Perturbation of hydrogen bonds in the adenine ... thymine base pair by Na+, Mg2+, Ca2+ and NH4+ cations

Perturbation of the hydrogen bonds in the adenine ... thymine base pair by Na+, Mg2+, Ca2+ and NH4+ cations has been investigated by means of ab initio SCF calculations with the STO-3G basis set. The geometry of adenine...thymine, as well as those of the perturbed pairs were optimized. Approach of any cation to thymine at O6 leads to destabilization of the adenine...thymine pair; divalent cations (Mg2+, Ca2+) have a profound effect on the structure of the base pair. The approach of a cation to other available sites (thymine: O2, adenine N1 and N3) leads, on the other hand, to stabilization of the base pair. If a water molecule is placed between the cation and the base pair, the structure and stability of the base pair are changed only negligibly.     

Perturbation of Hydrogen Bonds in the Adenine…Thymine Base Pair by Na+, Mg2+, Ca2+ and NH4 + Cations

Abstract

Perturbation of the hydrogen bonds in the adenine…thymine base pair by Na⁺, Mg²⁺, Ca²⁺ and NH₄ ⁺ cations has been investigated by means of ab initio SCF calculations with the STO-3G basis set. The geometry of adenine…thymine, as well as those of the perturbed pairs were optimized. Approach of any cation to thymine at 06 leads to destabilization of the adenine…thy mine pair; divalent cations (Mg²⁺, Ca²⁺) have a profound effect on the structure of the base pair. The approach of a cation to other available sites (thymine: O2, adenine N1 and N3) leads, on the other hand, to stabilization of the base pair. If a water molecule is placed between the cation and the base pair, the structure and stability of the base pair are changed only negligibly.     

Molecular mechanisms of transitions induced by cytosine analogue: comparative quantum-chemical study

Using the simplest molecular models at the MP2/6-311++G(2df,pd)//B3LYP/6-311++G(d,p) level of the theory it has been shown for the first time that in addition to traditional incorporational errors caused by facilitated (compared with the canonical DNA bases cytosine (Cyt)) tautomerization of 6-(2-deoxy-beta-D-ribofuranosyl)-3,4-dihydro-6H,8H-pyrimido[4,5-c][1,2]oxazin-7-one (DCyt), this mutagen causes the replication errors, increasing one million times the population of mispair Gua.DCyt* (asterisk marked mutagenic tautomer) as compared with mispair Gua.Cyt*. It is also proved that DCyt in addition to traditional incorporational errors also induces similar errors by an additional mechanism - due to a facilitated tautomerization of the wobble base pair Ade.DCyt (compared to the same pair Ade.Cyt) to a mispair Ade.DCyt* which is quasirisomorphic Watson-Crick base pair. Moreover, the obtained results allowed interpreting non-inconsistently the existing experimental NMR data.     

Deamination features of 5-hydroxymethylcytosine,a radical and enzymatic DNA oxidation product

Geometric consequences of electron delocalization were studied for all possible adenine tautomers in aqueous solution by means of ab initio methods {PCM(water)//DFT(B3LYP)/6-311+G(d,p)} and compared to those in the gas phase {DFT(B3LYP)/6-311+G(d,p)}. To measure the consequences of any type of resonance conjugation (π-π, n-π, and σ-π), the geometry-based harmonic oscillator model of electron delocalization (HOMED) index, recently extended to the isolated (DFT) and hydrated (PCM//DFT) molecules, was applied to the molecular fragments (imidazole, pyrimidine, 4-aminopyrimidine, and purine) and also to the whole tautomeric system. For individual tautomers, the resonance conjugations and consequently the bond lengths strongly depend on the position of the labile protons. The HOMED indices are larger for tautomers (or their fragments) possessing the labile proton(s) at the N rather than C atom. Solvent interactions with adenine tautomers slightly increase the resonance conjugations. Consequently, they slightly shorten the single bonds and lengthen the double bonds. When going from the gas phase to water solution, the HOMED indices increase (by less than 0.15 units). There is a good relation between the HOMED indices estimated in water solution and those in the gas phase for the neutral and ionized forms of adenine. Subtle effects, being a consequence of intramolecular interactions between the neighboring groups, are so strongly reduced by solvent that the relation between the HOMED indices and the relative energies for the neutral adenine tautomers seems to be better in water solution than in the gas phase.

