectrometric Investigation on a Model Dinucleoside Phosphotriester. J. Am. Soc. Mass Spectrom. 1997, 8, 1257–1261.CrossRefGoogle Scholar

Copyright information

© American Society for Mass Spectrometry 2007

Authors and Affiliations

  1. 1.Department of Chemistry and BiochemistryUniversity of BernBernSwitzerland

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