Charge effects for differentiation of oligodeoxynucleotide isomers containing 8-oxo-dG residues

Short Communication

Abstract

Dissociation reactions of a series of multiply charged oligodeoxynucleotide (ODN) 12-mer anions were studied using an ion trap mass spectrometer. These mixed nucleobase 12-mers fragment first by loss of a neutral nucleobase (A, G, C, and/or 5-methyl-cytosine) followed by cleavage at 3′ C-O bond of the sugar from which the base is lost to produce the complementary sequence ions, i.e., [a – B] and w type of ions. No detectable loss of 8-oxo-guanine and/or thymine from these 12-mers is observed under gentle collision conditions in the ion trap. The primary loss of a nucleobase and the subsequent backbone cleavage to generate sequence ions strongly depend on the charge state of the parent molecular ion. For low charge states (2- and 3-), product ions due to the loss of a neutral guanine base and related sequence ions are dominant in the tandem mass spectra. However, preferential loss of a neutral adenine becomes the primary reaction channel from the 5- charge state of the molecular ion. Such charge state dependent fragmentation behavior was utilized to determine the site of 8-oxo-dG residue in a series of structural isomers. The position of 8-oxo-dG residue can be simply determined from the fragmentation pattern of 3- charge state, but not of 5- charge state. It is suggested that in addition to specific modification that affects the N-glycosidic bond strength, total charge content of an ODN is an important factor for determining the differential fragmentation behavior.

References

  1. 1.
    Barry, J. P.; Vouros, P.; Vanschepdael, A.; Law, S. J. Mass and Sequence Verification of Modified Oligonucleotides Using Electrospray Tandem Mass Spectrometry. J. Mass Spectrom. 1995, 30, 993–1006.CrossRefGoogle Scholar
  2. 2.
    Tang, W.; Zhu, L.; Smith, L. M. Controlling DNA Fragmentation in MALDI-MS by Chemical Modification. Anal. Chem. 1997, 69, 302–312.CrossRefGoogle Scholar
  3. 3.
    Wang, Y. S.; Taylor, J. S.; Gross, M. L. Differentiation of Isomeric Photomodified Oligodeoxynucleotides by Fragmentation of Ions Produced by Matrix-Assisted Laser Desorption Ionization and Electrospray Ionization. J. Am. Soc. Mass Spectrom. 1999, 10, 329–338.CrossRefGoogle Scholar
  4. 4.
    Harsch, A.; Sayer, J. M.; Jerina, D. M.; Vouros, P. HPLC-MS/MS Identification of Positionally Isomeric Benzo[c]phenanthrene Diol Epoxide Adducts in Duplex DNA. Chem. Res. Toxicol. 2000, 13, 1342–1348.CrossRefGoogle Scholar
  5. 5.
    Wang, Y. S.; Taylor, J. S.; Gross, M. L. Isolation and Mass Spectrometric Characterization of Dimeric Adenine Photoproducts in Oligodeoxynucleotides. Chem. Res. Toxicol. 2001, 14, 738–745.CrossRefGoogle Scholar
  6. 6.
    Christian, N. P.; Reilly, J. P.; Mokler, V. R.; Wincott, F. E.; Ellington, A. D. Elucidation of the Initial Step of Oligonucleotide Fragmentation in Matrix-Assisted Laser Desorption/ Ionization Using Modified Nucleic Acids. J. Am. Soc. Mass Spectrom. 2001, 12, 744–753.CrossRefGoogle Scholar
  7. 7.
    McLuckey, S. A.; Vaidyanathan, G.; Habibi-Goudarzi, S. Charged versus Neutral Nucleobase Loss from Multiply Charged Oligonucleotide Anions. J. Mass Spectrom. 1995, 30, 1222–1229.CrossRefGoogle Scholar
  8. 8.
    McLuckey, S. A.; Vaidyanathan, G. Charge State Effects in the Decompositions of Single-Nucleobase Oligonucleotide Polyanions. Int. J. Mass Spectrom. Ion Processes 1997, 162, 1–16.CrossRefGoogle Scholar
  9. 9.
    McLuckey, S. A.; Habibi-Goudarzi, S. Decompositions of Multiply Charged Oligonucleotide Anions. J. Am. Chem. Soc. 1993, 115, 12085–12095.CrossRefGoogle Scholar
  10. 10.
    Little, D. P.; Aaserud, D. J.; Valaskovic, G. A.; McLafferty, F. W. Sequence Information from 42–108-mer DNAs (Complete for a 50-mer) by Tandem Mass Spectrometry. J. Am. Chem. Soc. 1996, 118, 9352–9359.CrossRefGoogle Scholar
  11. 11.
    Zhu, L.; Parr, G. R.; Fitzgerald, M. C.; Nelson, C. M.; Smith, L. M. Oligonucleotide Fragmentation in MALDI/TOF Mass Spectrometry Using 355-nm Radiation. J. Am. Chem. Soc. 1995, 117, 6048–6056.CrossRefGoogle Scholar
  12. 12.
    Klassen, J. S.; Schnier, P. D.; Williams, E. R. Blackbody Infrared Radiative Dissociation of Oligonucleotide Anions. J. Am. Soc. Mass Spectrom. 1998, 9, 1117–1124.CrossRefGoogle Scholar
  13. 13.
    Beckman, K. B.; Ames, B. N. Oxidative Decay of DNA. J. Biol. Chem. 1997, 272, 19633–19636.CrossRefGoogle Scholar
  14. 14.
    Muddiman, D. C.; Cheng, X.; Udseth, H. R.; Smith, R. D. Charge-State Reduction with Improved Signal Intensity of Oligonucleotides in Electrospray Ionization Mass Spectrometry. J. Am. Soc. Mass Spectrom. 1996, 7, 697–706.Google Scholar
  15. 15.
    Griffey, R. H.; Sasmor, H.; Greig, M. J. Oligonucleotide Charge States in Negative Ionization Electrospray Mass Spectrometry Are a Function of Solution Ammonium Ion Concentration. J. Am. Soc. Mass Spectrom. 1997, 8, 155–160.CrossRefGoogle Scholar
  16. 16.
    McLuckey, S. A.; Van Berkel, G. J.; Glish, G. L. Tandem Mass Spectrometry of Small, Multiply Charged Oligonucleotides. J. Am. Soc. Mass Spectrom. 1992, 3, 60–70.CrossRefGoogle Scholar
  17. 17.
    Bialkowski, K.; Cysewski, P.; Olinski, R. Effect of 2′-deoxyguanosine Oxidation at C8 Position on N-glycosidic Bond Stability. Z. Naturforsch. C 1996, 51, 119–122.Google Scholar
  18. 18.
    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
  19. 19.
    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
  20. 20.
    Greco, F.; Liguori, A.; Sindona, G.; Uccella, N. Gas-Phase Proton Affinity of Deoxyribonucleosides and Related Nucleo-bases by Fast Atom Bombardment Tandem Mass Spectrometry. J. Am. Chem. Soc. 1990, 112, 9092–9096.CrossRefGoogle Scholar

Copyright information

© American Society for Mass Spectrometry 2002

Authors and Affiliations

  1. 1.Environmental Molecular Sciences LaboratoryPacific Northwest National LaboratoryRichlandUSA

Personalised recommendations