Na+, Mg2+, and Zn2+ binding to all tautomers of adenine, cytosine, and thymine and the eight most stable keto/enol tautomers of guanine: a correlated ab initio quantum chemical study

Interactions of adenine, cytosine, guanine, and thymine with Na(+), Mg(2+), and Zn(2+) cations were studied using an approximate resolution of identity correlated second-order MP2 (RI-MP2) method with the TZVPP ([5s3p2d1f/3s2p1d]) basis set. All existing tautomers of adenine, cytosine, and thymine and the eight most stable keto/enol tautomers of guanine were considered. Cations bind mostly in a bidentate manner, and stabilization energies of these complexes are larger than those in the case when cations bind in a unidentate manner. The cation...Y (Y equal to N or O) distances for divalent metals are shorter than those for Na(+) and for Zn(2+) are mostly shorter than the Mg(2+)...Y distance. The intermolecular distances between the cation and the base for complexes containing adenine and cytosine are systematically shorter than those for complexes containing guanine and thymine. Only for cytosine the canonical keto/amino tautomer structure with ions represents the global minimum. For guanine, the metalated canonical form is again the most stable, but its stabilization energy is within less than 5% of the stabilization energies of the two other rare tautomers, which indicates that the canonical form and these two rare tautomers could coexist. The canonical structures of adenine and thymine in the presence of ions are considerably less stable (by more than 10%) than the complexes of the rare tautomers. It can be concluded that the interaction of Na(+), Mg(2+), and Zn(2+) cations with cytosine in the gas phase will not induce the change of the canonical form to the rare tautomeric form. In the case of isolated guanine, the equilibrium of the canonical form with rare tautomers can be found. For isolated adenine and thymine the presence of rare tautomers is highly probable.     

Thermal desorption behavior and binding properties of DNA bases and nucleosides on gold

A comparison of the binding of DNA bases (adenine, cytosine, guanine, and thymine) and nucleosides (2'deoxyadenosine, 2'deoxycytidine, 2'deoxyguanosine, and thymidine) to gold thin films is presented. Desorption of monolayer/submonolayer and multilayer films of the adsorbates on gold studied via temperature-programmed desorption (TPD) and reflection-absorption infrared (RAIR) spectroscopy reveals that there are major differences in the binding affinities of the different bases to gold, for example, thymine DeltaHdes = 111 +/- 2 kJ/mol compared to guanine DeltaHdes = 146 +/- 2 kJ/mol. The differences can be rationalized by molecular structures of the bases and their binding modes to gold surfaces deduced from IR data. Similar trends in desorption energies, shifted to lower desorption energy by more than 10 kJ/mol, are observed for deoxynucleoside layers on gold thin films.     

On the structure and desorption dynamics of DNA bases adsorbed on gold: a temperature-programmed study

The structure and desorption dynamics of mono- and multilayer samples of adenine, cytosine, guanine, and thymine on polycrystalline gold thin films are studied using temperature-programmed desorption-infrared reflection absorption spectroscopy (TPD-IRAS) and temperature-programmed desorption-mass spectroscopy (TPD-MS). It is shown that the pyrimidines, adenine and guanine, adsorb to gold in a complex manner and that both adhesive (adenine) and cohesive (guanine) interactions contribute the apparent binding energies to the substrate surface. Adenine displays at least two adsorption sites, including a high-energy site (210 degrees C, approximately 136 kJ/mol), wherein the molecule coordinates to the gold substrate via the NH2 group in an sp3-like, strongly perturbed, nonplanar configuration. The purines, cytosine and thymine, display a less complicated adsorption/desorption behavior. The desorption energy for cytosine (160 degrees C, approximately 122 kJ/mol) is similar to those obtained for adenine and guanine, but desorption occurs from a single site of dispersed, nonaggregated cytosine. Thymine desorbs also from a single site but at a significantly lower energy (100 degrees C, approximately 104 kJ/mol). Infrared data reveal that the monolayer architectures discussed herein are structurally very different from those observed for the bases in the bulk crystalline state. It is also evident that both pyrimidines and purines adsorb on gold with the plane of the molecule in a nonparallel orientation with respect to the substrate surface. The results of this work are discussed in the context of improving the understanding of the design of capturing oligonucleotides or DNA strands for bioanalytical applications, in particular, for gold nanoparticle-based assays.     

