- Flight of a cytidine deaminase complex with an imperfect transition state analogue inhibitor: Mass spectrometric evidence for the presence of a trapped water molecule
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Cytidine deaminase (CDA) binds the inhibitor zebularine as its 3,4-hydrate (Kd ~ 10-12 M), capturing all but ~5.6 kcal/mol of the free energy of binding expected of an ideal transition state analogue (Ktx ~ 10-16 M). On the basis of its entropic origin, that shortfall was tentatively ascribed to the trapping of a water molecule in the enzyme-inhibitor complex, as had been observed earlier for product uridine [Snider, M. J., and Wolfenden, R. (2001) Biochemistry 40, 11364-11371]. Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) of CDA nebularized in the presence of saturating 5-fluorozebularine reveals peaks corresponding to the masses of E2Zn2W2 (dimeric Zn-CDA with two water molecules), E2Zn2W2Fz, and E2Zn2W2Fz2, where Fz represents the 3,4-hydrate of 5-fluorozebularine. In the absence of an inhibitor, E 2Zn2 is the only dimeric species detected, with no additional water molecules. Experiments conducted in H218O indicate that the added mass W represents a trapped water molecule rather than an isobaric ammonium ion. This appears to represent the first identification of an enzyme-bound water molecule at a subunit interface (active site) using FTICR-MS. The presence of a 5-fluoro group appears to retard the decomposition of the inhibitory complex kinetically in the vapor phase, as no additional dimeric complexes (other than E2Zn2) are observed when zebularine is used in place of 5-fluorozebularine. Substrate competition assays show that in solution zebularine is released from CDA (koff > 0.14 s-1) much more rapidly than is 5-fluorozebularine (koff = 0.014 s-1), despite the greater thermodynamic stability of the zebularine complex.
- Schroeder, Gottfried K.,Zhou, Li,Snider, Mark J.,Chen, Xian,Wolfenden, Richard
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- Cytosine derivatives form hemiprotonated dimers in solution and the gas phase
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Hemiprotonated dimers of cytosine derivatives, implicated in the formation of the i-motif of DNA, have been created in solution and the gas phase. The mechanism of dimerization has been analyzed by mass spectrometry and multidimensional NMR spectroscopy.
- Moehlig, Aaron R.,Djernes, Katherine E.,Krishnan, V. Mahesh,Hooley, Richard J.
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- 5-FLUOROPYRIMIDINONE DERIVATIVES
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This present disclosure is related to the field of 5-fluoropyrimidinones and their derivatives and to the use of these compounds as fungicides.
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Page/Page column 29
(2011/02/24)
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- Cytosine modules in quadruple hydrogen bonded arrays
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Cytosine modules have been investigated for applications in supramolecular quadruple hydrogen bonded arrays. Notably, the importance of the C-5-H in the formation of unfolded and folded arrays by substitution to C-5-F was established. In addition, the incorporation of different alkyl chain lengths at N-1 and N-9 indicated that longer alkyl chains give rise to more of the unfolded rotamer, with the chain length and degree of unsaturation at N-1 having the major effect. Methyl cytosine modules were also able to readily form hetero-associated Upy-UCyt dimers as efficiently as the hexyl cytosine modules and a polyadipate telechelic polymer was used to prepare cytosine polymers.
- Greco, Elisabetta,Aliev, Abil E.,Lafitte, Valerie G. H.,Bala, Kason,Duncan, David,Pilon, Laura,Golding, Peter,Hailes, Helen C.
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experimental part
p. 2634 - 2642
(2011/01/12)
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- Glorination of Pyrimidines. Part 2. Mechanistic Aspects of the Reaction of Acetyl Hypofluorite with Uracil and Cytosine Derivatives
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The reaction of acetyl hypofluorite (AcOF) with uracil, cytosine, and some N-1-substituted derivatives dissolved in either acetic acid or water has been investigated.Analysis by radio-h.p.l.c., using (18)f as a tracer, and by (1)H n.m.r. revealed that a substituent at N-1 of uracil has a remarkable effect on the stability of the intermediate 6-acetoxy-5-fluoro-5,6-dihydrouracils.In addition, it was found that these cytosine adducts rapidly deaminate in water yielding their corresponding uracil analogues.
- Visser, W. M. Gerard,Herder, E. Renella,Kanter, Frans J. J. de,Herscheid D. M. Jacobus
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p. 1203 - 1208
(2007/10/02)
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- Stereochemistry of the Formation of 4-Alkoxyimino-5,6-dihydro-6-alkoxyaminopyrimidin-2(1H)-ones from Cytosines and Hydroxylamines
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High resolution 1H and 19F n.m.r. data together with deuterium labelling studies are presented which reveal that the addition of hydroxylamines across the 5,6-double bond of cytosines is predominantly trans.The 4-alkoxyimino-5,6-dihydro-6-alkoxyaminopyrimidin-2(1H)-one products show syn/anti isomerism about the 4-alkoxyimino-group dependent on the substituent at N(3) (H or Me, respectively) and conformational changes throughout the molecules which are dependent on the substituents at N(1) (H or Me) and C(5) (H or F).
- Atkins, Paul J.,Hall, C. Dennis
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p. 155 - 160
(2007/10/02)
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