RNA Fragmentation in MALDI Mass Spectrometry Studied by H/D-Exchange: Mechanisms of General Applicability to Nucleic Acids

Journal of the American Society for Mass Spectrometry

Volumn 17, Issue 10, 2006, Pages 1353-1368

  Andersen, Thomas E ^a   Kirpekar, Finn ^a   Haselmann, Kim F ^a  

^a UNIVERSITY OF SOUTHERN DENMARK   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

DEUTERIUM; DNA; HYDROGEN; HYDROXYLATION; MASS SPECTROMETRY; POSITIVE IONS;

BACKBONE CLEAVAGES; MALDI MASS SPECTROMETRY; RNA FRAGMENTATION;

RNA;

DEUTERIUM; DNA FRAGMENT; HYDROGEN; NUCLEIC ACID; NUCLEIC ACID BASE; RNA;

ARTICLE; CHEMICAL REACTION; DEUTERIUM HYDROGEN EXCHANGE; FRAGMENTATION REACTION; GAS; INFORMATION; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY;

DATA INTERPRETATION, STATISTICAL; DEUTERIUM; DNA; GLYCOSIDES; HYDROGEN; HYDROXYLATION; NUCLEIC ACIDS; RNA; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION;

EID: 33748984285     PISSN: 10440305     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jasms.2006.05.018     Document Type: Article

References (28)

