Gas-phase conformations and energetics of protonated 2′-deoxyadenosine and adenosine: IRMPD action spectroscopy and theoretical studies

Journal of Physical Chemistry B

Volumn 119, Issue 7, 2015, Pages 2795-2805

  Wu, R R ^a   Yang, Bo ^a   Berden, G ^b   Oomens, J ^b,c   Rodgers, M T ^a  

^a WAYNE STATE UNIVERSITY   (United States)

^b RADBOUD UNIVERSITY NIJMEGEN   (Netherlands)

^c UNIVERSITY OF AMSTERDAM   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

ELECTRONIC STRUCTURE; ELECTRONS; ELECTROSPRAY IONIZATION; FREE ELECTRON LASERS; GASES; GROUND STATE; HYDROGEN BONDS; IONIZATION; IONIZATION OF GASES; OPTICAL PARAMETRIC OSCILLATORS; PARAMETRIC OSCILLATORS; PHOTOIONIZATION;

ACTION SPECTROSCOPY; ELECTRONIC STRUCTURE CALCULATIONS; GAS PHASE CONFORMATIONS; GAS-PHASE STABILITY; HYDROXYL SUBSTITUENTS; INFRARED MULTIPLE PHOTON DISSOCIATIONS; LOW-ENERGY CONFORMATIONS; RELATIVE STABILITIES;

PROTONATION;

2'-DEOXYADENOSINE; ADENOSINE; DEOXYADENOSINE DERIVATIVE; GAS; PROTON;

CHEMICAL MODEL; CHEMISTRY; CONFORMATION; GAS; HYDROGEN BOND; INFRARED SPECTROPHOTOMETRY; PROCEDURES; THERMODYNAMICS; VIBRATION;

ADENOSINE; DEOXYADENOSINES; GASES; HYDROGEN BONDING; MODELS, CHEMICAL; MOLECULAR CONFORMATION; PROTONS; SPECTROPHOTOMETRY, INFRARED; THERMODYNAMICS; VIBRATION;

EID: 84923343950     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp509267k     Document Type: Article

References (59)