Nucleotides. Part XLVIII. Synthesis of 2′-amino-2′-deoxyarabinonucleoside phosphoramidite building blocks

Chemical syntheses of 2′-amino-2′-deoxyarabinonucleosides of uracil, thymine, cytosine, adenine, and guanine and their conversion into suitably protected 3′-phosphoramidite building blocks 24–28 for oligonucleotide synthesis are described. The 2-(4-nitrophenyl)ethoxycarbonyl (npeoc) group was used for protection of the aglycon and the 2′-amino functions.     

Electronic structure and spectroscopy of nucleic acid bases: ionization energies, ionization-induced structural changes, and photoelectron spectra

We report high-level ab initio calculations and single-photon ionization mass spectrometry study of ionization of adenine (A), thymine (T), cytosine (C), and guanine (G). For thymine and adenine, only the lowest-energy tautomers were considered, whereas for cytosine and guanine we characterized the five lowest-energy tautomeric forms. The first adiabatic and several vertical ionization energies were computed using the equation-of-motion coupled-cluster method for ionization potentials with single and double substitutions. Equilibrium structures of the cationic ground states were characterized by DFT with the ωB97X-D functional. The ionization-induced geometry changes of the bases are consistent with the shapes of the corresponding molecular orbitals. For the lowest-energy tautomers, the magnitude of the structural relaxation decreases in the following series, G > C > A > T, the respective relaxation energies being 0.41, 0.32, 0.25, and 0.20 eV. The computed adiabatic ionization energies (8.13, 8.89, 8.51-8.67, and 7.75-7.87 eV for A, T, C, and G, respectively) agree well with the onsets of the photoionization efficiency (PIE) curves (8.20 ± 0.05, 8.95 ± 0.05, 8.60 ± 0.05, and 7.75 ± 0.05 eV). Vibrational progressions for the S(0)-D(0) vibronic bands computed within double-harmonic approximation with Duschinsky rotations are compared with previously reported experimental photoelectron spectra and differentiated PIE curves.     

核酸水解产物嘌呤、嘧啶碱基在BDS柱上的分离及测定

 用高效液相色谱法测定了核酸水解的中间产物及最终产物 6种嘌呤、嘧啶碱基 ,探讨了色谱柱、流动相等对其分离的影响 ,确定了最佳色谱条件为 :HypersilBDS C18柱 ,乙腈 0 1mol/LKH2 PO4 (H3 PO4 调节 pH至4 0 5 ) (体积比为 2∶98)作流动相 ,紫外检测器在 2 6 0nm波长下检测。方法的精密度在 3%以内 ,回收率在 82 %～ 114%。方法应用于酵母核酸样品的测定中 ,取得了很好的结果。     

Gas-phase theoretical prediction of the metal affinity of copper(I) ion for DNA and RNA bases

The most stable tautomeric forms of free DNA and RNA bases were considered as substrates for the interaction of Cu(+) ion. Several suitable attachment sites were selected that involved mono- and bi-coordination of the cation. B3LYP/6-311 + G(2df,2p) bond energies showed that copper ion has the major affinity for guanine and cytosine bases. The proposed values of Cu(+) ion affinity are 59.9, 60.0, 80.2, 88.0 and 69.0 kcal mol(-1) for uracil, thymine, cytosine, guanine and adenine, respectively. The preference for the mono- or bi-coordination depends on the particular tautomer for each base.     

Oligonucleotide cross-linking with copper ions. Spectral and quantum chemical study

Copper(II) complexes with synthetic oligonucleotides consisting of repeating adenine–thymine and guanine–cytosine complementary base pairs have been studied by UV spectroscopy and simulated by DFT quantum chemical calculations at the B3LYP/6-311G++(d,p) level of theory with inclusion of solvation (hydration) effects. The obtained data suggest selective interaction of copper(II) ions with guanine–cytosine complementary pairs, followed by DNA cross-linking at those sites.     

