Interaction Of Cytosine Research Articles

Stacking interaction of cytosine with carbon nanotubes: MP2, DFT and Raman spectroscopy study

We employed the Raman spectroscopy and the MP2 and DFT (with the MPWB1K, M05, M05-2X and MPW1B95 functionals) calculations to study the interaction of cytosine with SWCNTs (single-wall carbon nanotubes). The Raman spectra of SWCNT and SWCNT-cytosine films showed that the non-covalent interaction results in a down-shift of the frequency of the most intensive band of the SWCNT at 1590 cm −1 (the G-mode). The interaction energy in the complex formed by cytosine with a fragment of the zigzag(10, 0) SWCNT calculated at the MP2/6-311++G(2d,p) level of theory is −62.4 kJ/mol.

Structural and electronic changes of cytosine upon addition of atomic sulfur

When sulfur becomes a contaminant it may affect important biophysical and biochemical processes. In this work, we investigate the interaction of cytosine with atomic sulfur. We find two equally probable places where sulfur may link cytosine. The changes in energetics and variations in the vibrational spectra, dipole moment, charge populations and electron density with respect to isolated cytosine are quantified. The computations are performed according to the Kohn–Sham version of density functional theory. We conclude on the possibility that sulfur may locally interfere in the formation of the Watson–Crick pairs and in the stacking of contiguous nucleic acid bases of the DNA/ RNA helix.

Volumetric investigations of solute–solvent interactions of cytosine and their methyl-, methoxy-, and hydroxy-derivatives in methanol and N, N-dimethylformamide at 25 °C

Experimentally determined densities of cytosine and their methyl-, methoxy-, and hydroxy-derivatives at 25 °C in methanol and N, N-dimethylformamide are presented. The apparent molar volumes and then the partial molar volumes V 2 0 were calculated. Together with previously obtained V 2 0 for aqueous solutions of compounds studied: (1) the transfer functions Δ V 2,tr 0 water–methanol, water– N, N-dimethylformamide; (2) the contributions to V 2 0 value which correspond to substitution on cytosine moiety of a hydrogen atom on a N, O, C atom by CH 3 group and replacement of a hydrogen on N 4 by an OH group were determined and discussed. Structural parameters: molecular accessible surface S M areas and their atomic partition S N, S O, S H(N,O), molecular volumes V 2 M of compounds studied were calculated. Its enables to determine the correlations between volumetric properties and structural parameters according to the model which is based on the assumptions that density of solvation shell α depends on polarity P and the structure of the hydrophobic compounds. The transfer functions Δ V 2,tr 0 water–methanol, water– N, N-dimethylformamide were also calculated and discussed.

Binding of nucleobases to a dizinc macrocyclic complex. Supramolecular assembling of dinuclear clusters through N–H⋯O and C–H⋯O hydrogen bonding

The interaction of cytosine (CyH), thymine (TH) and uracil (UH) with the dinuclear Zn(II) complexes of ligand 1,4,7,16,19,22-hexaza-10,13,25,28-tetraoxacyclotriacontane (L) has been studied by means of potentiometric titrations (0.1 mol dm −3 NMe 4NO 3, 298.1 K), and 1H NMR measurements. The equilibrium constants for the formation of the ternary complexes with the nucleobases indicate that the [Zn 2L] 4+ complex displays similar binding features towards thymine and uracil. The dizinc complex forms stable 1:1 and 1:2 complexes with both deprotonated thymine and uracil at neutral or slightly alkaline pH values. The constants for the addition of first and second substrate molecules are almost equal indicating that each nucleobase is coordinated, almost independently, by one metal ion of [Zn 2L] 4+. This feature is confirmed by the crystal structures of [Zn 2LT 2] 2+ and [Zn 2LU 2] 2+. In the [Zn 2LA 2] 2+ (A −=T −, U −) complexes the two metal ions have almost the same coordination environment and each Zn(II) is coordinated to three nitrogens of the macrocycle and to a deprotonated nitrogen of the nucleobases. In the crystal packing the dinuclear clusters give rise to a supramolecular architecture based on infinite pillars of [Zn 2LA 2] 2+ (A −=T −, U −) assembled via hydrogen bonding. Cytosine forms only 1:1 adducts with the dizinc complex and the stability constants values suggest that the deprotonated nucleobase bridges the two metal ions.