1. Hanus, M.; Ryjacek, F.; Kabelac, M.; Kubar, T.; Bogdan, T. V.; Trygubenko, S. A.; Hobza, P. Correlated Ab Initio Study of Nucleic Acid Bases and Their Tautomers in the Gas Phase, in a Microhydrated Environment and in Aqueous Solution. Guanine: Surprising Stabilization of Rare Tautomers in Aqueous Solution J. Am. Chem. Soc. 2003, 125, 7678-7688
2. Guallar, V.; Douhal, A.; Moreno, M.; Lluch, J. M. DNA Mutations Induced by Proton and Charge Transfer in the Low-lying Excited Singlet Electronic States of the DNA Base Pairs: A Theoretical Insight J. Phys. Chem. A 1999, 103, 6251-6256
3. Sniden, R. R. DNA Structure and Function; Academic Press: San Diego, 1994, pp 15-22.
4. Hermann, T.; Patel, D. J. Stitching Together RNA Tertiary Architectures J. Mol. Biol. 1999, 294, 829-849
5. van Dam, L.; Ouwerkerk, N.; Brinkmann, A.; Raap, J.; Levitt, M. H. Solid-State NMR Determination of Sugar Ring Pucker in C-13-Labeled 2′-Deoxynucleosides Biophys. J. 2002, 83, 2835-2844
6. Rich, A.; Nordheim, A.; Wang, A. H. The Chemistry and Biology of Left-Handed Z-DNA J. Annu. Rev. Biochem. 1984, 53, 791-846
7. Waalkes, T. P.; Abeloff, M. D.; Ettinger, D. S.; Woo, K. B.; Gehrke, C. W.; Kuo, K. C.; Borek, E. Modified Ribonucleosides As Biological Markers For Patients With Small Cell-Carcinoma of the Lung Eur. J. Cancer Clin. Oncol. 1982, 18, 1267-1274
8. Mitchell, E. P.; Evans, L.; Schultz, P.; Madsen, R.; Yarbro, J. W.; Gehrke, C. W.; Kuo, K. Modified Nucleosides in Human Serum J. Chromatogr. 1992, 581, 31-40
9. Perigaud, C.; Gosselin, G.; Imbach, J. L. Stereospecific Synthesis of Chiral Acyclic Analogs of Guanosine Bioorg. Med. Chem. Lett. 1992, 2, 677-680
10. Perigaud, C.; Gosselin, G.; Imbach, J. L. Nucleoside Analogs As Chemotherapeutic-Agents: A Review Nucleosides Nucleotides 1992, 11, 903-945
11. McPherson, A.; Jurnak, F.; Wang, A.; Kolpal, F.; Rich, A.; Molineux, I.; Fitzgerald, P. The Structure of A DNA Unwinding Protein and Its Complexes With Oligodeoxynucleotides by X-Ray-Diffraction Biophys. J. 1980, 32, 155-173
12. Delamaza, L. M.; Carter, B. J. Molecular Structure of Adeno-Associated Virus Variant DNA J. Biol. Chem. 1980, 255, 3194-3203
13. Guo, Q.; Min, L.; Churchill, M. E. A.; Tullius, T. D.; Kallenbach, N. R. Asymmetric Structure of A Three-Arm DNA Junction Biochemistry 1990, 29, 10927-10934
14. Pina, B.; Truss, M.; Ohlenbusch, H.; Postma, J.; Beato, M. DNA Rotational Positioning in A Regulatory Nucleosome is Determined By Base Sequence: An Algorithm to Model the Preferred Superhelix Nucleic Acids Res. 1990, 18, 6981-6987
15. 4-Methoxycytosine. Guanine Base-Pairs in Z-DNA J. Mol. Biol. 1990, 216, 773-781
16. Florian, J.; Leszczynski, J. Theoretical Investigation of the Molecular-Structure of the Pi-Kappa DNA-Base Pair J. Biomol. Struct. Dyn. 1995, 12, 1055-1062
17. Santamaria, R.; Quirozgutierrez, A.; Juarez, C. Structures and Energetic Properties of B-DNA Nucleotides J. Mol. Struct.: THEOCHEM 1995, 357, 161-170
18. Triolo, A.; Arcamone, F. M.; Raffaelli, A.; Salvadori, P. Non-Covalent Complexes Between DNA-Binding Drugs and Double-Stranded Deoxyoligonucleotides: A Study by Ionspray Mass Spectrometry J. Mass. Spectrom. 1997, 32, 1186-1194
19. Wang, Z.; Wan, K. X.; Ramanathan, R.; Taylor, J. S.; Gross, M. L. Structure and Fragmentation Mechanism of Isomeric T-Rich Oligodeoxynucleotides: A Comparison of Four Tandem Mass Spectrometric Methods J. Am. Soc. Mass Spectrom. 1998, 9, 683-691
20. Cheatham, T. E.; Srinivasan, J.; Case, D. A.; Kollman, P. A. Molecular Dynamics and Continuum Solvent Studies of the Stability of polyG-polyC and polyA-polyT DNA Duplexes in Solution J. Biomol. Struct. Dyn. 1998, 16, 265-280
