Protonation preferentially stabilizes minor tautomers of the halouracils: IRMPD action spectroscopy and theoretical studies

Journal of the American Society for Mass Spectrometry

Volumn 23, Issue 9, 2012, Pages 1469-1478

  Crampton, K T ^a   Rathur, A I ^a   Nei, Y W ^a   Berden, G ^b   Oomens, J ^b,c   Rodgers, M T ^a  

^a WAYNE STATE UNIVERSITY   (United States)

^b FOM INSTITUTE FOR PLASMA PHYSICS RIJNHUIZEN   (Netherlands)

^c UNIVERSITY OF AMSTERDAM   (Netherlands)

Author keywords

5 Bromouracil; 5 Chlorouracil; 5 Fluorouracil; 5 Iodouracil; 6 Chlorouracil; Free electron laser; Infrared multiple photon dissociation; Protons; Tautomerization

Indexed keywords

5-BROMOURACIL; 5-CHLOROURACIL; 5-FLUOROURACIL; 5-IODOURACIL; 6-CHLOROURACIL; INFRARED MULTIPLE PHOTON DISSOCIATIONS; TAUTOMERIZATIONS;

DISSOCIATION; ELECTRONIC STRUCTURE; FREE ELECTRON LASERS; PHOTONS; PROTONATION; PROTONS; RNA;

HYDROGEN BONDS;

5 BROMOURACIL; 6 CHLOROURACIL; CHLOROURACIL; FLUOROURACIL; HALOGEN; IODOURACIL; UNCLASSIFIED DRUG; URACIL DERIVATIVE;

ARTICLE; BINDING AFFINITY; CHEMICAL ANALYSIS; CHEMICAL BINDING; CONFORMATIONAL TRANSITION; HALOGENATION; INFRARED MULTIPLE PHOTON DISSOCIATION ACTION SPECTROSCOPY; INTERMETHOD COMPARISON; MATHEMATICAL COMPUTING; MOLECULAR INTERACTION; MOLECULAR STABILITY; NUCLEIC ACID SYNTHESIS; PROCESS OPTIMIZATION; PROTON TRANSPORT; SPECTROSCOPY; STRUCTURE ANALYSIS; TAUTOMER; TAUTOMERIZATION; THEORETICAL STUDY;

HYDROCARBONS, HALOGENATED; ISOMERISM; MASS SPECTROMETRY; PHOTOCHEMICAL PROCESSES; PROTONS; SPECTROPHOTOMETRY, INFRARED; THERMODYNAMICS; URACIL;

EID: 84865706798     PISSN: 10440305     EISSN: 18791123     Source Type: Journal    
DOI: 10.1007/s13361-012-0434-7     Document Type: Article

References (41)

