Base-pairing energies of proton-bound homodimers determined by guided ion beam tandem mass spectrometry: Application to cytosine and 5-substituted cytosines

Analytical Chemistry

Volumn 85, Issue 22, 2013, Pages 11000-11006

  Yang, Bo ^a   Wu, R R ^a   Rodgers, M T ^a  

^a WAYNE STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

5-FLUOROCYTOSINE; B3LYP CALCULATIONS; COLLISION-INDUCED DISSOCIATION; GUIDED ION BEAM TANDEM MASS SPECTROMETRIES; MENTAL RETARDATION; METHYLATED DNAS; PERMETHYLATION; RELATED SYSTEMS;

ALKYLATION; DNA; HALOGENATION; HANDICAPPED PERSONS; MASS SPECTROMETRY; METHYLATION; OLIGONUCLEOTIDES;

PROTONS;

CYTOSINE; DNA; DRUG DERIVATIVE; ION; PROTON;

ARTICLE; BASE PAIRING; CHEMISTRY; CONFORMATION; ELECTROSPRAY MASS SPECTROMETRY; METHODOLOGY; NUCLEOTIDE MOTIF; TANDEM MASS SPECTROMETRY; THEORETICAL MODEL;

BASE PAIRING; CYTOSINE; DNA; IONS; MODELS, THEORETICAL; NUCLEIC ACID CONFORMATION; NUCLEOTIDE MOTIFS; PROTONS; SPECTROMETRY, MASS, ELECTROSPRAY IONIZATION; TANDEM MASS SPECTROMETRY;

EID: 84888386452     PISSN: 00032700     EISSN: 15206882     Source Type: Journal    
DOI: 10.1021/ac402542g     Document Type: Article

References (55)