21. Kurnikov, I. V.; Tong, G. S. M.; Madrid, M.; Beratan, D. N. Hole Size and Energetics in Double Helical DNA: Competition Between Quantum Delocalization and Solvation Localization J. Phys. Chem. B 2002, 106, 7-10
22. Rueda, M.; Kalko, S. G.; Luque, F. J.; Orozco, M. The Structure and Dynamics of DNA in the Gas Phase J. Am. Chem. Soc. 2003, 125, 8007-8014
23. Guo, X. H.; Bruist, M. F.; Davis, D. L.; Bentzley, C. M. Secondary Structural Characterization of Oligonucleotide Strands Using Electrospray Ionization Mass Spectrometry Nucleic Acids Res. 2005, 33, 3659-3666
24. Balthasart, F.; Plavec, J.; Gabelica, V. Ammonium Ion Binding to DNA G-Quadruplexes: Do Electrospray Mass Spectra Faithfully Reflect the Solution-Phase Species? J. Am. Soc. Mass Spectrom. 2013, 24, 1-8
25. Jaeger, J. A.; Turner, D. H.; Zuker, M. Predicting Optimal and Suboptimal Secondary Structure For RNA Methods Enzymol. 1990, 183, 281-306
26. Estes, P. A.; Cooke, N. E.; Liebhaber, S. A. A Native RNA Secondary Structure Controls Alternative Splice-Site Selection and Generates 2 Human Growth-Hormone Isoforms J. Biol. Chem. 1992, 267, 14902-14908
27. Gutell, R. R.; Power, A.; Hertz, G. Z.; Putz, E. J.; Stormo, G. D. Identifying Constraints on the Higher-Order Structure of RNA: Continued Development and Application of Comparative Sequence-Analysis Methods Nucleic Acids Res. 1992, 20, 5785-5795
28. Davis, D. R. Stabilization of RNA Stacking by Pseudouridine Nucleic Acids Res. 1995, 23, 5020-5026
29. Jones, S.; Daley, D. T. A.; Luscombe, N. M.; Berman, H. M.; Thornton, J. M. Protein-RNA Interactions: A Structural Analysis Nucleic Acids Res. 2001, 29, 943-954
30. Gooch, B. D.; Beal, P. A. Recognition of Duplex RNA by Helix-Threading Peptides J. Am. Chem. Soc. 2004, 126, 10603-10610
31. Koculi, E.; Hyeon, C.; Thirumalai, D.; Woodson, S. A. Charge Density of Divalent Metal Cations Determines RNA Stability J. Am. Chem. Soc. 2007, 129, 2676-2682
32. Zhang, A. Y. Q.; Bugaut, A.; Balasubramanian, S. A Sequence-Independent Analysis of the Loop Length Dependence of Intramolecular RNA G-Quadruplex Stability and Topology Biochemistry 2011, 50, 7251-7258
33. Philips, A.; Milanowska, K.; Lach, G.; Boniecki, M.; Rother, K.; Bujnicki, J. M. MetalionRNA: Computational Predictor of Metal-Binding Sites in RNA Structures Bioinformatics 2012, 28, 198-205
34. Nir, E.; Imhof, P.; Kleinermanns, K.; de Vries, M. S. REMPI Spectroscopy of Laser Desorbed Guanosines J. Am. Chem. Soc. 2000, 122, 8091-8092
35. Stueber, D.; Grant, D. M. C-13 and N-15 Chemical Shift Tensors in Adenosine, Guanosine Dihydrate, 2′-Deoxythymidine, and Cytidine J. Am. Chem. Soc. 2002, 124, 10539-10551
36. Wu, R. R.; Yang, B.; Berden, G.; Oomens, J.; Rodgers, M. T. Gas Phase Conformations and Energetics of Protonated 2′-Deoxyguanosine and Guanosine: IRMPD Action Spectroscopy and Theoretical Studies J. Phys. Chem. B 2014, 118, 14774-14784
37. Murgia, S.; Lampis, S.; Zucca, P.; Sanjust, E.; Monduzzi, M. Nucleotide Recognition and Phosphate Linkage Hydrolysis at a Lipid Cubic Interface J. Am. Chem. Soc. 2010, 132, 16176-16184
38. Adelfinskaya, O.; Terrazas, M.; Froeyen, M.; Marliere, P.; Nauwelaerts, K.; Herdewijin, P. Polymerase-Catalyzed Synthesis of DNA From Phosphoramidate Conjugates of Deoxynucleotides and Amino Acids Nucleic Acids Res. 2007, 35, 5060-5072
39. Knowles, J. R. The Mechanism of Biotin-Dependent Enzymes Annu. Rev. Biochem. 1989, 58, 195-221