1. Watson, J.D., Crick, F.H.: Genetic implications of the structure of deoxyribonucleic acid. Nature 171, 964-767 (1953)
2. Sowers, L.C., Shaw, B.R., Veigl, M.L., Sedwick, W.D.: DNA base modification: Ionized base pairs and mutagenesis. Mutat. Res. 177, 201-218 (1987) (Pubitemid 17045656)
3. Lowdin, P.O.: Proton tunneling in DNA and its biological applications. Rev. Mod. Phys. 35, 724-732 (1963)
4. Kool, E.T.: Hydrogen bonding, base stacking, and steric effects in DNA replication. Annu. Rev. Biophys. Biomol. Struct. 30, 1-22 (2001) (Pubitemid 32566154)
5. Topal, M.D., Fresco, J.R.: Complementary base pairing and the origin of substitution mutations. Nature 263, 285-289 (1976)
6. Freese, E.: The specific mutagenic effect of base analogues on Phage T4. J. Mol. Biol. 1, 87-105 (1959)
7. Katritzky, A.R., Waring, A.J.: Tautomeric azines, I. Tautomerism of 1-methyluracil and 5-bromo-1-methyluracil. J. Chem. Soc. 1540-1544 (1962)
8. Fresco, J.R., Broitman, S., Lane, A.E.: Base pair mismatching and nearest-neighbor effects in transition mutations. In: Alberts, B., Fox, C.F. (Eds.) Mechanistic studies of DNA replication and genetic recombination. Academic Press: New York, pp. 753-768 (1980)
9. Singer, B., Kusmierek, J.T.: Chemical mutagenesis. Annu. Rev. Biochem. 51, 655-693 (1982) (Pubitemid 12024692)
10. Salpin, J.-Y., Guillaumont, S., Tortajada, J., MacAleese, L., Lemaire, J., Maître, P.: Infrared spectra of protonated uracil, thymine, and cytosine. Chem. Phys. Chem. 8, 2235-2244 (2007)
11. Modrich, P., Lahue, R.: Mismatch repair in replication fidelity, genetic recombination and cancer biology. Annu. Rev. Biochem. 65, 101-134 (1996)
12. Stanbridge, E.J.: Human tumor suppressor genes. Annu. Rev. Genet. 24, 615-657 (1990) (Pubitemid 120011561)
13. Fearon, E.R., Vogelstein, B.: A genetic model for colorectal tumorigenesis. Cell 61, 759-767 (1990)
14. Bishop, J.M.: Molecular themes in oncogenesis. Cell 64, 235-248 (1991)
15. Nei, Y.-w., Akinyemi, T.E., Steill, J.D., Oomens, J., Rodgers, M. T.: Infrared multiple photon dissociation action spectroscopy of protonated uracil and thiouracils: Effects of thio-keto substitution on gas-phase conformation. Int. J. Mass Spectrom. 297, 139-151 (2010)
16. Yang, Z., Rodgers, M.T.: Influence of halogenation on the properties of uracil and its noncovalent interactions with alkali metal ions. Threshold collision-induced dissociation and theoretical studies. J. Am. Chem. Soc. 126, 16217-16226 (2004) (Pubitemid 39627633)
17. Nei, Y.-w., Akinyemi, T.E., Kaczan, C.M., Steill, J.D., Oomens, J., Rodgers, M.T.: Infrared multiple photon dissociation action spectroscopy of sodiated uracil and thiouracils: Effects of thio-keto substitution on gas-phase conformation. Int. J. Mass Spectrom. 308, 191-202 (2011)
18. Wang, H.-p., Xu, W.-g., Zhang, H.-x.: Theoretical studies on structure and electron affinity of 5-and 6-halouracils. Chem. Res. Chinese U. 25, 388-396 (2009)
19. Leszczynski, J.: Tautomerism of uracil: The final chapter? Fourth-order electron correlation contributions to the relative energies of tautomers. J. Phys. Chem. 96, 1649-1653 (1992)
20. Bakker, J.M., Sinha, R.K., Besson, T., Brugnara, M., Tosi, P., Salpin, J.-Y., Maître, P.: Direct evidence for tautomerization of the uracil moiety within the Pb2+/uridine-5′-monophosphate complex: A combined tandem mass spectrometry and IRMPD study. J. Phys. Chem. A 112, 12393-12400 (2009)
21. Orozco, M., Hernández, B., Luque, F.J.: Tautomerism of 1-methyl derivatives of uracil, thymine, and 5-bromouracil. Is tautomerism the basis for the mutagenicity of 5-bromouridine? J. Phys. Chem. B 102, 5228-5233 (1998) (Pubitemid 128576750)
22. Scanlan, M.J., Hillier, I.H.: An ab initio study of tautomerism of uracil, thymine, 5-fluorouracil, and cytosine. J. Am. Chem. Soc. 106, 3737-3745 (1984) (Pubitemid 14055256)
23. Tian, S.X., Zhang, C.F., Zhang, Z.J., Chen, X.J., Xu, K.Z.: How many uracil tautomers are there? Density functional studies of stability ordering of tautomers. Chem. Phys. Lett. 242, 217-225 (1999)