Comparison of gas phase intrinsic properties of cytosine and thymine nucleobases with their O-alkyl adducts: different hydrogen bonding preferences for thymine versus O-alkyl thymine

In recent years, there has been increasing interest in damaged DNA and RNA nucleobases. These damaged nucleobases can cause DNA mutation, resulting in various diseases such as cancer. Alkylating agents are mutagenic and carcinogenic in a variety of prokaryotic and eukaryotic organisms. The present study employs density functional theory (DFT/B3LYP) with the 6-311++G(d,p) basis set to investigate the effect of chemical damage in O-alkyl pyrimidines such as O⁴-methylthymine, O²-methylcytosine and O²-methylthymine. We compared the intrinsic properties, such as proton affinities, gas phase acidities, equilibrium tautomerization and nucleobase pair’s hydrogen bonding properties, of these molecules with those in the normal nucleobases thymine and cytosine. The results are of interest for chemical reasons and also possibly for biological purposes since biological media can be quite non-polar. Furthermore, we found that N1-H of O⁴-methylthymine is less acidic than N1-H of thymine, suggesting that alkyl DNA glycosylase enzyme cannot discriminate this damaged nucleobase from a normal thymine nucleobase. This result indicates that the conjugated base anion of O⁴-methylthymine would be a worse leaving group and O⁴-methylthymine is repaired in genome by demethylation rather than enzyme-catalyzed excision at N1.     

Quantum-chemical investigation of tautomerization ways of Watson-Crick DNA base pair guanine-cytosine

A novel physico-chemical mechanism of the Watson-Crick DNA base pair Gua.Cyt tautomerization Gua.Cyt*<---->Gua.Cyt<---->Gua*.Cyt (mutagenic tautomers of bases are marked by asterisks) have been revealed and realized in a pathway of single proton transfer through two mutual isoenergetic transition states with Gibbs free energy of activation 30.4 and 30.6 kcal/mol and they are ion pairs stabilized by three (N2H...N3, N1H...N4- and O6+H...N4-) and five (N2H...O2, N1H...O2, N1H...N3, O6+H...N4- and 06+H...N4-) H-bonds accordingly. Stable base pairs Gua-Cyt* and Gua*.Cyt which dissociate comparably easy into monomers have acceptable relative Gibbs energies--12.9 and 14.3 kcal/mol--for the explanation of the nature of the spontaneous transitions of DNA replication. Results are obtained at the MP2/6-311++G(2df,pd)//B3LYP/6-31 1++G(d,p) level of theory in vacuum approach.     

A quantum-dynamics study of the prototropic tautomerism of guanine and its contribution to spontaneous point mutations in Escherichia coli

High-level quantum-chemical and quantum-dynamics calculations are reported on the tautomerization equilibrium and rate constants of guanine and its complexes with one and two water molecules. The results are used to estimate the fraction of guanine present in the cell during DNA synthesis as the unwanted tautomer that forms an irregular base pair with thymine, thus giving rise to a spontaneous GC --> AT point mutation. A comparison of the estimated mutation frequency with the observed frequency in Escherichia coli is used to analyze two proposed mechanisms, differing in the extent of equilibration reached in the tautomerization reaction. In the absence of water, the equilibrium concentration of tautomeric forms is relatively large, but the barrier to their formation is high. If water is present, tautomeric forms are less favored, but water molecules may serve as efficient proton conduits causing rapid tautomerization. It is tentatively concluded that the mechanism in which a high tautomerization barrier keeps the tautomeric transformation far from a state of equilibrium is more likely than a mechanism in which water and/or polymerases produce a low equilibrium concentration of the tautomeric forms.     

