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Journal of Physical Chemistry B
Volumn 111, Issue 14, 2007, Pages 3800-3812
A kinetic and thermodynamic study of the glycosidic bond cleavage in deoxyuridine
Author keywords

[No Author keywords available]
Indexed keywords

HYDROLYSIS; NUCLEOPHILES; NUCLEOTIDES; PROTON TRANSFER; REACTION KINETICS; THERMODYNAMIC PROPERTIES;
EID: 34248204233     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp063841m     Document Type: Article
Times cited : (35)
References (114)
  • 88
    • 84906361569 scopus 로고    scopus 로고
    • The H4′-C4′-C5′-O5′ dihedral angle is approximately equal to 180° in DNA, and therefore the hydroxyl and methoxyl groups were added in the same orientation in our models. However, we note that many enzymes catalyze a base flipping step prior to glycosidic bond cleavage, which changes the alignment of the phosphodiester backbone.
    • The H4′-C4′-C5′-O5′ dihedral angle is approximately equal to 180° in DNA, and therefore the hydroxyl and methoxyl groups were added in the same orientation in our models. However, we note that many enzymes catalyze a base flipping step prior to glycosidic bond cleavage, which changes the alignment of the phosphodiester backbone.
  • 90
    • 84906390013 scopus 로고    scopus 로고
    • 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, Pomelli, 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, Keit
    • 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.; Pomelli, 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 03, revision C.02 and D.01; Gaussian, Inc.: Wallingford, CT, 2004.
  • 91
    • 84906390014 scopus 로고    scopus 로고
    • It has been determined experimentally that the sugar puckering for RNA and A-DNA is C3′-endo, while it is C2′-endo in B-DNA
    • It has been determined experimentally that the sugar puckering for RNA and A-DNA is C3′-endo, while it is C2′-endo in B-DNA.
  • 92
    • 84906361565 scopus 로고    scopus 로고
    • We note that the IRCs typically lead to reactant complexes with C3′-endo sugar puckering and the energy difference between the C3′-endo and the C2′-endo conformations is small, where model 1 predicts the C3′-endo conformation to be 5 kj mol-1 more stable and model 4-CH3 predicts C2′-endo to be 1 kJ mol -1 more stable. Since conversion between different sugar conformations is expected to be a low-energy process, we utilized reactant complexes with C3′-endo puckering in all pathways for consistency
    • -1 more stable. Since conversion between different sugar conformations is expected to be a low-energy process, we utilized reactant complexes with C3′-endo puckering in all pathways for consistency.
  • 95
    • 84906375873 scopus 로고    scopus 로고
    • Although IRCs for the first and second steps should ideally lead to the same intermediate complex, two structures with slightly different water orientations were obtained for model 4-CH3, which differ by only 1.4 kJ mol-1. Since we expect a low barrier for water migration, we report only the relative energy for the intermediate obtained by following the IRC from the first step
    • -1. Since we expect a low barrier for water migration, we report only the relative energy for the intermediate obtained by following the IRC from the first step.
  • 114
    • 84906361566 scopus 로고    scopus 로고
    • The 6-311+G(2df,2p) basis set was used in conjunction with MPWB1K, MPW1B95, and PWB6K hybrid density functional methods as implemented in Truhlar's benchmarking studies (see refs 60-62).
    • The 6-311+G(2df,2p) basis set was used in conjunction with MPWB1K, MPW1B95, and PWB6K hybrid density functional methods as implemented in Truhlar's benchmarking studies (see refs 60-62).

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