Kinetics and activation parameter analysis for the prebiotic oligocytidylate formation on Na(+)-montmorillonite at 0-100 degrees C

The kinetic analysis of the temperature dependence of the formation of oligocytidylate (oligo(C)) from the 5'-monophosphorimidazolide moiety of cytidine (ImpC) in the presence of Na (+)-montmorillonite (Na (+)-Mont) catalyst has been carried out at 0-100 degrees C. The rate constants for the formation of oligo(C), hydrolysis of ImpC with and without Na (+)-Mont and degradation of oligo(C) were determined. The apparent activation parameters were 30.8 +/- 3.9 kJ mol (-1) ( Ea), 28.3 +/- 4.0 kJ mol (-1) (Delta H++), and -231 +/- 13 J mol (-1) K (-1) (Delta S++) for the formation of the 2-mer; 45.6 +/- 2.9 kJ mol (-1) ( Ea), 43.0 +/- 3.0 kJ mol (-1) (Delta H++), -164 +/- 10 J mol (-1) K (-1) (Delta S++) for the 3-mer; and 45.2 +/- 0.6 kJ mol (-1) ( Ea), 42.7 +/- 0.7 kJ mol (-1) (Delta H++), -159 +/- 2 J mol (-1) K (-1) (Delta S++) for the 4-mer in the presence of Na (+)-Mont. An increasing trend for the rate constants for the formation of oligo(C) in the order 2-mer < 3-mer <4-mer was observed at high temperatures, which is consistent with that observed at low temperatures. These analyses implied for the first time that the associate formation between an activated nucleotide monomer and an elongating oligonucleotide prior to the phosphodiester bond formation during the elongation of an oligonucleotide on a clay surface would be based on the interaction between the two reactants at the phosphoester and/or ribose moieties rather than at the nucleotide bases. The hydrolysis rate of ImpC at 25-100 degrees C was 5.3-10.6 times greater in the presence of Na (+)-Mont than in its absence. Although the degradation of oligo(C) in the presence of Na (+)-Mont was slower than the formation of the 3-mer and longer oligo(C) on Na (+)-Mont, its yield decreased with temperature. This is mainly because the ratios of the rate constant of the 2-mer formation to those of ImpC hydrolysis and the 3-mer and 4-mer formation decrease with an increase in temperature, which is attributed to the enthalpy and entropy changes for the formation of the 2-mer. This trend resembles the case of the template-directed formation of oligo(G) on a poly(C) template but is different from the Pb (2+)-ion-catalyzed oligo(C) formation. According to the kinetics and activation parameter analyses regarding the clay reaction and other prebiotic polymerase models, the possible pathways for the oligonucleotide formation are discussed and compared.     

Electrochemical response of oligonucleotides on carbon paste electrode

Electrochemical response of synthetic oligonucleotides with different DNA bases sequences was investigated to find relationships between a chain composition and a signal. All DNA mononucleotides present electroactivity at a carbon paste electrode yielding anodic peaks at potentials: 1.00 (GMP), 1.28 (AMP), 1.47 (TMP) and 1.53 V (CMP). Also 15-mer homooligonucleotides show respective anodic peaks. Electrochemical response of 15- and 19-mer oligonucleotides consisting of all four DNA bases in different amounts was determined by the composition of oligonucleotide chain. When the contribution of different bases in oligonucleotide was balanced two anodic peaks were obtained that can be attributed to guanine and adenine moieties. Thymine residue is shown as a separate peak in voltammogram when its content in oligonucleotide chain is close to 50% of the total number of bases. Cytosine also yields a peak at its significant contribution in oligonucleotide chain and both pyrimidinic moieties produce catalytic waves easier when one of them is dominating or when only one pyrimidine derivative is present in a chain. Guanine is the easiest oxidized base and it produces a peak even at its minimal contribution (one guanine residue in 19-mer oligonucleotide). Guanine peak potential is dependent on oligonucleotide concentration and oligonucleotide composition. The lowest oligonucleotide concentration detected by guanine peak was 12.5 nM whereas detected by thymine peak was 90 nM.     