基于密度泛函理论研究Watson–Crick碱基对中的氢键特征(英文)

基于密度泛函理论(DFT)研究腺嘌呤、胸腺嘧啶、鸟嘌呤、胞嘧啶以及腺嘌呤胸腺嘧啶碱基对、鸟嘌呤胞嘧啶碱基对。在DFT-B3LYP/6-31G**水平上利用自然键轨道理论分析研究结果显示,互补碱基对的结构和电子特征有利于氢键的形成。本文中讨论几何结构、电子结构、分子轨道和能量对于氢键形成的影响。此研究结果将有助于更好的理解AT和GC碱基对中氢键与它们的结构特性之间的关系。     

Density functional studies on the electron affinities of DNA and RNA bases

Influence of basis sets on electron affinities (EAs) of DNA and RNA bases has been investigated using density functional method (B3LYP functional) with different basis sets (6-31G, TZVP and 6-311+ + G**). Effect of some PBE functionals namely, PBEOP, PBELYP and PBEVWN, on EA values of the nucleobases was studied using basis set which predicted the most reliable values with B3LYP functional. Observation of the trends in the values of EA and dipole moment of the molecules enable us to identify the features of a basis set that shows the presence of dipole-bound state of some of the nucleobases. The vertical electron affinities with B3LYP and PBEOP functionals are close to the experimental values. The adiabatic electron affinities of uracil and thymine were found to be positive for basis set with diffuse functions using B3LYP functional. Adenine does not have a stable covalently bound anion at all levels of basis sets and functionals. The sign of adiabatic electron affinity value of cytosine is inconsistent with that of experimental value but in agreement with previous theoretical results. For guanine the adiabatic electron affinity value with 6-311+ + G** basis set was found to be very high as comparison with other two basis sets confirming the formation of mixed covalent-dipole character.     

A theoretical and experimental investigation of the electronic spectra and tautomerization of nucleobases

The electronic structures of all possible tautomers of uracil, thymine, cytosine, adenine and guanine have been carefully examined within the MNDO-MO frame-work. Equilibrium geometries are determined and the relative stabilities are discussed. Allowance for solvent effect on the stabilities is made by assuming a tetrahedral solvent cage with the DNA base occupying its centre. The electronic absorption spectra of the studied DNA bases, in solvents of different polarities are recorded and discussed. Assignments of the observed bands are facilitated using MNDO-CI computations. It is suggested that in solution the DNA bases are in some statistical mixtures of the most stable tautomers, and the Watson-Crick (WC) structure cannot account for the observed spectra alone.     

Propeller-twisted adenine.thymine and guanine.cytosine base pairs tend to buckle and stagger in opposite directions.

Base pairs are propeller-twisted, buckled and staggered in DNA fragment crystals. These deformations were analyzed with isolated Watson-Crick base pairs using empirical potentials and buckle was found to almost linearly correlate with propeller. Interestingly, the thymine.adenine pair favours negative buckling for propellers mostly observed in DNA crystals while positive buckling is preferred by the cytosine.guanine pair. The propeller also induces opposite staggers in the adenine.thymine and guanine.cytosine base pairs.     

Variable temperature infrared spectroscopy of cytosine-guanine base pairs: tautomerism versus polarization.

