Decameric uracil complexes around Li+

Journal of Mass Spectrometry

Volumn 45, Issue 7, 2010, Pages 740-749

  Zins, Emilie Laure ^a,b   Pepe, Claude ^b   Schröder, Detlef ^a  

^a INSTITUTE OF ORGANIC CHEMISTRY AND BIOCHEMISTRY   (Czech Republic)

^b Centre National de la Recherche Scientifique Université Pierre et Marie Curie Paris 6 Sorbonne Universités   (France)

Author keywords

Effective; ESI MS MS; Fragmentation pattern; Geometry optimizations; Magic numbers; Noncovalent complexes; Nucleobases; Temperature

Indexed keywords

ELECTROSPRAY IONIZATION; GEOMETRY; IONIZATION OF GASES; MASS SPECTROMETRY; MODEL STRUCTURES;

FRAGMENTATION PATTERNS; GEOMETRY OPTIMIZATIONS; MAGIC NUMBERS; NON-COVALENT COMPLEXES; NUCLEOBASES;

DENSITY FUNCTIONAL THEORY;

LITHIUM; URACIL; MONOVALENT CATION;

AB INITIO CALCULATION; ARTICLE; CHEMICAL STRUCTURE; DENSITY FUNCTIONAL THEORY; ELECTROSPRAY MASS SPECTROMETRY; FRAGMENTATION REACTION; GAS; PRIORITY JOURNAL; QUANTUM CHEMISTRY; CHEMISTRY; KINETICS; PROCEDURES; QUANTUM THEORY;

CATIONS, MONOVALENT; KINETICS; LITHIUM; MODELS, MOLECULAR; QUANTUM THEORY; SPECTROMETRY, MASS, ELECTROSPRAY IONIZATION; URACIL;

EID: 77954453729     PISSN: 10765174     EISSN: 10969888     Source Type: Journal    
DOI: 10.1002/jms.1764     Document Type: Article

References (44)

