Infrared multiple photon dissociation (IRMPD) spectroscopy of the proton-bound dimer of 1-methylcytosine in the gas phase

Journal of Physical Chemistry Letters

Volumn 1, Issue 19, 2010, Pages 2891-2897

  Oomens, Jos ^a,b   Moehlig, Aaron R ^c   Morton, Thomas Hellman ^c,d  

^a FOM INSTITUTE FOR PLASMA PHYSICS RIJNHUIZEN   (Netherlands)

^b UNIVERSITY OF AMSTERDAM   (Netherlands)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d UNIVERSITÉ PARIS SUD   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ELECTRONS; FREE ELECTRON LASERS; MONOMERS; POSITIVE IONS; PROTONATION;

ACTION SPECTROSCOPY; CARBONYL OXYGEN; EXCHANGEABLE HYDROGEN; IN-PLANE BENDING; INFRARED MULTIPLE PHOTON DISSOCIATIONS; LOWER FREQUENCIES; PROTON BOUND DIMER; STRONG ABSORPTIONS;

DIMERS;

EID: 77957925168     PISSN: None     EISSN: 19487185     Source Type: Journal    
DOI: 10.1021/jz101080x     Document Type: Article

References (60)

1. Blackburn, E. H. The Telomere and Telomerase: Nucleic Acid-Protein Complexes Acting in a Telomere Homeostasis System. A Review Biochemistry 1997, 62, 1196-1201
2. Gottschling, D. E.; Stoddard., B. Telomeres: Structure of a Chromosome's Aglet Curr. Biol. 1999, R164-R167
3. Burge, S.; Parkinson, G. N.; Hazel, P.; Todd, A. K.; Neidle, S. Quadruplex DNA: Sequence, Topology, and Structure Nucleic Acids Res. 2006, 34, 5402-5415
4. Simonsson, T.; Pecinka, P.; Kubista, M. DNA Tetraplex Formation in the Control Region of c-myc Nucleic Acids Res. 1998, 26, 1167-1172
5. Siddiqui-Jain, A.; Grand, C. L.; Bearss, D. J.; Hurley, L. H. Direct Evidence for a G-Quadruplex in a Promoter Region and its Targeting with a Small Molecule to Repress c-MYC Transcription Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 11593-11598
6. Sun, D.; Hurley, L. H. Biochemical Techniques for the Characterization of G-Quadruplex Structures: EMSA, DMS Footprinting, and DNA Polymerase Stop Assay Methods Mol. Biol. 2010, 608, 65-79
7. Guo, K.; Pourpak, A.; Beetz-Rogers, K.; Gokhale, V.; Sun, D.; Hurley, L. H. Formation of Pseudosymmetrical G-Quadruplex and i -Motif Structures in the Proximal Promoter Region of the RET Oncogene J. Am. Chem. Soc. 2007, 129, 10220-10228
8. Sun, D.; Hurley, L. H. The Importance of Negative Superhelicity in Inducing the Formation of G-Quadruplex and i -Motif Structures in the c-Myc Promoter: Implications for Drug Targeting and Control of Gene Expression J. Med. Chem. 2009, 52, 2863-2874
9. Dai, J.; Ambrus, A.; Hurley, L. H.; Yang, D. A Direct and Nondestructive Approach To Determine the Folding Structure of the I-Motif DNA Secondary Structure by NMR J. Am. Chem. Soc. 2009, 131, 6102-6104
10. Gehring, K.; Leroy, J.-L.; Guéron, M. A Tetrameric DNA Structure with Protonated Cytosine·Cytosine Base Pairs Nature 1993, 363, 561-565
11. Leroy, J.-L.; Gehring, K.; Kettani, K. A.; Guéron, M. Acid Multimers of Oligodeoxycytidine Strands: Stoichiometry, Base-Pair Characterization, and Proton Exchange Properties Biochemistry 1993, 32, 6019-6031
12. Leroy, J.-L.; Guéron, M.; Mergny, J.-L.; Hélène, C. Intramolecular Folding of a Fragment of the Cytosine-Rich Strand of Telomeric DNA into an i -Motif Nucleic Acids Res. 1994, 22, 1600-1606
13. Leroy, J.-L. Cytidine Protonation and Base-Pair Intercalation in Nucleic Acid Structures: The i -Motif Nucleic Acids Res. 2002, 7-8
14. Esmaili, N.; Leroy, J.-L. i -Motif Solution Structure and Dynamics of the d(AACCCC) and d(CCCCAA) Tetrahymena Telomeric Repeats Nucleic Acids Res. 2005, 33, 213-224
15. A. Phan, A.; Mergny, J.-L. Human Telomeric DNA: G-Quadruplex, i -Motif and Watson-Crick Double Helix Nucleic Acids Res. 2002, 30, 4618-4625
16. Leroy, J.-L. The Formation Pathway of i -Motif Tetramers Nucleic Acids Res. 2009, 37, 4127-4134