1. Wells, R. D. J. Biol. Chem. 1996, 271, 2875-2878
2. Mitas, M. Nucleic Acids Res. 1997, 25, 2245-2253
3. McLenan, Y.; Polussa, J.; Tassone, F.; Hagerman, R. Curr. Genomics 2011, 12, 216-224
4. Garber, K. B.; Visootsak, J.; Warren, S. T. Eur. J. Hum. Genet. 2008, 16, 666-672
5. Pieretti, M.; Zhang, F.; Fu, Y.-H; Warren, S. T.; Oostra, B. A.; Caskey, C. T.; Nelson, D. L. Cell 1991, 66, 817-822
6. Darlow, J. M.; Leach, D. R. F. J. Mol. Biol. 1998, 275, 3-16
7. Gehring, K.; Leroy, J.-L.; Guéron, M. A Nature 1993, 363, 561-565
8. Fotjík, P.; Vorlícková, M. Nucleic Acids Res. 2001, 29, 4684-4690
9. Rosu, F.; Gabelica, V.; Joly, L.; Grégoire, G.; Pauw, E. D. Phys. Chem. Chem. Phys. 2010, 12, 13448-13454
10. Oomens, J.; Moehlig, A. R.; Morton, T. H. J. Phys. Chem. Lett. 2010, 1, 2891-2897
11. Yang, B.; Wu, R. R.; Berden, G.; Oomens, J.; Rodgers, M. T. J. Phys. Chem. B 2013, 10.1021/jp405105w
12. Sutcliffe, J. S.; Nelson, D. L.; Zhang, F.; Pieretti, M.; Caskey, C. T.; Saxe, D.; Warren, W. T. Hum. Mol. Genet. 1992, 1, 397-400
13. Oberlé, I.; Rousseau, F.; Heitz, D.; Kretz, C.; Devys, D.; Hanauer, A.; Boué, J.; Bertheas, M. F.; Mandel, J. L. Science 1991, 252, 1097-1102
14. Valinluck, V.; Liu, P.; Kang, J. I., Jr.; Burdzy, A.; Sowers, L. C. Nucleic Acids Res. 2005, 33, 3057-3064
15. Vanetich, K. M.; Santi, D. V. Adv. Exp. Med. Biol. 1998, 244, 113-124
16. Smith, S. S.; Kaplan, B. E.; Sowers, L. C.; Newman, E. M. Proc. Natl. Acad. Sci. U.S.A. 1992, 89, 4744-4748
17. Klimasauskas, S.; Kumar, S.; Roberts, R. J.; Cheng, X. Cell 1994, 76, 357-369
18. Rodgers, M. T. J. Phys. Chem. A. 2001, 105, 2374-2383
19. Teloy, E.; Gerlich, D. Chem. Phys. 1974, 4, 417-427
20. Gerlich, D. Inhomogeneous RF Fields: A Versatile Tool for the Study of Processes with Slow Ions. Diplomarbeit, University of Freiburg, Federal Republic of Germany, 1971.
21. Gerlich, D. In State-Selected and State-to-State Ion-Molecule Reaction Dynamics, Part 1. Experiment; Ng, C.-Y.; Baer, M., Eds.; Advances in Chemical Physics, Vol. 82; Wiley: New York, 1992; pp 1-176.
22. Dalleska, N. F.; Honma, K.; Armentrout, P. B. J. Am. Chem. Soc. 1993, 115, 12125-12131
23. Aristov, N.; Armentrout, P. B. J. Phys. Chem. 1986, 90, 5135-5140
24. Hales, D. A.; Armentrout, P. B. J. Cluster Sci. 1990, 1, 127-142
25. 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 A.1; Gaussian, Inc., Wallingford, CT, 2009.
26. Weigend, F.; Ahlrichs, R. Phys. Chem. Chem. Phys. 2005, 7, 3297-3305
27. Feller, D. J. Comput. Chem. 1996, 17, 1571-1586
28. Schuchardt, K. L.; Didier, B. T.; Elsethagen, T.; Sun, L.; Gurumoorthi, V.; Chase, J.; Li, L.; Windus, T. L. J. Chem. Inf. Model. 2007, 47, 1045-1052
29. Hay, P. J.; Wadt, W. R. J. Chem. Phys. 1985, 82, 299-310
30. Peterson, K. A.; Figgen, D.; Goll, E.; Stoll, H.; Dolg, M. J. Chem. Phys. 2003, 119, 11113-11123
31. Smith, S. M.; Markevitch, A. N.; Romanov, D. A.; Li, X.; Levis, R. J.; Schlegel, H. B. J. Phys. Chem. A 2000, 108, 11063-11072
32. Peng, C.; Schlegel, H. B. Isr. J. Chem. 1993, 33, 449-454
33. Exploring Chemistry with Electronic Structures Methods, 2 nd ed.; Foresman, J. B.; Frisch, Æ., Eds.; Gaussian Inc.: Pittsburgh, PA, 1996; p 64.
34. Boys, S. F.; Bernardi, R. Mol. Phys. 1979, 19, 553-566
35. van Duijneveldt, F. B.; van Duijneveldt-van de Rijdt, J. G. C. M.; van Lenthe, J. H. Chem. Rev. 1994, 94, 1873-1885
36. Muntean, F.; Armentrout, P. B. J. Chem. Phys. 2001, 115, 1213-1228
37. Beyer, T. S.; Swinehart, D. S. Commun. ACM 1973, 16, 379
38. Stein, S. E.; Rabinovitch, B. S. J. Chem. Phys. 1973, 58, 2438-2445
39. Stein, S. E.; Rabinovitch, B. S. Chem. Phys. Lett. 1977, 49, 183-188
40. Khan, F. A.; Clemmer, D. E.; Schultz, R. H.; Armentrout, P. B. J. Phys. Chem. 1993, 97, 7978-7987
41. Rodgers, M. T.; Ervin, K. M.; Armentrout, P. B. J. Chem. Phys. 1997, 106, 4499-4508
42. Chesnavich, W. J.; Bowers, M. T. J. Phys. Chem. 1979, 83, 900-905
43. Chen, Y.; Rodgers, M. T. J. Am. Soc. Mass. Spectrom. 2012, 23, 2020-2030
44. Austin, C. A.; Chen, Y.; Rodgers, M. T. Int. J. Mass Spectrom. 2012, 330, 27-34
45. Armentrout, P. B.; Yang, B.; Rodgers, M. T. J. Phys. Chem. B 2013, 117, 3771-3781
46. Nose, H.; Chen, Y.; Rodgers, M. T. J. Phys. Chem. A 2013, 117, 4316-4330
47. Nose, H.; Rodgers, M. T. ChemPlusChem 2013, 78, 1109-1123
48. Sim, F.; St-Amant, A.; Pápai, I.; Salahub, D. R. J. Am. Chem. Soc. 1992, 114, 4391-4400
49. Laasonen, K.; Parrinello, M.; Car, R.; Lee, C.; Vanderbilt, D. Chem. Phys. Lett. 1993, 207, 208-213
50. Kim, K.; Jordan, K. D. J. Phys. Chem. 1994, 98, 10089-10094
51. Del Bene, J. E.; Person, W. B.; Szczepaniak, K. J. Phys. Chem. 1995, 99, 10705-10707
52. Novoa, J. J.; Sosa, C. J. Phys. Chem. 1995, 99, 15837-15845
53. Hobza, P.; Šponer, J.; Reschel, T. J. Comput. Chem. 1995, 16, 1315-1325
54. Suhai, S. J. Phys. Chem. 1995, 99, 1172-1181
55. Valdés, H.; Klusák, V.; Pitoňák, M.; Exner, O.; Starý, I.; Hobza, P.; Rulisek, L. J. Comput. Chem. 2008, 29, 861-870