This report describes an infrared (IR) spectroscopic study of a model cytosine-guanine base pair. This base pair is part of a self-consistent experimental system based on lipophilic ribose derivatives of cytidine (C), guanosine (G) and O6-methylguanosine (O6MeG) that are soluble in non-aqueous, low dielectric solvents at appreciable concentrations. Previous experiments on this system have revealed different rotation dynamics for the amino bonds within the CG base pair, an observation that could be explained by the presence of rare tautomers (P.O. Lowdin, Reviews of Modern Physics 35,724 (1963)), or by mutual polarization of the base pairs (L.D. Williams, N.G. Williams and B.R. Shaw,J.Am.Chem.Soc. 112,829 (1990)). The IR spectra in the OH and NH stretching region indicate formation of hydrogen-bonded CG base pairs and self associates in 1,2-dichlorobenzene over a temperature range from 10 to 290K. Changes in the lineshapes and intensities of the IR bands with temperature correlate with phase transitions of the solvent, but no evidence is seen for an OH stretching band that would indicate the formation of hydroxyl tautomers within base pairs. Similarly, the relative intensities of the C = O stretching bands of CG in cyclohexane solution remain constant over this same temperature range, confirming that within the base pair, the tautomeric states of the bases remain essentially unperturbed in the 2-amino/6-keto form of G and the 2-keto/4-amino form of C. The spectra of O6-MeG aid in the band assignments, since this molecule is frozen in an equivalent of the 2-amino/6-hydroxyl tautomer, but without the OH group and its associated stretching band. We conclude that the probability of tautomerism does not appear to be sufficient to explain the different rotation dynamics for the two amino bonds of the CG base pair. Rather it is argued that mutual polarization within the base pair, which would increase the bond order of the amino bond of C within the base pair, can explain the results without the formation of unconventional tautomers.     

Crystal structure of human methyl-binding domain IV glycosylase bound to abasic DNA

The mammalian repair protein MBD4 (methyl-CpG-binding domain IV) excises thymine from mutagenic G·T mispairs generated by deamination of 5-methylcytosine (mC), and downstream base excision repair proteins restore a G·C pair. MBD4 is also implicated in active DNA demethylation by initiating base excision repair of G·T mispairs generated by a deaminase enzyme. The question of how mismatch glycosylases attain specificity for excising thymine from G·T, but not A·T, pairs remains largely unresolved. Here, we report a crystal structure of the glycosylase domain of human MBD4 (residues 427-580) bound to DNA containing an abasic nucleotide paired with guanine, providing a glimpse of the enzyme-product complex. The mismatched guanine remains intrahelical, nestled into a recognition pocket. MBD4 provides selective interactions with the mismatched guanine (N1H, N2H(2)) that are not compatible with adenine, which likely confer mismatch specificity. The structure reveals no interactions that would be expected to provide the MBD4 glycosylase domain with specificity for acting at CpG sites. Accordingly, we find modest 1.5- to 2.7-fold reductions in G·T activity upon altering the CpG context. In contrast, 37- to 580-fold effects were observed previously for thymine DNA glycosylase. These findings suggest that specificity of MBD4 for acting at CpG sites depends largely on its methyl-CpG-binding domain, which binds preferably to G·T mispairs in a methylated CpG site. MBD4 glycosylase cannot excise 5-formylcytosine (fC) or 5-carboxylcytosine (caC), intermediates in a Tet (ten eleven translocation)-initiated DNA demethylation pathway. Our structure suggests that MBD4 does not provide the electrostatic interactions needed to excise these oxidized forms of mC.     

Investigation of the intermolecular proton transfer in the supersystems adenine-methanol/ethanol/i-propanol: MP2 and DFT levels study

Twelve H-bonded supersystems constructed between the adenine tautomers and methanol, ethanol, and i-propanol were studied at the B3LYP and MP2 levels of theory using 6-311G(d,p) and 6-311++G(d,p) basis functions. The thermodynamic parameters of the complex formations were calculated in order to estimate the exact stability of the supersystems. It was proven that the calculated energy barriers of the alcohol-assisted proton transfers are about 60% lower than those of the intramolecular proton transfers in adenine found earlier (Gu and Leszczynski in J Phys Chem A 103:2744–2750, 1999). Figure H-bonded complex between i-propanol and adenine     

Dependence of substrate binding and catalysis on pH, ionic strength, and temperature for thymine DNA glycosylase: Insights into recognition and processing of G·T mispairs