2-aza-2'-deoxyadenosine: synthesis, base-pairing selectivity, and stacking properties of oligonucleotides

2-Aza-2'-deoxyadenosine (2, z2Ad) is synthesized via its 1,N6-etheno derivative 7 and enzymatically deaminated to 2-aza-2'-deoxyinosine (3). Compound 2 is converted into the phosphoramidite building block 10b. This is employed in solid-phase oligonucleotide synthesis. The 2-azapurine base forms a strong base pair with guanine, but a much weaker one with adenine, thymine, and cytosine. Oligonucleotide duplexes with dangling nucleotide residues, such as 2-aza-2'-deoxyadenosine and 7-deaza-2'-deoxyadenosine (4, c7Ad), either on one or both termini, are synthesized, and the thermal stability of the duplexes is correlated with the hydrophobic properties of the dangling nucleotide residues.     

At nonzero temperatures, stacked structures of methylated nucleic acid base pairs and microhydrated nonmethylated nucleic acid base pairs are favored over planar hydrogen-bonded structures: a molecular dynamics simulations study

The dynamic structure of all ten possible nucleic acid (NA) base pairs and methylated NA base pairs hydrated by a small number of water molecules (from 1 to 16) was determined by using molecular dynamics simulations in the NVE microcanonical and NVT canonical ensembles with the Cornell force field (W. D. Cornell, P. Cieplak, C. I. Bayly, I. R. Gould, K. M. Merz, D. M. Ferguson, D. C. Spellmeyer, T. Fox, J. E. Caldwell, P. Kollman, J. Am. Chem. Soc. 1995, 117, 5179). The presence of one water molecule does not affect the structure of any hydrogen-bonded (H-bonded) nonmethylated base pair. An equal population of H-bonded and stacked structures of adenine...adenine, adenine...guanine and adenine... thymine pairs is reached if as few as two water molecules are present, while obtaining equal populations of these structures in the case of adenine...cytosine, cytosine...thymine, guanine... guanine and guanine...thymine required the presence of four water molecules, and in the case of guanine...cytosine, six. A comparable population of planar, H-bonded and stacked structures for cytosine...cytosine and thymine... thymine base pairs was only obtained if at least eight water molecules hydrated a pair. Methylation of bases changed the situation dramatically and stacked structures were favoured over H-bonded ones even in the absence of water molecules in most cases. Only in the case of methyl cytosine...methyl cytosine, methyl guanine...methyl guanine and methyl guanine...methyl cytosine pairs were two, two or six water molecules, respectively, needed in order to obtain a comparable population of planar, H-bonded and stacked structures. We believe that these results give clear evidence that the preferred stacked structure of NA base pairs in the microhydrated environment, and also apparently in a regular solvent, is due to the hydrophilic interaction of a small number of water molecules. In the case of methylated bases, it is also due to the fact that the hydrogen atoms most suitable for the formation of H-bonds have been replaced by a methyl group. A preferred stacked structure is, thus, not due to a hydrophobic interaction between a large bulk of water molecules and the base pair, as believed.     

Natural resonance structures and aromaticity of the nucleobases

Natural resonance theory (NRT) and nucleus- independent chemical shift (NICS) analyses have been applied to the standard nucleobases adenine, guanine, cytosine, uracil, and thymine. The molecular electron densities were obtained from density functional theory calculations at the B3LYP level and ab initio calculations at the HF, MP2, and CCD levels. Compared with the dominance of the two Kekulé structures in benzene, the structural modifications in the forms of endocyclic heteroatoms and exocyclic substituents introduce various degrees of charge separation in nucleobases. As a result, the leading resonance structures for cytosine, uracil, and thymine are found to be covalent structures, but their weightings decrease to ~30% in the NRT expansion. For adenine and guanine, the covalent structures have weightings of ~20%, and the leading ionic resonance structures have weightings of as high as about 8%. Methods that include electron correlation effects, B3LYP, MP2, and CCD, give smaller weightings for the covalent structures than HF. However, MP2 and CCD results often include “strange” resonance structures with connections between unbonded vicinal atoms, making DFT at the B3LYP level the better choice for calculating these molecules’ electron density. The NICS at the ring center shows that the six-membered rings in cytosine, uracil, thymine, and guanine are nonaromatic with NICS within − 3 to − 1 ppm, while it is − 7.3 ppm for the six-membered ring in adenine. The NICS of the five-membered rings of adenine and guanine is around − 12 ppm, a slight decrease from the value of − 15.0 ppm for pyrrole.     

