Fragmentation of Oligoribonucleotides from Gas-Phase Ion-Electron Reactions

Journal of the American Society for Mass Spectrometry

Volumn 17, Issue 10, 2006, Pages 1369-1375

  Yang, Jiong ^a   Håkansson, Kristina ^a  

^a UNIVERSITY OF MICHIGAN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DISSOCIATION; DNA; ELECTRON SOURCES; ION SOURCES; REACTION KINETICS; RNA;

COLLISION ACTIVATED DISSOCIATION (CAD); ELECTRON CAPTURE DISSOCIATION (ECD); ELECTRON DETACHMENT DISSOCIATION (EDD); ION ELECTRON REACTIONS;

GENETIC ENGINEERING;

ION; NUCLEIC ACID BASE; OLIGORIBONUCLEOTIDE; PHOSPHATE; RNA;

ARTICLE; ELECTRON CAPTURE DETECTION; ELECTRON DETACHMENT DISSOCIATION; GAS; RNA CLEAVAGE; TECHNIQUE;

CHROMATOGRAPHY, HIGH PRESSURE LIQUID; CYCLOTRONS; FOURIER ANALYSIS; MASS SPECTROMETRY; OLIGORIBONUCLEOTIDES; PHOSPHATES;

EID: 33748986566     PISSN: 10440305     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jasms.2006.05.006     Document Type: Article

References (49)