Repair of G·T mismatches arising from deamination of 5-methylcytosine (m(5)C) involves excision of thymine and restoration of a G·C pair via base excision repair (BER). Thymine DNA glycosylase (TDG) is one of two mammalian enzymes that can specifically remove thymine from G·T mispairs. While TDG can excise other bases, it maintains stringent specificity for a CpG context, suggesting deaminated m(5)C is an important biological substrate. Recent studies reveal TDG is essential for embryogenesis; it helps to maintain an active chromatin complex and initiates BER to counter aberrant de novo CpG methylation, which may involve excision of actively deaminated m(5)C. The relatively weak G·T activity of TDG has been implicated in the hypermutability of CpG sites, which largely involves C→T transitions arising from m(5)C deamination. Thus, it is important to understand how TDG recognizes and process substrates, particularly G·T mispairs. Here, we extend our detailed studies of TDG by examining the dependence of substrate binding and catalysis on pH, ionic strength, and temperature. Catalytic activity is relatively constant for pH 5.5-9, but falls sharply for pH>9 due to severely weakened substrate binding, and, potentially, ionization of the target base. Substrate binding and catalysis diminish sharply with increasing ionic strength, particularly for G·T substrates, due partly to effects on nucleotide flipping. TDG aggregates rapidly and irreversibly at 37°C, but can be stabilized by specific and nonspecific DNA. The temperature dependence of catalysis reveals large and unexpected differences for G·U and G·T substrates, where G·T activity exhibits much steeper temperature dependence. The results suggest that reversible nucleotide flipping is much more rapid for G·T substrates, consistent with our previous findings that steric effects limit the active-site lifetime of thymine, which may account for the relatively weak G·T activity. Our findings provide important insight into catalysis by TDG, particularly for mutagenic G·T mispairs.     

Density-functional study on the equilibria in the ThDP activation

The equilibria among the various ionization and tautomeric states involved in the activation of ThDP is addressed using high level density functional theory calculations, X3LYP/6-311++G(d,p)//X3LYP(PB)/6-31++G(d,p). This study provides the first theoretically derived thermodynamic data for the internal equilibria in the activation of ThDP. The role of the medium polarity on the geometry and thermodynamics of the diverse equilibria of ThDP is addressed. The media chosen are cyclohexane and water, as paradigms of apolar and polar media. The results suggest that all ionization and tautomeric states are accessible during the catalytic cycle, even in the absence of substrate, being APH⁺ the form required to interconvert the AP and IP tautomers; and the generation of the ylide proceeds via the formation of the IP form. Additionally, the calculated ΔG° values allow to calculate all the equilibrium constants, including the pK_C2 for the thiazolium C2 atom whose ionization is believed to initiate the catalytic cycle.     

The physico-chemical “anatomy” of the tautomerization through the DPT of the biologically important pairs of hypoxanthine with DNA bases: QM and QTAIM perspectives

The biologically important tautomerization of the Hyp·Cyt, Hyp*·Thy and Hyp·Hyp base pairs to the Hyp*·Cyt*, Hyp·Thy* and Hyp*·Hyp* base pairs, respectively, by the double proton transfer (DPT) was comprehensively studied in vacuo and in the continuum with a low dielectric constant (ε?=?4) corresponding to hydrophobic interfaces of protein–nucleic acid interactions by combining theoretical investigations at the B3LYP/6-311++G(d,p) level of QM theory with QTAIM topological analysis. Based on the sweeps of the energetic, electron-topological, geometric and polar parameters, which describe the course of the tautomerization along the intrinsic reaction coordinate (IRC), it was proved that the tautomerization through the DPT is concerted and asynchronous process for the Hyp·Cyt and Hyp*·Thy base pairs, while concerted and synchronous for the Hyp·Hyp homodimer. The continuum with ε?=?4 does not affect qualitatively the course of the tautomerization reaction for all studied complexes. The nine key points along the IRC of the Hyp·Cyt?Hyp*·Cyt* and Hyp*·Thy?Hyp·Thy* tautomerizations and the six key points of the Hyp·Hyp?Hyp*·Hyp* tautomerization have been identified and fully characterized. These key points could be considered as electron-topological “fingerprints” of concerted asynchronous (for Hyp·Cyt and Hyp*·Thy) or synchronous (for Hyp·Hyp) tautomerization process via the DPT. It was found, that in the Hyp*·Cyt*, Hyp·Thy*, Hyp·Hyp and Hyp*·Hyp* base pairs all H-bonds are significantly cooperative and mutually reinforce each other, while the C2H…O2 H-bond in the Hyp·Cyt base pair and the O6H…O4 H-bond in the Hyp*·Thy base pair behave anti-cooperatively, i.e., they become weakened, while two others become strengthened.     

