Conformationally Driven Gas-Phase H/D Exchange of Dinucleotide Negative Ions

Journal of the American Society for Mass Spectrometry

Volumn 18, Issue 10, 2007, Pages 1827-1834

  Balbeur, Dorothée ^a   Dehareng, Dominique ^a   De Pauw, Edwin ^a  

^a UNIVERSITY OF LIÈGE   (Belgium)

Author keywords

[No Author keywords available]

Indexed keywords

EXCHANGEABLE HYDROGEN; HETEROATOM BEARING;

COMPUTER SIMULATION; CYCLOTRON RESONANCE; DEUTERIUM; FOURIER TRANSFORMS; HYDROGEN; REACTION KINETICS;

NEGATIVE IONS;

DEUTERIUM; DINUCLEOTIDE; HYDROGEN; METHANOL; METHANOL H 2; UNCLASSIFIED DRUG;

ARTICLE; ATOM; CONFORMATION; DENSITY FUNCTIONAL THEORY; GAS; ION CYCLOTRON RESONANCE MASS SPECTROMETRY; ION EXCHANGE; MASS SPECTROMETER; MOLECULAR MODEL; REACTION ANALYSIS; REACTION TIME; SIMULATION;

ANIONS; COMPUTER SIMULATION; DEUTERIUM EXCHANGE MEASUREMENT; GASES; KINETICS; MODELS, CHEMICAL; MODELS, MOLECULAR; MOTION; NUCLEIC ACID CONFORMATION; OLIGONUCLEOTIDES; PHASE TRANSITION; SPECTROMETRY, MASS, ELECTROSPRAY IONIZATION; SPECTROSCOPY, FOURIER TRANSFORM INFRARED;

EID: 34548680490     PISSN: 10440305     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jasms.2007.07.014     Document Type: Article

References (26)