17. 4 Association into Supra Molecular i -Motif Structures Nucleic Acids Res. 2010, 38, 3817-3826
18. Marsh, R. E.; Bierstedt, R.; Eichhorn, E. L. The Crystal Structure of Cytosine-5-acetic Acid Acta Crystallogr. 1962, 15, 310-316
19. Langridge, R.; Rich, A. Molecular Structures of Helical Polycytidylic Acid Nature 1963, 198, 725-728
20. Guschlbauer, W. Protonated Polynucleotide Structures, I. The Thermal Denaturation of Polycyticylic Acid in Acid Solution Proc. Natl. Acad. Sci. U.S.A. 1967, 57, 1441-1448
21. Holm, A. I. S.; Nielsen, L. M.; Kohler, B.; Vrønning Hoffmann, S.; Brøndsted Nielsen, S. Electronic Coupling between Cytosine Bases in DNA Single Strands and i -Motifs Revealed from Synchrotron Radiation Circular Dichroism Experiments Phys. Chem. Chem. Phys. 2010, 12, 3426-3420
22. Kistenmacher, T. J.; Rossi, M.; Marzilli, L. G. A Model for the Interrelationship Between Asymmetric Interbase Hydrogen Bonding and Base-Base Stacking in Hemiprotonated Polyribocytidylic Acid: Crystal Structure of 1-Methylcytosine Hemihydroiodide Hemihydrate Biopolymers 1978, 17, 2581-2585
23. Kistenmacher, T. J.; Rossi, M; Caradonna, J. P.; Marzilli, L. G. Solution and Solid State Studies on the Interactions of Protonated Cytosine Salts. III. Interpyrimidine Base Stacking and Asymmetric Interbase Hydrogen Bonding in the Structure of 1-Methylcytosine Hemihydroiodide Hemihydrate Adv. Mol. Relax. Interact. Processes 1979, 15, 119-133
24. Fujinami, F.; Ogawa, K.; Arakawa, Y.; Shirotake, S.; Fujii, S.; Tomita, K.-I. The Structure of the Complex Cytosinium Hemitetrachlorozincate-Cytosine Acta Crystallogr., Sect. B 1979, 35, 968-970
25. - (X = Cl, CN) and Cytosine and Guanine Model Nucleobases: Salt Formation with (Hemi-) Protonated Bases, Coordination, and Oxidative Degradation of Guanine Inorg. Chim. Acta 1998, 283, 223-232
26. Armentano, D.; De Munno, G.; Di Donna, L.; Sindona, G.; Giorgi, G.; Salvini, L. Self-Assembling of Cytosine Nucleoside into Triply-Bound Dimers in Acid Media. A Comprehensive Evaluation of Proton-Bound Pyrimidine Nucleosides by Electrospray Tandem Mass Spectrometry, X-ray Diffractometry, and Theoretical Calculations J. Am. Soc. Mass Spectrom. 2004, 15, 268-279
27. 2H]I-Structure and Stability of a Dimeric Threefold Hydrogen-Bonded 1-Methylcytosinium 1-Methylcytosine Cation Org. Biomol. Chem. 2004, 2, 2513-2516
28. 2H] I, an Asymmetric Base Pair Acta Crystallogr., Sect. E 2005, E61, o320-o322
29. 4TCNQ Radical Anion and Methoxy Adduct Anion Chem. Lett. 2006, 35, 1342-1343
30. 2TCNQ Salt Solid State Sci. 2008, 10, 1364-1368
31. Bosnjakovič-Pavlovič, N; Spasojevič-de Biré, A.; Tomaz, I.; Bouhmaida, N.; Avecilla, F.; Mioc, U. B.; Pessoa, J. C.; Ghermani, N. E. Electronic Properties of a Cytosine Decavanadate: Toward a Better Understanding of Chemical and Biological Properties of Decavanadates Inorg. Chem. 2009, 48, 9742-9753
32. Sponer, J.; Leszczynski, J.; Vetterl, V.; Hobza, P. J. Base Stacking and Hydrogen Bonding in Protonated Cytosine Dimer: The Role of Molecular Ion-Dipole and Inductive Interactions J. Biomol. Struct. Dyn. 1996, 13, 695-706
33. Borah, B.; Wood, J. L. The Cytidine-Cytidinium Complex: Infrared and Raman Spectroscopic Studies J. Mol. Struct. 1976, 30, 13-30
34. Han, S. Y.; Oh, H. B. Theoretical Study of the Ionic Hydrogen Bond in the Isolated Proton-Bound Dimer of Cytosine Chem. Phys. Lett. 2006, 432, 269-274
35. Gabelica, V.; Rosu, F.; De Pauw, E.; Lemaire, J.; Gillet, J.-C.; Poully, J.-C.; Lecomte, F.; Grégoire, G.; Schermann, J.; Desfrançois, C. Infrared Signatures of DNA G-Quadruplexes in the Gas Phase J. Am. Chem. Soc. 2008, 130, 1810-1811
36. Rajabi, K.; Theel, K.; Gillis, E. A.; Beran, G.; Fridgen, T. D. The Structure of the Protonated Adenine Dimer by Infrared Multiple Photon Dissociation Spectroscopy and Electronic Structure Calculations J. Phys. Chem. A 2009, 113, 8099-8107