Rates of water exchange for two cobalt(II) heteropolyoxotungstate compounds in aqueous solution

Polyoxometalate ions are used as ligands in water-oxidation processes related to solar energy production. An important step in these reactions is the association and dissociation of water from the catalytic sites, the rates of which are unknown. Here we report the exchange rates of water ligated to Co(II) atoms in two polyoxotungstate sandwich molecules using the (17)O-NMR-based Swift-Connick method. The compounds were the [Co(4)(H(2)O)(2)(B-α-PW(9)O(34))(2)](10-) and the larger αββα-[Co(4)(H(2)O)(2)(P(2)W(15)O(56))(2)](16-) ions, each with two water molecules bound trans to one another in a Co(II) sandwich between the tungstate ligands. The clusters, in both solid and solution state, were characterized by a range of methods, including NMR, EPR, FT-IR, UV-Vis, and EXAFS spectroscopy, ESI-MS, single-crystal X-ray crystallography, and potentiometry. For [Co(4)(H(2)O)(2)(B-α-PW(9)O(34))(2)](10-) at pH 5.4, we estimate: k(298)=1.5(5)±0.3×10(6) s(-1), ΔH(≠)=39.8±0.4 kJ mol(-1), ΔS(≠)=+7.1±1.2 J mol(-1) K(-1) and ΔV(≠)=5.6 ±1.6 cm(3) mol(-1). For the Wells-Dawson sandwich cluster (αββα-[Co(4)(H(2)O)(2)(P(2)W(15)O(56))(2)](16-)) at pH 5.54, we find: k(298)=1.6(2)±0.3×10(6) s(-1), ΔH(≠)=27.6±0.4 kJ mol(-1) ΔS(≠)=-33±1.3 J mol(-1) K(-1) and ΔV(≠)=2.2±1.4 cm(3) mol(-1) at pH 5.2. The molecules are clearly stable and monospecific in slightly acidic solutions, but dissociate in strongly acidic solutions. This dissociation is detectable by EPR spectroscopy as S=3/2 Co(II) species (such as the [Co(H(2)O)(6)](2+) monomer ion) and by the significant reduction of the Co-Co vector in the XAS spectra.     

Ultratrace determination of adenine in the presence of copper by adsorptive stripping voltammetry

An electrochemical stripping procedure for ultra-trace measurements of adenine is described based on the adsorption of the adenine-copper complex on a static mercury drop electrode. Cyclic voltammetry was used to characterize the interfacial and redox behavior. Optimum experimental conditions were found when using a 0.005 M NaOH solution containing 0.4 ppm of copper, an accumulation potential of -0.30 V, a scan rate of 100 mV s(-1) and a linear scan mode. There is a linear response to adenine concentration in the range of 0.1-1.0 ppb and the detection limit for 6 min accumulation time was of 4.0 ppt (3.0x10(-11) M). Proper conditions for measuring the adenine in presence of guanine, thymine and cytosine were also investigated. The method was applied for the determination of adenine in a sample of single-stranded calf thymus DNA.     

Polarized fluorescence and estimated lifetimes of the DNA bases at room temperature

Polarized fluorescence spectra are presented for thymine, cytosine, adenine and guanine in neutral aqueous solution and in rigid neutral ethylene glycol-water (6:4) at ca. ?125°C. For thymine and cytosine at 25°C the polarization is nearly as high as in rigid media. Analysis yields fluorescence lifetime (τf) estimates of ?2 ps. This limits the likelihood that emission is from a minor species or via a forbidden transition. The lower room temperature polarization for adenine and guanine indicates τf's of ≈ 10 ps which allows for emission from a fluorescent tautomer or via a slightly forbidden transition.     