Escherichia coli cytosine deaminase: the kinetics and thermodynamics for binding of cytosine to the apoenzyme and the Zn 2+ holoenzyme are similar

Recombinant Escherichia coli cytosine deaminase is purified as a mixture of Zn 2+ and Fe 2+ forms of the enzyme. Fe 2+ is removed readily by o-phenanthroline to yield apoenzyme (apoCDase) that contains <0.2 mol of Zn 2+per mol of subunit. ApoCDase was efficiently reconstituted to Zn 2+CDase by treatment with ZnCl 2. The interaction of cytosine with apoCDase and Zn 2+CDase was investigated at pH 7.5 and 25°C by monitoring changes in intrinsic protein fluorescence. The values for the kinetic data K 1, k 2, and k 3 for Zn 2+CDase were 0.25 mM, 80 s −1, and 38 s −1, respectively. The value for k −2 was statistically indistinguishable from zero. The analogous values for K 1, k 2, and k −2, ( k 3=0) for apoCDase were 0.157 mM, 186 s −1 and ∼0.8 s −1, respectively. The overall dissociation constant of apoCDase for cytosine was 0.00069 mM, whereas the K m of Zn 2+CDase for cytosine was 0.20 mM. The pre-steady state phase of the reaction was associated with an absorbance increase at 280 nm that was attributed to solvent perturbation of the spectrum of cytosine or enzyme. Formation of the Fe 2+CDase–cytosine complex was too rapid to monitor by these techniques.

Theoretical study of the protonation and deprotonation of cytosine. Implications for the interaction of cytosine with water

The geometries, harmonic vibrational frequencies and energies of the two stable cyclic structures of the keto tautomer of cytosine complexed with water are computed using density functional theory (B3LYP) combined with the 6-31++G(d,p) basis set. The effect of complex formation with water on the pyramidalization of the amino group is discussed. The proton affinities of the oxygen and nitrogen atoms and the deprotonation enthalpies of the three NH bonds of cytosine are computed at the same level of theory. The deprotonation enthalpies of the two NH bonds of the amino group differ by 23 kJ mol −1 from each other and this reflects the asymmetric deformation of the amino group. The most stable hydrogen bond between cytosine and water is formed at the acceptor atom characterized by the lowest proton affinity and at the NH group having the highest acidity. The results are compared with data obtained at the same level of theory for the uracil– and thymine–water complexes. For the three nucleobases, the intermolecular distances and the energies of the hydrogen bonds formed at the different sites depend on the proton affinity and the deprotonation enthalpy of these sites. The dominance of the proton donor capacity in determining the hydrogen-bond energies and the cooperativity in the cyclic structures are discussed.

Subsite binding in an RNase: structure of a barnase-tetranucleotide complex at 1.76-A resolution.

A set of subsites in barnase has been proposed from kinetic studies. A specific substrate analog, the tetradeoxynucleotide, CGAC, has been designed from this information. We report the crystal structure of its complex with barnase at 1.76-A resolution. The structure was solved by molecular replacement from a model of free barnase and refined to a crystallographic R factor of 19.0%. The stoichiometry of the asymmetric unit dimeric complex is [barnase:d(CGAC)]2, with 2-fold noncrystallographic symmetry. Each barnase molecule binds one oligonucleotide whereby the recognition site is occupied by guanine, and all three phosphate groups of the nucleotide make electrostatic interactions with basic residues in a strongly electropositive region at the bottom of the active site. The active-site His 102 packs against the adenine base of the nucleotide in an almost identical manner to the guanine base in the barnase-d(GpC) complex and defines a possible subsite in the Michaelis complex. The overall protein structure is unchanged on forming the complex with d(CGAC), but there are small differences in the active site and in crystal packing regions. The protein coordinates will be useful for theoretical calculations since some disorder induced by packing constraints in the crystals of the free enzyme are absent in the crystals of the complex. The interface of the dimer is formed by a His 102-adenine-adenine-His 102 face-to-face ring stack directly on the 2-fold axis. The edge of the adenine-adenine stack packs closely onto the face of a 3'-cytosine-3'-cytosine interaction, which has a "base-pair"-like conformation but too great a separation of the bases to form hydrogen bonds. This unusual arrangement is the major stabilizing interaction within the dimeric complex, since there are no direct protein-protein interactions. Using the structure of the complex as a starting point for model building, the nature of the enzyme-substrate and enzyme-transition state complexes is investigated.

Quantitative phosphorescence study of interactions of cytosine and cytidine and its nucleotides in frozen aqueous solution: Evidence for anomalous heavy-atom effect

Phosphorescence vs. pH titration curves of cytosine, cytidine, cytidine-5′-mono-phosphate (CMP), -diphosphate (CDP) and -triphosphate (CTP) were obtained in methanol/water 10/90 v/v and in various aqueous sodium halide solutions frozen at 77°K. As shown by the shape of the titration curve, molecular aggregates or “puddles” of cytosine and cytidine were shown to occur only in relatively concentrated frozen solution (10 −3 M), these aggregates being dissociated in dilute frozen solutions (≤10 −4 M) or in ∼ 1 M sodium chloride. No molecular aggregation could be found even in concentrated solutions of CMP, CDP, and CTP. Lower concentrations of sodium bromide or iodide (10 −1 M) were demonstrated to give “reversed” sigmoidal phosphorescence titration curves in the case of cytidine, due to an anomalously large heavy-atom enhancement factor in acidic solution, ranging between 30 and 50.