1. J. R. Williamson, M. K. Raghuraman, T. R. Cech. Monovalent cationin-duced structure of telomeric DNA: the G-quartet model. Cell (Cambridge, MA, United States) 1989, 59, 871.
2. R. Otero, M. Schock, L. M. Molina, E. Laegsgaard, I. Stensgaard, B. Hammer, F. Besenbacher. Guanine quartet networks stabilized by cooperative hydrogen bonds. Angew. Chem. Int. Ed. Engl. 2005, 44, 2270.
3. E. S. Baker, S. L. Bernstein, M. T. Bowers. Structural characterization of G-quadruplexes in deoxyguanosine clusters using ion mobility mass spectrometry. J. Am. Soc.Mass Spectrom. 2005, 16, 989.
4. M. S. Kaucher, Y. F. Lam, S. Pieraccini, G. Gottarelli, J. T. Davis. Using diffusion NMR to characterize guanosine self-association: Insights into structure and mechanism. Chem. Eur. J. 2005, 11, 164.
5. J. T. Davis. G-quartets 40 years later: from 5′-GMP to molecular biology and supramolecular chemistry. Angew. Chem. Int. Ed. Engl. 2004, 43, 668.
6. 23Na NMR. J. Am. Chem. Soc. 2002, 124, 742.
7. S. Sakamoto, K. Nakatani, I. Saito, K. Yamaguchi. Formation and destruction of the guanine quartet in solution observed by cold-spray ionizationmass spectrometry. Chem. Commun. (Camb.) 2003, 6, 788.
8. C. C. Hardin, T. Watson, M. Corregan, C. Bailey. Cation-dependent transition between the quadruplex and Watson-Crick hairpin forms of d(CGCG3GCG). Biochemistry 1992, 31, 833.
9. E. M. B. Janke, A. Dunger, H.H. Limbach, K.Weisz. Hydrogen bonding in complexes of adenosine and 4-thiouridine: a low-temperature NMR study. Magn. Reson. Chem. 2001, 39, S177.
10. J. Gu, J. Leszczynski. Isoguanine complexes: quintet versus tetrad. J. Phys. Chem. B 2003, 107, 6609.
11. S. C. Nanita, E. Sokol, R. Graham Cooks. Alkali metal cationized serine clusters studied by sonic spray ionization tandem mass spectrometry. J. Am. Soc.Mass Spectrom. 2007, 18, 856.
12. K. J. Koch, T. Aggerholm, S. C. Nanita, R. G. Cooks. Clustering of nucleobases with alkali metals studied by electrospray ionization tandem mass spectrometry: implications for mechanisms of multistrand DNA stabilization. J.Mass Spectrom. 2002, 37, 676.
13. S. A. Hofstadler; R. H. Griffey. Analysis of noncovalent complexes of DNA and RNA by mass spectrometry. Chem. Rev. 2001, 101, 377.
14. C. L. Gatlin, F. Turecek, T. Vaisar. Determination of soluble Cu(I) and Cu(II) species in jet fuel by electrospray ionization mass spectrometry. Anal. Chem. 1994, 66, 3950.
15. T. Aggerholm, S. C. Nanita, K. J. Koch, R. G. Cooks. Clustering of nucleosides in the presence of alkali metals: Biologically relevant quartets of guanosine, deoxyguanosine and uridine observed by ESI-MS/MS. J.Mass Spectrom. 2003, 38, 87.
16. E. L. Zins, S. Rochut, C. Pepe. Theoretical and experimental study of cationized uracil complexes in gas phase. J. Mass Spectrom. 2009, 44, 40.
17. J. M. Daniel, S. D. Friess, S. Rajagopalan, S. Wendt, R. Zenobi. Quantitative determination of noncovalent binding interactions using soft ionization mass spectrometry. Int. J. Mass Spectrom. 2002, 216, 1.
18. L.Ma, M. Iezzi, M. S. Kaucher, Y. F. Lam, J. T.Davis. Cation exchange in lipophilic G-quadruplexes: not all ion binding sites are equal. J. Am. Chem. Soc. 2006, 128, 15269.
19. B. N. Pramanik, A. K. Ganguli, M. L. Gross. Applied Electrospray Mass Spectrometry. Marcel Dekker, Inc: New York, Basel, 2002.
20. J. Gu, J. Leszczynski. Structures and properties of the planar G C G C tetrads: ab initio HF and DFT studies. J. Phys. Chem. A 2000, 104, 6308.
21. J. Gu, J. Leszczynski. Isoguanine: from base pair to tetrad. J. Phys. Chem. A 2003, 107, 9447.
22. M. Meyer, J. Suehnel. Self-association of isoguanine nucleobases and molecular recognition of alkaline ions: tetrad vs pentad structures. J. Phys. Chem. A 2003, 107, 1025.
23. C. Roberts, J. C. Chaput, C. Switzer. Beyond guanine quartets: cation-induced formation of homogenous and chimeric DNA tetraplexes incorporating iso-guanine and guanine. Chem. Biol. 1997, 4, 899.