24. Feyer, V., Plekan, O., Richter, R., Coreno, M., V.-llosera, G., Prince, K.C., Trofimov, A.B., Zaytseva, I.L., Moskovskaya, T.E., Gromov, E.V., Schirmer. J.: Tautomerism in cytosine and uracil: An experimental and theoretical core level spectroscopic study. J. Phys. Chem. A 113, 5736-5742 (2009)
25. Hu, X., Li, H., Zhang, L., Han, S.: Tautomerism of uracil and 5-bromouracil in a microcosmic environment with water and metal ions. What roles do metal ions play? J. Phys. Chem. B 111, 9347-9354 (2007) (Pubitemid 47280535)
26. Brown, D.J.; Evans, R.F.; Cowden, W.B.; Fenn M.D. In: The Pyrimidines; Chemistry of Heterocyclic Compounds A Series of Monographs 52; John Wiley and Sons: New York, 1994
27. Pérez, A., Tuckerman, M., Hjalmarson, H.P., von Lillienfeld, O.A.: Enol tautomers of Watson-Crick base pair models are metastable because of nuclear quantum effects. J. Am. Chem. Soc. 132, 11510-11515 (2010)
28. Heidelberger, C., Chaudhuri, N.K., Danneberg, P., Mooren, D., Griesbach, L., Duschinsky, R., Schnitzer, R.J., Pleven, E., Scheiner, J.: Fluorinated pyridimines: A new class of tumor-inhibitory compounds. Nature 179, 663-666 (1957)
29. Bernhard, H., J.-Arand, E., Bernhard, G., Heike, M., Klein, O., Riemann, J.F., Meyer zum Büschenfelde, K.H., Dippold, W., Knuth, A.: Treatment of advanced pancreatic cancer with 5-fluorouracil, folinic acid and interferon alpha-2A: Results of a phase II trial. Br. J. Cancer. 71, 102-105 (1995)
30. Neoptolemos, J.P., Stocken, D.D., Smith, C.T., Bassi, C., Ghaneh, P., Owen, E., Moore, M., Padbury, R., Doi, R., Smith, D., Buchler, M.W.: Adjuvant 5-fluorouracil and folinic acid versus observation for pancreatic cancer: Composite data from the ESPAC-1 and -3(v1) trials. Br. J. Cancer. 100, 246-250 (2009)
31. Meyerhardt, J.A., Mayer, R.J., Engl, N.: Systematic therapy for colorectal cancer. N. Engl. J. Med. 352, 476-487 (2005)
32. Noordhuis, P., Holwerda, U., van der Wilt, C.L., van Groeningen, C.J., Smid, K., Meijer, S., Pinedo, H.M., Peter, G.J.: 5-Fluorouracil incorporation into RNA and DNA in relation to thymidylate synthase inhibition of human colorectal cancers. Ann. Oncol. 15, 1025-1032 (2004) (Pubitemid 39089778)
33. Mauro, D.J., De Riel, J.K., Tallarida, R.J., Sirover, M.A.: Mechanisms of excision of 5-fluorouracil by uracil DNA glycosylase in normal human cells. Mol. Pharmacol. 43, 854-857 (1993) (Pubitemid 23178859)
34. Valle, J.J., Eyler, J.R., Oomens, J., Moore, D.T., van der Meer, A.F.G., von Helden, 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 spectra of gaseous ions. Rev. Sci. Instrum. 76, 023103-023110 (2005)
35. 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. 128, 517-525 (2006) (Pubitemid 43157545)
36. Polfer, N.C., Oomens, J.: Reaction products in mass spectrometry elucidated by infrared spectroscopy. Phys. Chem. Chem. Phys. 9, 3804-3817 (2007)
37. Oepts, D., van der Meer, A.F.G., van Amersfoort, P.W.: The freeelectron laser user facility FELIX. Infrared Phys. Technol. 36, 297-308 (1995)
38. Oomens, J., Sartakov, B.G., Meijer, G., von Helden, G.: Gas-phase infrared multiple photon dissociation spectroscopy of mass-selected molecular ions. Int. J. Mass Spectrom. 254, 1-19 (2006)
39. Armentrout, P.B., Rodgers, M.T., Oomens, J., Steill, J.D.: Infrared multiphoton dissociation spectroscopy of cationized serine: Effects of alkali-metal cation size on gas-phase conformation. J. Phys. Chem. A 112, 2248-2257 (2008)
40. Rodgers, M.T., Armentrout, P.B., Oomens, J., Steill, J.D.: Infrared multiphoton dissociation spectroscopy of cationized threonine: Effects of alkali-metal cation size on gas-phase conformation. J. Phys. Chem. A. 112, 2258-2267 (2008)
41. Frisch, M.J.; Trucks, G.W.; Schlegel, H.B.; Scuseria, G.E.; Robb, M.A.; Cheeseman, J.R.; Montgomery, J.A. Jr.; 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.; Bakken, V.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomeli, 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.; Pople, J. A. Gaussian 09, Revision A.02. Gaussian, Inc.: Wallingford CT, 2004