Infrared spectra of uracil and thymine in an argon matrix

High-resolution IR spectra of uracil, thymine, methyl-derivatives of uracil and 5,6-dihydrouracil are obtained using the matrix isolation method.     

Reductive catabolism of uracil and thymine by Burkholderia cepacia

Catabolism of uracil and thymine in Burkholderia cepacia ATCC 25416 was shown to occur using a reductive pathway. The first pathway enzyme, dihydropyrimidine dehydrogenase, was shown to utilize NADPH as its nicotinamide cofactor. Growth of B. cepacia on pyrimidine bases as the nitrogen source instead of on ammonium sulfate increased dehydrogenase activity at least 32-fold. The second and third reductive pathway enzymes, dihydropyrimidinase and N-carbamoyl-β-alanine amidohydrolase, respectively, exhibited activities elevated more than 21-fold when pyrimidine or dihydropyrimidine bases served as the nitrogen source rather than ammonium sulfate. The pathway enzyme activities were induced after growth on 5-methylcytosine. Received: 17 January 1997 / Accepted: 5 May 1997     

Degradation of the pyrimidine bases uracil and thymine by Escherichia coli B

Degradation of the pyrimidine bases uracil and thymine by Escherichia coli B was investigated. The known products of the reductive pathway of pyrimidine base catabolism were tested to determine if they could support the growth of E. coli B cells as sole sources of nitrogen or carbon. As might be expected if the reductive pathway was present, it was found that dihydrouracil, N-carbamoyl-beta-alanine, beta-alanine, dihydrothymine and beta-aminoisobutyric acid could sustain the growth of the bacterial cells as sole nitrogen sources by at least a fourteen-fold greater level than that observed if they were included as sole carbon sources. The existence of the reductive pathway of pyrimidine base degradation was confirmed in this micro-organism, since dihydrouracil, N-carbamoyl-beta-alanine and beta-alanine were detected following thin-layer chromatographic separation of the catabolic products of uracil and dihydrouracil.     

Covalent hybridization of CNT by thymine and uracil: A computational study

We have investigated the electronic and structural properties of covalent functionalization of the tip of (5,0) carbon nanotube (CNT) by di-keto and keto-enol forms of thymine (T) and uracil (U) nucleobases. Density functional theory (DFT) calculations have been performed to optimize the investigated structures and to calculate the properties such as dipole moment, bond length, band gap, total energy, binding energy and quadrupole coupling constant. The results indicated that, due to the functionalization of CNT by T and U, the hybrids exhibit new properties in which they are similar in both types of CNT-T and CNT-U hybrids.     

Hydrogen-bonding preferences in 2,6-diaminopurine: uracil (thymine) and 8-methyl adenine:uracil (thymine) complexes

We present molecular mechanical calculations on 2,6-diaminopurine (2,6-DAP):uracil (thymine) and 8-methyladenine (8-methyl A): uracil (thymine) hydrogen-bonded complexes of various geometries, namely, Watson-Crick (normal and reverse), Hoogsteen (normal and reverse), and purine N3 type. In contrast to earlier calculations [Ornstein, R. L. & Fresco, J. R. (1983) Proc. Natl. Acad. Sci. USA 80 , 5171–5175], the 2,6-DAP:uracil (thymine) complexes are predicted to be Watson-Crick and the 8-methyladenine:uracil (thymine) to be Hoogsteen. The results presented here are more consistent with the observed crystallographic preferences.     

Hydration of uracil and thymine methylderivatives: a Monte Carlo simulation

The simulation performed shows that under methylation of uracil and thymine NH-groups the interaction energy between a base and water (Uwb) is increased. It is also detected that the increase in this energy was observed in the 1st and the 3rd sectors. These conclusions do not confirm the assumption made in the literature on the character of an interaction between methylated bases and water. According to this assumption, when the NH-groups are methylated, the energy of Uwb in these sectors decreases as a result of the van der Waals interactions between a methyl group and water, whose energy compensates the increase in the Uwb energy due to the breaking of an H-bond. Regularity of water molecules near a hydrophobic group under the hydration of polar molecules is detected for the first time.     