37. Oepts, D.; van der Meer, A. F. G.; van Amersfoort, P. W. The Free-Electron Laser Facility FELIX Infrared Phys. Technol. 1995, 36, 297-308
38. Polfer, N. C.; Oomens, J. Reaction Products in Mass Spectrometry Elucidated with Infrared Spectroscopy Phys. Chem. Chem. Phys. 2007, 9, 3804-2817
39. + Stretching Frequency Angew. Chem., Int. Ed. 2008, 47, 2106-2108
40. Steill, J. D.; Oomens, J. Action Spectroscopy of Gas-Phase Carboxylate Anions by Multiple Photon IR Electron Detachment/Attachment J. Phys. Chem. A 2009, 113, 4941-4946
41. Oomens, J.; Morton, T. H. Structures of Products from Positive Ion-Molecule Reactions by Means of Vibrational Spectroscopy Eur. J. Mass Spectrom. 2010, 16, 313-319
42. Salpin, J.-Y.; Guillaumont, S.; Tortajada, J.; MacAleese, L.; Lemaire, J.; Maître, P. Infrared Spectra of Protonated Uracil, Thymine and Cytosine Chem. Phys. Chem. 2007, 8, 2235-2244
43. Liu, M.; Li, T.; Cardoso, D. S.; Fu, Y.; Lee, J. K. Gas Phase Thermochemical Properties of Pyrimidine Nucleobases J. Org. Chem. 2008, 73, 9283-9291
44. Yao, C.; Tureček, F.; Polce, M. J.; Wesdemiotis, C. Proton and Hydrogen Atom Adducts to Cytosine. An Experimental and Computational Study Int. J. Mass Spectrom. 2007, 265, 106-123
45. + Iminol Tautomer for Base Mispairing J. Am. Chem. Soc. 1993, 115, 760-767
46. Szczesniak, M.; Leszczynski, J.; Person, W. B. Identification of the Imino-Oxo Form of 1-Methylcytosine J. Am. Chem. Soc. 1992, 114, 2731-2733
47. Yao, C.; Cuadrado-Peinado, M. L.; Polášek, M.; Turečk, F. Gas-Phase Tautomers of Protonated 1-Methylcytosine. Preparation, Energetics, and Dissociation Mechanisms J. Mass Spectrom. 2005, 40, 1417-1428
48. Bowen, R. D. Ion-Neutral Complexes Acc. Chem. Res. 1991, 24, 364-371
49. Morton, T. H. The Reorientation Criterion and Positive Ion-Neutral Complexes Org. Mass Spectrom. 1992, 27, 353-368
50. Longevialle, P. Ion-Neutral Complexes in the Unimolecular Reactivity of Organic Cations in the Gas Phase Mass Spectrom. Rev. 1992, 11, 157-192
51. McAdoo, D. J.; Morton, T. H. Gas Phase Analogues of Cage Effects Acc. Chem. Res. 1993, 26, 295-302
52. Morton, T. H. Collisional Activation and Dissociation: Decomposition via Ion-Neutral Complexes; The Encyclopedia of Mass Spectrometry Armentrout, P. B., Ed.; Elsevier: London, 2003; Vol. 1, pp 467 - 479.
53. Morton, T. H. Theoretical Models for Ion-Neutral Complexes in Unimolecular Ion Decompositions. The Encyclopedia of Mass Spectrometry; Nibbering, N. M. M., Ed.; Elsevier: London, 2004; Vol. 4, pp 165 - 173.
54. Julian, R. R.; Ly, T.; Finaldi, A. M.; Morton, T. H. Dissociation of a Protonated Secondary Amine in the Gas Phase via an Ion-Neutral Complex Int. J. Mass Spectrom. 2007, 265, 302-307
55. Sivaramakrishnan, R.; Michael, J. V.; Klippenstein, S. J. Direct Observation of Roaming Radicals in the Thermal Decomposition of Acetaldehyde J. Phys. Chem. A 2010, 114, 755-765
56. Harding, L. B.; Georgievskii, Y.; Klippenstein, S. J. Roaming Radical Kinetics in the Decomposition of Acetaldehyde J. Phys. Chem. A 2010, 114, 765-777
57. Mautner (Meot-Ner), M. Ion Thermochemistry of Low-Volatility Compounds in the Gas Phase. 2. Intrinsic Basicities and Hydrogen-Bonded Dimers of Nitrogen Heterocyclics and Nucleic Bases J. Am. Chem. Soc. 1979, 101, 2396-2403
58. Mautner (Meot-Ner), M. The Ionic Hydrogen Bond Chem. Rev. 2005, 105, 213-284
59. Oh, H.-B.; Lin, C.; Hwang, H.; Zabrouskov, V.; Zhai, H.; Carpenter, B.; McLafferty, F. W. Infrared Photodissociation of Electrosprayed Ions in a Fourier Transform Mass Spectrometer J. Am. Chem. Soc. 2005, 127, 4076-4083
60. Helfer, D.L., II; Ramachandra, S. H.; Leonard, N. J. Selective Alkylation and Aralkylation of Cytosine at the 1-Position J. Org. Chem. 1981, 46, 4803-4804