24. M. Meyer, T. Steinke, M. Brandl, J. Suhnel. Density functional study of guanine and uracil quartets and of guanine quartet/metal ion complexes. J. Comput. Chem. 2000, 22, 109.
25. 2+). J. Phys. Chem. 1996, 100, 7250.
26. J. Gu, J. Leszczynski.Aremarkable alteration in the bonding pattern: an HF and DFT study of the interactions between themetal cations and the Hoogsteen hydrogen-bonded G-tetrad. J. Phys. Chem. A 2000, 104, 6308.
27. M. Meyer, T. Steinke, M. Brandl, J. Suhnel. Density functional study of guanine and uracil quartets and of guanine quartet/metal ion complexes. J. Comput. Chem. 2000, 22, 109.
28. C. Pepe, S. Rochut, J. P. Paumard, J. C. Tabet. Ab initio calculations of proton affinities of glycine, proline, cysteine and phenylalanine: Comparison with the experimental values obtained using an electrospray ionisation ion trapmass spectrometer. Rapid Commun. Mass Spectrom. 2004, 18, 307.
29. M. J. Frisch, G.W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, V. G. Zakrzewski, J. A. Montgomery, J. R. E. Stratmann, J. C. Burant, S. Dapprich, J. M. Millam, A. D. Daniels, K. N. Kudin, M. C. Strain, O. Farkas, J. Tomasi, V. Barone, M. Cossi, R. Cammi, B. Mennucci, C. Pomelli, C. Adamo, S. Clifford, J. Ochterski, G. A. Petersson, P. Y. Ayala, Q. Cui, K.Morokuma, N. Rega, P. Salvador, J. J. Dannenberg, D. K.Malick, A. D. Rabuck, K. Raghavachari, J. B. Foresman, J. Cioslowski, J. V. Ortiz, A. G. Baboul, B. B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, I. Komaromi, R. Gomperts, R. L. Martin, D. J. Fox, T. Keith, M. A. Al-Laham, C. Y. Peng, A. Nanayakkara, M. Challacombe, P. M. W. Gill, B. Johnson, W. Chen, M. W. Wong, J. L. Andres, C. Gonzalez, M. Head-Gordon, E. S. Replogle, J. A. Pople. Gaussian 03. Gaussian, Inc.: Pittsburgh, PA, 2002.
30. M. P. Waller, A. Robertazzi, J. A. Platts. Hybrid density functional theory for π stackings interactions: applications to benzene, pyridine and DNA bases. J. Comput. Chem. 2006, 27, 491.
31. A. Robertazzi, J. A. Platts. Gas-phase DNA oligonucleotide structures. A QM/MM and atoms in molecules study. J. Phys. Chem. A 2006, 110, 3992.
32. A. Robertazzi, J. A. Platts. A QM/MM study of cisplatin-DNA oligonucleotides: from simple models to realistic systems. Chem. Eur. J. 2006, 12, 5747.
33. K. Gkionis, J. A. Platts, J. G. Hill. Insights into DNA binding of ruthenium arene complexes: role of hydrogen bonding and π stacking. Inorg. Chem. 2008, 47, 3893.
34. K. Gkionis, J. G. Hill, S. P. Oldfield, J. A. Platts. Performance of Becke's half-and-half functional for non-covalent interactions: energetics, geometries and electron densities. J. Mol. Model. 2009, 15, 1051.
35. B. S. Jursic. Density functional theory and ab initio study of bond dissociation energy for peroxonitrous acid and peroxyacetyl nitrate. J.Mol. Struct. THEOCHEM 1996, 370, 65.
36. M. Buehl, D. Peters, R. Herges. Substituent effects on 61Ni NMR chemical shifts. Dalton Trans. 2009, 30, 6037.
37. S. Gronert. Quadrupole ion trap studies of fundamental organic reactions. Mass Spectrom. Rev. 2005, 24, 100.
38. +-catalyzed gas-phase oxidation of ethane by N2O. Angew.Chem. Int. Ed. Engl. 1990, 29, 1431.
39. + with benzene. Int. J. Mass Spectrom. 2000, 203, 155.
40. + complexes (L = pyridine, bipyridine, and phenanthroline). Z. Naturforsch., B: Chem. Sci. 2007, 62b, 309.
41. C. L. Ricketts, D. Schröder, C. Alcaraz, J. Roithová. Growth of larger hydrocarbon ions in the ionosphere of Titan. Chem. Eur. J. 2008, 14, 4779.
42. P. Longevialle. The role of ion dipole stabilized complexes in the unimolecular fragmentation of amides under electron impact. Org. Mass Spectrom. 1985, 20, 644.
43. S. Gronert. Estimation of effective ion temperatures in a quadrupole ion trap. J Am Soc Mass Spectrom 1998, 9, 845.
44. 2+: magic numbers, dissociation, and structure. Int. J. Mass Spectrom. 2000, 195/196, 667.