Interaction of glucosamine with uracil and thymine: a computational study

Noncovalent interactions are ubiquitous and have been well recognized in chemistry, biology and material science. Yet, there are still recurring controversies over their natures, due to the wide range of noncovalent interaction terms. In this Essay, we employed the Valence Bond (VB) methods to address two types of interactions which recently have drawn intensive attention, i.e., the halogen bonding and the CH???HC dihydrogen bonding. The VB methods have the advantage of interpreting molecular structures and properties in the term of electron-localized Lewis (resonance) states (structures), which thereby shed specific light on the alteration of the bonding patterns. Due to the electron localization nature of Lewis states, it is possible to define individually and measure both polarization and charge transfer effects which have different physical origins. We demonstrated that both the ab initio VB method and the block-localized wavefunction (BLW) method can provide consistent pictures for halogen bonding systems, where strong Lewis bases NH₃, H₂O and NMe₃ partake as the halogen bond acceptors, and the halogen bond donors include dihalogen molecules and XNO₂ (X?=?Cl, Br, I). Based on the structural, spectral, and energetic changes, we confirm the remarkable roles of charge transfer in these halogen bonding complexes. Although the weak C-H???H-C interactions in alkane dimers and graphane sheets are thought to involve dispersion only, we show that this term embeds delicate yet important charge transfer, bond reorganization and polarization interactions.

     

The nature of protein dipole moments: experimental and calculated permanent dipole of alpha-chymotrypsin

The electric dichroism of alpha-chymotrypsin has been measured in buffers of various pH values and ion compositions. The stationary dichroism obtained as a function of the electric field strength is not compatible with an induced dipole mechanism and clearly shows that alpha-chymotrypsin is associated with a substantial permanent dipole moment. After correction for the internal directing electric field according to a sphere model, the dipole moment is 1.6 X 10(-27) C m at pH 8.3 (corresponding to 480 D). This value decreases with decreasing pH (to 1.2 X 10(-27) C m at pH 4.2), but is almost independent of the monovalent salt concentration in the range from 2 to 12 mM and of Mg2+ addition up to 1 mM. The assignment of the permanent dipole moment is confirmed by analysis of the dichroism rise curves. The dichroism decay time constants of (31 +/- 1) ns at 2 degrees C can be represented by a spherical model with a radius of 25-26 A, which is consistent with the known X-ray structure. The limiting linear dichroism is slightly dependent on the buffer composition and demonstrates subtle variations of the protein structure. As a complement to the experimental results, electric and hydrodynamic parameters of alpha-chymotrypsin have been calculated according to the known X-ray structure. Bead model simulations provide the center of diffusion, which is used to calculate dipole moments according to the equilibrium charge distribution evaluated from standard pK values.(ABSTRACT TRUNCATED AT 250 WORDS)     

Changes of fluorescence spectra of thymine in aqueous solution by radiation

Aqueous solution of thymine (5 X 10(-4) M, buffered at pH 7.0) was irradiated with 60Co gamma-rays under four different atmospheric conditions. In the presence of t-BuOH-N2, there was little increase in the fluorescence intensity as was previously reported in the radiolysis of cytosine. Under O2 there was also no significant increase differing from the case of cytosine. The fluorescence intensity was found to increase appreciably under N2O but it was less under N2 indicating that OH radical is mainly responsible for the formation of the highly fluorescent products. However, the fluorescence yields under these conditions were much lower in thymine radiolysis than cytosine radiolysis.     

Computation of the dipole moments of proteins.

A simple and computationally feasible procedure for the calculation of net charges and dipole moments of proteins at arbitrary pH and salt conditions is described. The method is intended to provide data that may be compared to the results of transient electric dichroism experiments on protein solutions. The procedure consists of three major steps: (i) calculation of self energies and interaction energies for ionizable groups in the protein by using the finite-difference Poisson-Boltzmann method, (ii) determination of the position of the center of diffusion (to which the calculated dipole moment refers) and the extinction coefficient tensor for the protein, and (iii) generation of the equilibrium distribution of protonation states of the protein by a Monte Carlo procedure, from which mean and root-mean-square dipole moments and optical anisotropies are calculated. The procedure is applied to 12 proteins. It is shown that it gives hydrodynamic and electrical parameters for proteins in good agreement with experimental data.