40. Crespo-Hernandez, C. E.; Cohen, B.; Hare, P. M.; Kohler, B. Ultrafast Excited-State Dynamics in Nucleic Acids Chem. Rev. 2004, 104, 1977-2019
41. Dodge-Kafka, K. L.; Kapiloff, M. S. The mAKAP Signaling Complex: Integration of cAMP, Calcium, and MAP Kinase Signaling Pathways Eur. J. Cell Biol. 2006, 85, 593-602
42. + Metabolism in Health and Disease Trends Biochem. Sci. 2007, 32, 12-19
43. Tu, B. P.; Weissman, J. S. Oxidative Protein Folding in Eukaryotes: Mechanisms and Consequences J. Cell Biol. 2004, 164, 341-346
44. Greco, F.; Liguori, A.; Sindona, G.; Uccella, N. Gas-Phase Proton Affinity of Deoxyribonucleosides and Related Nucleobases by Fast-Atom-Bombardment Tandem Mass-Spectrometry J. Am. Chem. Soc. 1990, 112, 9092-9096
45. Di Donna, L.; Napoli, A.; Sindona, G.; Athanassopoulos, C. A Comprehensive Evaluation of the Kinetic Method Applied in the Determination of the Proton Affinity of the Nucleic Acid Molecules J. Am. Soc. Mass Spectrom. 2004, 15, 1080-1086
46. Touboul, D.; Bouchoux, G.; Zenobi, R. Gas-Phase Protonation Thermochemistry of Adenosine J. Phys. Chem. B 2008, 112, 11716-11725
47. Valle, J. J.; Eyler, J. R.; Oomens, J.; Moore, D. T.; van der Meer, A. F. G.; von Heldon, G.; Meijer, G.; Hendrickson, C. L.; Marshall, A. G.; Blakney, G. T. Free Electron Laser-Fourier Transform Ion Cyclotron Resonance Mass Spectrometry Facility for Obtaining Infrared Multiphoton Dissociation Spectra of Gaseous Ions Rev. Sci. Instrum. 2005, 76, 023103-1-023103-7
48. Polfer, N. C.; Oomens, J.; Moore, D. T.; von Helden, G.; Meijer, G.; Dunbar, R. C. Infrared Spectroscopy of Phenylalanine Ag(I) and Zn(II) Complexes in the Gas Phase J. Am. Chem. Soc. 2006, 128, 517-525
49. Polfer, N. C.; Oomens, J. Reaction Products in Mass Spectrometry Elucidated with Infrared Spectroscopy Phys. Chem. Chem. Phys. 2007, 9, 3804-3817
50. Oepts, D.; van der Meer, A. F. G.; van Amersfoort, P. W. The Free-Electron-Laser User Facility FELIX Infrared Phys. Technol. 1995, 36, 297-308
51. HyperChem Computational Chemistry Software Package, version 5.0; Hypercube, Inc.: Gainsville, FL, 1997.
52. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Scalmani, G.; Barone, V.; Mennucci, B.; Petersson, G. A.; Gaussian 09, revision C.01; Gaussian, Inc.: Wallingford, CT, 2009.
53. Russo, N.; Toscano, M.; Grand, A.; Jolibis, F. Protonation of Thymine, Cytosine, Adenine, and Guanine DNA Nucleic Acid Bases: Theoretical Investigation into the Framework of Density Functional Theory J. Comput. Chem. 1998, 9, 989-1000
54. Turecek, F.; Chen, X. Protonated Adenine: Tautomers, Solvated Clusters, and Dissociation Mechanisms J. Am. Soc. Mass Spectrom. 2005, 16, 1713-1726
55. Gidden, J.; Bowers, M. T. Gas-Phase Conformations of Deprotonated and Protonated Mononucleotides Determined by Ion Mobility and Theoretical Modeling J. Phys. Chem. B 2003, 107, 12829-12837
56. Steill, J. D.; Oomens, J. Gas-Phase Deprotonation of p -Hydroxybenzoic Acid Investigated by IR Spectroscopy: Solution-Phase Structure is Retained upon ESI J. Am. Chem. Soc. 2009, 131, 13570-13571
57. Plutzer, C.; Nir, E.; de Vries, M. S.; Kleinermanns, K. IR-UV Double-Resonance Spectroscopy of the Nucleobase Adenine Phys. Chem. Chem. Phys. 2001, 3, 5466-5469
58. van Zundert, G. C. P.; Jaeqx, S.; Berden, G.; Bakker, J. M.; Kleinermanns, K.; Oomens, J.; Rijs, A. M. IR Spectroscopy of Isolated Neutral and Protonated Adenine and 9-Methyladenine ChemPhysChem 2011, 12, 1921-1927
59. Rajabi, K.; Gillis, E. A. L.; Fridgen, T. D. Structures of Alkali Metal Ion-Adenine Complexes by IRMPD Spectroscopy and Electronic Structure Calculations J. Phys. Chem. A 2010, 114, 3449-3456