Modeling and molecular mechanical studies of the cis-thymine glycol radiation damage lesion in DNA

Computer graphics and energy minimization techniques were used to construct a model of DNA containing cis-thymine glycol, an oxidation product of thymine formed in DNA by ionizing radiation. The model simulated an experimental DNA substrate used to study the effects of this lesion on DNA synthesis in vitro. The results derived from the model indicate that cis-thymine glycol lesions introduce localized perturbations of DNA structure. Specifically the model shows that interactions with the neighboring base pair on the 5' side are significantly destabilized by thymine glycol whereas interactions with the 3' base pair are stabilized by the lesion. The magnitude of these effects is modulated by the nucleotide sequence around the lesion, particularly by the nature of the base on the 3' side. The base pair formed between adenine and thymine glycol is energetically stable and shows minimal distortion, suggesting that this lesion retains the ability to direct the insertion of the correct nucleotide during DNA synthesis.     

Molecular recognition of B-DNA by Hoechst 33258.

The binding sites of Hoechst 33258, netropsin and distamycin on three DNA restriction fragments from plasmid pBR322 were compared by footprinting with methidiumpropyl-EDTA X Fe(II) [MPE X Fe(II)]. Hoechst, netropsin and distamycin share common binding sites that are five +/- one bp in size and rich in A X T DNA base pairs. The five base pair protection patterns for Hoechst may result from a central three base pair recognition site bound by two bisbenzimidazole NHs forming a bridge on the floor of the minor groove between adjacent adenine N3 and thymine O2 atoms on opposite helix strands. Hydrophobic interaction of the flanking phenol and N-methylpiperazine rings would afford a steric blockade of one additional base pair on each side.     

Mechanistic study of the structure–activity relationship for the free radical scavenging activity of baicalein

Density functional theory calculations were performed to evaluate the antioxidant activity of baicalein. The conformational behaviors of both the isolated and the aqueous-solvated species (simulated with the conductor-like polarizable continuum solvation model) were analyzed at the M052X/6-311 + G(d,p) level. The most stable tautomers of various forms of baicalein displayed three IHBs between O4 and OH5, O5 and OH6, and O6 and OH7. The most stable tautomer of the baicalein radical was obtained by dehydrogenating the hydroxyl at C6, while the most stable anion tautomer was obtained by deprotonating the C7 hydroxyl in gaseous and aqueous phases. The expected antioxidant activity of baicalein was explained by its ionization potentials (IPs) and homolytic O–H bond dissociation enthalpies (BDEs), which were obtained via the UM052X optimization level of the corresponding radical species. Heterolytic O–H bond cleavages (proton dissociation enthalpies, PDEs) were also computed. The calculated IP, BDE, and PDE values suggested that one-step H-atom transfer, rather than sequential proton loss–electron transfer or electron transfer–proton transfer, would be the most favorable mechanism for explaining the antioxidant activity of baicalein in the gas phase and in nonpolar solvents. In aqueous solution, the SPLET mechanism was more important.