1. Gard E., Green M.K., Bregar J., and Lebrilla C.B. Gas-Phase Hydrogen/Deuterium Exchange as a Molecular Probe for the Interaction of Methanol and Protonated Peptides. J. Am. Soc. Mass Spectrom 5 (1994) 623-631
2. 3. J. Am. Chem. Soc 117 (1995) 12840-12854
3. 2S. J. Am. Chem. Soc 120 (1998) 10187-10193
4. Robinson J.M., Greig M.J., Griffey R.H., Venkantraman M., and Laude D.A. Hydrogen/Deuterium Exchange of Nucleotides in the Gas Phase. Anal. Chem 70 (1998) 3566-3571
5. Freitas M.A., and Marshall A.G. Gas-Phase RNA and DNA Ions. 2. Conformational Dependence of the Gas-Phase H/D Exchange of Nucleotide 5′ Monophosphates. J. Am. Soc. Mass Spectrom 12 (2001) 780-785
6. Wyttenbach T., and Bowers M.T. The Hydrogen/Deuterium Exchange Mechanism. J. Am. Soc. Mass Spectrom 10 (1999) 9-14
7. Gree-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
8. Crestoni M.E., and Fornarini S. Gas-Phase Hydrogen/Deuterium Exchange of Adenine Nucleotides. J. Mass Spectrom 38 (2003) 854-861
9. Wang F., Freitas M.A., Marshall A.G., and Skyes B.D. Gas-Phase Memory of Solution-Phase Protein Conformation: H/D Exchange and Fourier Transform Ion Cyclotron Resonance Mass Spectrometry of the N-Terminal Domain of Cardiac Troponin C. Int. J. Mass Spectrom 192 (1999) 319-325
10. Herrmann K., Wysocki V., and Vorpagel E.R. Computational Investigation and Hydrogen/Deuterium Exchange of the Fixed Charge Derivative Tris(2,4,6-Trimethoxyphenyl) Phosphonium: Implication of the Aspartic Acid Cleavage Mechanism. J. Am. Soc. Mass Spectrom 16 (2005) 1067-1080
11. 3OD. Int. J. Mass Spectrom 249/250 (2006) 93-105
12. Reid G.E., Simpson R.J., and O'Hair R.A.J. Probing the Fragmentation Reactions of Protonated Glycine Oligomers Via Multistage Mass Spectrometry and Gas Phase Ion-Molecule Hydrogen/Deuterium Exchange. Int. J. Mass Spectrom 191 (1999) 209-230
13. Felix T., Reyzer M., and Brodbelt J. Hydrogen/Deuterium Exchange of Nucleoside Analogs in a Quadrupole Ion Trap Mass Spectrometer. Int. J. Mass Spectrom 191 (1999) 161-170
14. 2+. J. Am. Soc. Mass Spectrom 11 (2000) 711-721
15. Zhang J., and Brodbelt J.S. Gas-Phase Hydrogen/Deuterium Exchange and Conformations of Deprotonated Flavonoids and Gas-Phase Acidities of Flavonoids. J. Am. Chem. Soc 126 (2004) 5906-5919
16. Chipuk J.E., and Brodbelt J.S. Gas-Phase Hydrogen/Deuterium Exchange of 5′ and 3′ Mononucleotides in a Quadrupole ion Trap: Exploring the Role of Conformation and System Energy. J. Am. Soc. Mass Spectrom 18 (2007) 724-736
17. Gidden J., and Bowers M.T. Gas-Phase Conformational and Energetic Properties of Deprotonated Dinucleotides. Eur. Phys. J. D 20 (2002) 409-419
18. Goodner K.L., Milgram K.E., Williams K.R., Watson C.H., and Eyler J.R. Quantification of Ion Abundances in Fourier Transform Ion Cyclotron Resonance Mass Spectrometry. J. Am. Soc. Mass Spectrom 9 (1998) 1204-1212
19. Marshall A.G., Comisarow M.B., and Parisod G. Relaxation and Spectral Line Shape in Fourier Transform Ion Resonance Spectroscopy. J. Chem. Phys 71 (1979) 4434-4444
20. Nir E., Imhof P., Kleinermanns K., and de Vries M.S. REMPI Spectroscopy of Laser Desorbed Guanosines. J. Am. Chem. Soc 122 (2000) 8091-8092
21. Rodgers M.T., Campbell S., Marzluff E.M., and Beauchamp J.L. Low-Energy Collision-Induced Dissociation of Deprotonated Dinucleotides: Determination of the Energetically Favored Dissociation Pathways and the Relative Acidities of Nucleic Acid Bases. Int. J. Mass Spectrom. Ion Processes 137 (1994) 121-149
22. Gidden J., and Bowers M.T. Gas-Phase Conformation of Deprotonated and Protonated Mononucleotides Determined by Ion Mobility and Theoretical Modeling. J. Phys. Chem 107 (2003) 12829-12837
23. Liu D., Wyttenbach T., and Bowers M.T. Hydration of Mononucleotides. J. Am. Chem. Soc 128 (2006) 15155-15163
24. Saenger W. Principles of Nucleic Acid Structure (1984), Springer-Verlag, New York 14-23
25. Frisch M.J., Trucks G.W., Schlegel H.B., Scuseria G.E., Robb M.A., Cheeseman J.R., Montgomery Jr. J.A., Vreven T., Kudin K.N., Burant J.C., Millam J.M., Iyengar S.S., Tomasi J., Barone V., Mennucci B., Cossi M., Scalmani G., Rega N., Petersson G.A., Nakatsuji H., Hada M., Ehara M., Toyota K., Fukuda R., Hasegawa J., Ishida M., Nakajima T., Honda Y., Kitao O., Nakai H., Klene M., Li X., Knox J.E., Hratchian H.P., Cross J.B., Adamo C., Jaramillo J., Gomperts R., Stratmann R.E., Yazyev O., Austin A.J., Cammi R., Pomelli C., Ochterski J.W., Ayala P.Y., Morokuma K., Voth G.A., Salvador P., Dannenberg J.J., Zakrzewski V.G., Dapprich S., Daniels A.D., Strain M.C., Farkas O., Malick D.K., Rabuck A.D., Raghavachari K., Foresman J.B., Ortiz J.V., Cui Q., Baboul A.G., Clifford S., Cioslowski J., Stefanov B.B., Liu G., Liashenko A., Piskorz P., Komaromi I., Martin R.L., Fox D.J., Keith T., Al-Laham M.A., Peng C.Y., Nanayakkara A., Challacombe M., Gill P.M.W., Johnson B., Chen W., Wong M.W., Gonzalez C., and Pople J.A. Gaussian 03, Revision C. 02 (2004), Gaussian, Inc, Wallingford, CT
26. McDonnell L.A., Giannakopulos A.E., Derrick P.J., Tsybin Y.O., and Hakansson P.A. Theoretical Investigation of The Kinetic Energy of Ions Trapped in a Radio-Frequency Hexapole Ion Trap. Eur. J. Mass Spectrom 8 (2002) 181-189