1. Grotjahn L., Blocker H., and Frank R. Mass spectroscopic sequence-analysis of oligonucleotides. Biomed. Mass Spectrom 12 (1985) 514-524
2. Grotjahn L., Frank R., and Blocker H. Ultrafast sequencing of oligodeoxyribonucleotides by FAB-mass spectrometry. Nucleic Acids Res 10 (1982) 4671-4678
3. Wu J., and McLuckey S.A. Gas-phase fragmentation of oligonucleotide ions. Int. J. Mass Spectrom 237 (2004) 197-241
4. Phillips D.R., and McCloskey J.A. A comprehensive study of the low-energy collision-induced dissociation of dinucleoside monophosphates. Int. J. Mass Spectrom. Ion Processes 128 (1993) 61-82
5. Gross J., Leisner A., Hillenkamp F., Hahner S., Karas M., Schafer J., Lutzenkirchen F., and Nordhoff E. Investigations of the metastable decay of DNA under ultraviolet matrix-assisted laser desorption/ionization conditions with post-source decay analysis and hydrogen/deuterium exchange. J. Am. Soc. Mass Spectrom 9 (1998) 866-878
6. Wan K.X., Gross J., Hillenkamp F., and Gross M.L. Fragmentation mechanisms of oligodeoxynucleotides studied by H/D exchange and electrospray ionization tandem mass spectrometry. J. Am. Soc. Mass Spectrom 12 (2001) 193-205
7. Gross J., Hillenkamp F., Wan K.X., and Gross M.L. Metastable decay of negatively charged oligodeoxynucleotides analyzed with ultraviolet matrix-assisted laser desorption/ionization post-source decay and deuterium exchange. J. Am. Soc. Mass Spectrom 12 (2001) 180-192
8. McLuckey S.A., and Habibi-Goudarzi S. Decompositions of multiply-charged oligonucleotide anions. J. Am. Chem. Soc 115 (1993) 12085-12095
9. Wang Z., Wan K.X., Ramanathan R., Taylor J.S., and 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 9 (1998) 683-691
10. Kirpekar F., and Krogh T.N.R.N.A. fragmentation studied in a matrix-assisted laser desorption/ionization tandem quadrupole/orthogonal time-of-flight mass spectrometer. Rapid Commun. Mass Spectrom 15 (2001) 8-14
11. Schürch S., Bernal-Mendez E., and Leumann C.J. Electrospray tandem mass spectrometry of mixed-sequence RNA/DNA oligonucleotides. J. Am. Soc. Mass Spectrom 13 (2002) 936-945
12. Tromp J.M., and Schürch S. Gas-phase dissociation of oligoribonucleotides and their analogues studied by electrospray ionization tandem mass spectrometry. J. Am. Soc. Mass Spectrom 16 (2005) 1262-1268
13. Chou C.W., Limbach P.A., and Cole R.B. Fragmentation pathway studies of oligonucleotides in matrix-assisted laser desorption/ionization mass spectrometry by charge tagging and H/D exchange. J. Am. Soc. Mass Spectrom 13 (2002) 1407-1417
14. Jørgensen T.J.D., Bache N., Roepstorff P., Gardsvoll H., and Ploug M. Collisional activation by MALDI tandem time-of-flight mass spectrometry induces intramolecular migration of amide hydrogens in protonated peptides. Mol. Cell. Proteom 4 (2005) 1910-1919
15. Cerny R.L., Tomer K.B., Gross M.L., and Grotjahn L. Fast atom bombardment combined with tandem mass spectrometry for determining structures of small oligonucleotides. Anal. Biochem 165 (1987) 175-182
16. Takagi Y., Warashina M., Stec W.J., Yoshinari K., and Taira K. Recent advances in the elucidation of the mechanisms of action of ribozymes. Nucleic Acids Res 29 (2001) 1815-1834
17. Cassano A.G., Anderson V.E., and Harris M.E. Understanding the transition states of phosphodiester bond cleavage: insights from heavy atom isotope effects. Biopolymers 73 (2004) 110-129
18. Horton H.R., Moran L.A., Ochs R.S., Rawn J.D., and Scrimgeour K.G. Principles of biochemistry. 3rd ed. (2002), Prentice-Hall pp 605-607.
19. Boschenok J., and Sheil M.M. Electrospray tandem mass spectrometry of nucleotides. Rapid Commun. Mass Spectrom 10 (1996) 144-149
20. Ni J.S., Mathews M.A.A., and McCloskey J.A. Collision-induced dissociation of polyprotonated oligonucleotides produced by electrospray ionization. Rapid Commun. Mass Spectrom 11 (1997) 535-540
21. Nordhoff E., Karas M., Cramer R., Hahner S., Hillenkamp F., Kirpekar F., Lezius A., Muth J., Meier C., and Engels J.W. Direct mass-spectrometric sequencing of low-picomole amounts of oligodeoxynucleotides with up to 21 bases by matrix-assisted laser-desorption ionization mass spectrometry. J. Mass Spectrom 30 (1995) 99-112
22. Nordhoff E., Cramer R., Karas M., Hillenkamp F., Kirpekar F., Kristiansen K., and Roepstorff P. Ion stability of nucleic acids in infrared matrix-assisted laser desorption/ionization mass spectrometry. Nucleic Acids Res 21 (1993) 3347-3357
23. Wang B.H., Hopkins C.E., Belenky A.B., and Cohen A.S. Sequencing of modified oligonucleotides using in-source fragmentation and delayed pulsed ion extraction matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Int. J. Mass Spectrom 169 (1997) 331-350
24. Wan K.X., and 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 12 (2001) 580-589
25. Schneider K., and Chait B.T. Matrix-assisted laser-desorption mass-spectrometry of homopolymer oligodeoxyribonucleotides-influence of base composition on the mass-spectrometric response. Org. Mass Spectrom 28 (1993) 1353-1361
26. Nordhoff E., Kirpekar F., Karas M., Cramer R., Hahner S., Hillenkamp F., Kristiansen K., Roepstroff P., and Lezius A. Comparison of IR- and UV-matrix-assisted laser desorption/ionization mass spectrometry of oligodeoxynucleotides. Nucleic Acids Res 22 (1994) 2460-2465
27. Kirpekar F., Nordhoff E., Kristiansen K., Roepstorff P., Hahner S., and Hillenkamp F. 7-Deaza purine bases offer a higher ion stability in the analysis of DNA by matrix-assisted laser desorption/ionization mass spectrometry. Rapid Commun. Mass Spectrom 9 (1995) 525-531
28. Schneider K., and Chait B.T. Increased stability of nucleic acids containing 7-deaza-guanosine and 7-deaza-adenosine may enable rapid DNA sequencing by matrix-assisted laser desorption mass spectrometry. Nucleic Acids Res 23 (1995) 1570-1575