1. Johnston W.K., Unrau P.J., Lawrence M.S., Glasner M.E., and Bartel D.P. RNA-Catalyzed RNA Polymerization: Accurate and General RNA-Templated Primer Extension. Science 292 (2001) 1319-1325
2. Walter N.G., Harris D.A., Pereira M.J.B., and Rueda D. In the Fluorescent Spotlight: Global and Local Conformational Changes of Small Catalytic RNAs. Biopolymers 61 (2001) 224-242
3. Bevilacqua P.C., Brown T.S., Nakano S., and Yajima R. Catalytic Roles for Proton Transfer and Protonation in Ribozymes. Biopolymers 73 (2004) 90-109
4. Fürtig B., Richter C., and Wöhnert J. NMR Spectroscopy of RNA. Chem. Biochem 4 (2003) 936-962 H., S
5. Al-Hashimi H.M. Dynamics-Based Amplification of RNA Function and Its Characterization by Using NMR Spectroscopy. Chem. Biochem 6 (2005) 1506-1519
6. Selvin P.R. Fluorescence Resonance Energy Transfer. Methods Enzymol 246 (1995) 6264-6268
7. Zhuang X. Single-Molecule RNA Science. Annu. Rev. Biophys. Biomol. Struct 34 (2005) 399-414
8. Limbach P.A., Crain P.F., and McCloskey J.A. Molecular Mass Measurement of Intact Ribonucleic Acids Via Electrospray Ionization Quadrupole Mass Spectrometry. J. Am. Soc. Mass Spectrom 6 (1995) 27-39
9. Crain P.F., and McCloskey J.A. Applications of Mass Spectrometry to the Characterization of Oligonucleotides and Nucleic Acids. Curr. Opin. Biotechnol 9 (1998) 25-34
10. Polson A.G., Crain P.F., Pomerantz S.C., McCloskey J.A., and Bass B.L. The Mechanism of Adenosine to Inosine Conversion by the Double-Stranded RNA Unwinding/Modifying Activity: A High-performance Liquid Chromatography-Mass Spectrometry Analysis. Biochemistry 30 (1991) 11507-11514
11. Limbach P.A., Crain P.F., and McCloskey J.A. Summary: The Modified Nucleosides of RNA. Nucleic Acids Res 22 (1994) 2183-2196
12. Pomerantz S.C., and McCloskey J.A. Detection of the Common RNA Nucleoside Pseudouridine in Mixtures of Oligonucleotides by Mass Spectrometry. Anal. Chem 77 (2005) 4697-4697
13. Ni J., Pomerantz S.C., Rozenski J., Zhang Y., and McCloskey J.A. Interpretation of Oligonucleotide Mass Spectra for Determination of Sequence Using Electrospray Ionization and Tandem Mass Spectrometry. Anal. Chem 68 (1996) 1989-1999
14. Muddiman D.C., and Smith R.D. Sequencing and Characterization of Larger Oligonucleotides by Electrospray Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectrometry. Rev. Anal. Chem 17 (1998) 1-68
15. Benson L.M., Null A.P., and Muddiman D.C. Advantages of Thermococcus kodakaraenis (KOD) DNA Polymerase for PCR-Mass Spectrometry Based Analyses. J. Am. Soc. Mass Spectrom 14 (2003) 601-604
16. Banoub J.H., Newton R.P., Esmans E., Ewing D.F., and Mackenzie G. Recent Developments in Mass Spectrometry for the Characterization of Nucleosides, Nucleotides, Oligonucleotides, and Nucleic Acids. Chem. Rev 105 (2005) 1869-1916
17. Hofstadler S.A., Sannes-Lowery K.A., and Hannis J.C. Analysis of Nucleic Acids by FTICR MS. Mass Spectrom. Rev 24 (2005) 265-285
18. Wu J., and McLuckey S.A. Gas-Phase Fragmentation of Oligonucleotide Ions. Int. J. Mass Spectrom 237 (2004) 197-241
19. Little D.P., Chorush R.A., Speir J.P., Senko M.W., Kelleher N.L., and McLafferty F.W. Rapid Sequencing of Oligonucleotides by High-Resolution Mass-Spectrometry. J. Am. Chem. Soc 116 (1994) 4893-4897
20. Little D.P., Aaserud D.J., Valaskovic G.A., and McLafferty F.W. Sequence Information from 42-108-mer DNAs (Complete for a 50 mer) by Tandem Mass Spectrometry. J. Am. Chem. Soc 118 (1996) 9352-9359
21. Sannes-Lowery K.A., and Hofstadler S.A. Sequence Confirmation of Modified Oligonucleotides Using IRMPD in the External Reservoir of an Electrospray Ionization Fourier Transform Ion Cyclotron Mass Spectrometer. J. Am. Soc. Mass Spectrom 14 (2003) 825-833
22. Sannes-Lowery K.A., Drader J.J., Griffey R.H., and Hofstadler S.A. Fourier Transform Ion Cyclotron Resonance Mass Spectrometry as a High Throughput Affinity Screen to Identify RNA Binding Ligands. Trends Anal. Chem 19 (2000) 481-491
23. McLuckey S.A., Van Berkel G.J., and Glish G.L. Tandem Mass Spectrometry of Small, Multiply-charged Oligonucleotides. J. Am. Soc. Mass Spectrom 3 (1992) 60-70
24. McLafferty F.W., Horn D.M., Breuker K., Ge Y., Lewis M.A., Cerda B., Zubarev R.A., and Carpenter B.K. Electron Capture Dissociation of Gaseous Multiply Charged Ions by Fourier Transform Ion Cyclotron Resonance. J. Am. Soc. Mass Spectrom 12 (2001) 245-249
25. Zubarev R.A. Reactions of Polypeptide Ions with Electrons in the Gas Phase. Mass Spectrom. Rev 22 (2003) 57-77