Common semiopen conformations of Mg2+-free Ras, Rho, Rab, Arf, and Ran proteins combined with GDP and their similarity with GEF-bound forms

A computational study was performed on the Mg(2+)-free conformations of the small guanine nucleotide-binding proteins (GNBPs): Ras, Rho, Rab, Arf, and Ran, which were complexed with GDP. Molecular dynamics (MD) simulation was executed for each complex for the duration of 3.0 ns to investigate the effects of Mg(2+) ions on the GNBPs' structure. The results indicated that all Mg(2+)-free GNBPs formed a groove between the switch region and the nucleotide-binding site. In some GNBP families, the release of Mg(2+) was reported to play an important role in binding the guanine nucleotide-exchanging factor (GEF) promoting the GDP/GTP exchange reaction. Interestingly, the grooves, which appeared in the MD simulations, were similar to the grooves experimentally observed in the GNBP-GEF complex. We also calculated the Mg(2+)-bound GNBPs to compare with the Mg(2+)-free forms. No groove was observed in the Mg(2+)-bound GNBPs. These results demonstrated a regulatory role of Mg(2+) ion to prepare a template for the GEF binding. Moreover, the results suggested that the release of Mg(2+) ion lead to the GEF-GNBP binding.     

带电组氨酸侧链与DNA碱基间非键作用强度的理论研究

采用MP2方法和6-31+G(d,p)基组优化得到了带有一个正电荷的组氨酸侧链与4个DNA碱基间形成的18个氢键复合物的气相稳定结构, 从文献中获取了组氨酸侧链与DNA碱基间形成的12个堆积和T型复合物的气相稳定结构, 使用包含基组重叠误差(BSSE)校正的MP2方法和aug-cc-pVTZ基组及密度泛函理论M06-2X-D3方法和aug-cc-pVDZ基组计算了这些复合物的结合能. 研究结果表明, 包含BSSE校正的M06-2X-D3方法和aug-cc-pVDZ基组能够给出较准确的结合能; 气相条件下, 组氨酸侧链与同种DNA碱基间的离子氢键作用明显强于堆积作用和T型作用, 组氨酸侧链最易通过离子氢键与胞嘧啶C和鸟嘌呤G作用形成氢键复合物, 组氨酸与胞嘧啶C和鸟嘌呤G间的T型作用强于与腺嘌呤A和胸腺嘧啶T间的离子氢键作用; 水相条件下, 组氨酸侧链与同种DNA碱基间的离子氢键作用仍明显强于堆积作用和T型作用, 组氨酸侧链更易与胞嘧啶C和鸟嘌呤G相互作用形成氢键复合物, 但是最强的组氨酸侧链与胞嘧啶C间的T型作用明显弱于与腺嘌呤A和胸腺嘧啶T间的离子氢键作用, 说明水相条件下组氨酸侧链与DNA碱基间主要通过离子氢键作用形成氢键复合物.     

Investigation of proton transport tautomerism in clusters of protonated nucleic acid bases (cytosine, uracil, thymine, and adenine) and ammonia by high-pressure mass spectrometry and ab initio calculations

The energetics of the ion-molecule interactions and structures of the clusters formed between protonated nucleic acid bases (cytosine, uracil, thymine, and adenine) and ammonia have been studied by pulsed ionization high-pressure mass spectrometry (HPMS) and ab initio calculations. For protonated cytosine, uracil, thymine, and adenine with ammonia, the measured enthalpies of association with ammonia are -21.7, -27.9, -22.1, and -17.5 kcal mol-1, respectively. Different isomers of the neutral and protonated nucleic acid bases as well as their clusters with ammonia have been investigated at the B3LYP/6-31+G(d,p) level of theory, and the corresponding binding energetics have also been obtained. The potential energy surfaces for proton transfer and interconversion of the clusters of protonated thymine and uracil with ammonia have been constructed. For cytosine, the experimental binding energy is in agreement with the computed binding energy for the most stable isomer, CN01-01, which is derived from the enol form of protonated cytosine, CH01, and ammonia. Although adenine has a proton affinity similar to that of cytosine, the binding energy of protonated adenine to ammonia is much lower than that for protonated cytosine. This is shown to be due to the differing types of hydrogen bonds being formed. Similarly, although uracil and thymine have similar structures and proton affinities, the binding energies between the protonated species and ammonia are different. Strikingly, the addition of a single methyl group, in going from uracil to thymine, results in a significant structural change for the most stable isomers, UN01-01 and TN03-01, respectively. This then leads to the difference in their measured binding energies with ammonia. Because thymine is found only in DNA while uracil is found in RNA, this provides some potential insight into the difference between uracil and thymine, especially their interactions with other molecules.