26. Zubarev R.A. Electron Capture Dissociation Tandem Mass Spectrometry. Curr. Opin. Biotechnol 15 (2004) 12-16
27. Cooper H.J., Håkansson K., and Marshall A.G. The Role of Electron Capture Dissociation in Biomolecular Analysis. Mass Spectrom. Rev 24 (2005) 201-222
28. Håkansson K., Hudgins R.R., Marshall A.G., and O'Hair R.A.J. Electron Capture Dissociation and Infrared Multiphoton Dissociation of Oligodeoxynucleotide Dications. J. Am. Soc. Mass Spectrom 14 (2003) 23-41
29. Schultz K.N., and Håkansson K. Rapid Electron Capture Dissociation of Mass-Selectively Accumulated Oligodeoxynucleotide Dications. Int. J. Mass Spectrom 234 (2004) 123-130
30. Horn D.M., Breuker K., Frank A.J., and McLafferty F.W. Kinetic Intermediates in the Folding of Gaseous Protein Ions Characterized by Electron Capture Dissociation Mass Spectrometry. J. Am. Chem. Soc 123 (2001) 9792-9799
31. Budnik B.A., Haselmann K.F., and Zubarev R.A. Electron Detachment Dissociation of Peptide Dianions: An Electron-Hole Recombination Phenomenon. Chem. Phys. Lett 342 (2001) 299-302
32. Yang J., Mo J., Adamson J.T., and Håkansson K. Characterization of Oligodeoxynucleotides by Electron Detachment Dissociation Fourier Transform Ion Cyclotron Resonance Mass Spectrometry. Anal. Chem 77 (2005) 1876-1882
33. Schürch S., Bernal-Méndez E., and Leumann C.J. Electrospray Tandem Mass Spectrometry of Mixed-Sequence RNA/DNA Oligonucleotides. J. Am. Soc. Mass Spectrom 13 (2002) 936-945
34. Tromp J.M., and Schurch S. Gas-Phase Dissociation of Oligoribonucleotides and Their Analogs Studied by Electrospray Ionization Tandem Mass Spectrometry. J. Am. Soc. Mass Spectrom 16 (2005) 1262-1268
35. de Köning L.J., Nibbering N.M.M., van Orden S.L., and Laukien F.H. Mass Selection of Ions in a Fourier Transform Ion Cyclotron Resonance Trap using Correlated Harmonic Excitation Fields (CHEF). Int. J. Mass Spectrom. Ion Processes 165 (1997) 209-219
36. Breuker K., Oh H., Cerda B.A., Horn D.M., and McLafferty F.W. Hydrogen Atom Loss in Electron Capture Dissociation: A Fourier Transform Ion Cyclotron Resonance Study with Single Isotopomeric Ubiquitin Ions. Eur. J. Mass Spectrom 8 (2002) 177-180
37. Green-Church K.B., and Limbach P.A. Mononucleotide Gas-Phase Proton Affinities as Determined by the Kinetic Method. J. Am. Soc. Mass Spectrom 11 (2000) 24-32
38. Green-Church K.B., Limbach P.A., Freitas M.A., and Marshall A.G. Gas-Phase Hydrogen/Deuterium Exchange of Positively Charged Mononucleotides by Use of Fourier-Transform Ion Cyclotron Resonance Mass Spectrometry. J. Am. Soc. Mass Spectrom 12 (2001) 268-277
39. 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
40. 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
41. Berdys J., Anusiewicz I., Skurski P., and Simons J. Damage to Model DNA Fragments from Very Low-Energy (<1 eV) Electrons. J. Am. Chem. Soc 126 (2004) 6441-6447
42. Li X., Sevilla M.D., and Sanche L. Density Functional Theory Studies of Electron Interaction with DNA: Can Zero eV Electrons Induce Strand Breaks?. J. Am. Chem. Soc 125 (2003) 13668-13669
43. McFarland M.A., Chalmers M.J., Quinn J.P., Hendrickson C.L., and Marshall A.G. Evaluation and Optimization of Electron Capture Dissociation Efficiency in Fourier Transform Ion Cyclotron Resonance Mass Spectrometry. J. Am. Soc. Mass Spectrom 16 (2005) 1060-1066
44. Griffey R.H., Greig M.J., Robinson J.M., and Laude D.A. Gas-Phase Hydrogen-Deuterium Exchange in Phosphorothioate d(GTCAG) and d(TCGAT). Rapid Commun. Mass Spectrom 13 (1999) 113-117
45. Kjeldsen F., Silivra O.A., Ivonin I.A., Haselmann K.F., Gorshkov M., and Zubarev R.A. C-α-C Backbone Fragmentation Dominates in Electron Detachment Dissociation of Gas-Phase Polypeptide Polyanions. Chem. Eur. J 11 (2005) 1803-1812
46. 2- in the Gas Phase. J. Phys. Chem. A 105 (2001) 10468-10474
47. Hush N.S., and Cheung A.S. Ionization Potentials and Donor Properties of Nucleic Acid Bases and Related Compounds. Chem. Phys. Lett 34 (1975) 11-13
48. Budnik B.A., Haselmann K.F., Elkin Y.N., Gorbach V.I., and Zubarev R.A. Applications of Electron-Ion Dissociation Reactions for Analysis of Polycationic Chitooligosaccharides in Fourier Transform Mass Spectrometry. Anal. Chem 75 (2003) 5994-6001
49. Olsen J.V., Haselmann K.F., Nielsen M.L., Budnik B.A., Nielsen P.E., and Zubarev R.A. Comparison of Electron Capture Dissociation and Collisionally Activated Dissociation of Polycations of Peptide Nucleic Acids. Rapid Commun. Mass Spectrom 15 (2001) 969-974