Effects of OH radical addition on proton transfer in the guanine-cytosine base pair

Double proton transfer (PT) reactions in guanine-cytosine OH radical adducts are studied by the hybrid density functional B3LYP approach. Concerted and stepwise proton-transfer processes are explored between N1(H) on guanine (G) and N3 on cytosine (C), and between N4(H) on C and O6 on G. All systems except GC6OH display a concerted mechanism. 8OHGC has the highest dissociation energy and is 1.2 kcal/mol more stable than the nonradical GC base pair. The origin of the interactions are investigated through the estimation of intrinsic acid-basic properties of the *OH-X monomer (X = G or C). Solvent effects play a significant role in reducing the dissociation energy. The reactions including *OH-C adducts have significantly lower PT barriers than both the nonradical GC pair and the *OH-G adducts. All reactions are endothermic, with the GC6OH --> GC6OHPT reaction has the lowest reaction energy (4.6 kcal/mol). In accordance with earlier results, the estimated NBO charges show that the G moiety carries a slight negative charge (and C a corresponding positive one) in each adduct. The formation of a partial ion pair may be a potential factor leading to the PT reactions being thermodynamically unfavored.     

Electron affinity of the guanine-cytosine base pair and structural perturbations upon anion formation

The adiabatic electron affinity (AEA) for the Watson-Crick guanine-cytosine (GC) DNA base pair is predicted using a range of density functional methods with double- and triple-zeta plus polarization plus diffuse (DZP++ and TZ2P++) basis sets in an effort to bracket the true electron affinity. The methods used have been calibrated against a comprehensive tabulation of experimental electron affinities (Chem.Rev. 2002, 102, 231). Optimized structures for GC and the GC anion are compared to the neutral and anionic forms of the individual bases as well as Rich's 1976 X-ray structure for sodium guanylyl-3',5'-cytidine nonahydrate, GpC.9H(2)O. Structural distortions and natural population (NPA) charge distributions of the GC anion indicate that the unpaired electron is localized primarily on the cytosine moiety. Unlike treatments using second-order perturbation theory (MP2), density functional theory consistently predicts a substantial positive adiabatic electron affinity for the GC pair (e.g., TZ2P++/B3LYP: +0.48 eV). The stabilization of C(-) via three hydrogen bonds to guanine is sufficient to facilitate adiabatic binding of an electron to GC and is also consistent with the positive experimental electron affinities obtained by photoelectron spectroscopy of cytosine anions incrementally microsolvated with water molecules. The pairing (dissociation) energy for GC(-) (35.6 kcal/mol) is determined with inclusion of electron correlation and shows the anion to have greater thermodynamic stability; the pairing energy for neutral GC (TZ2P++/B3LYP 23.9 kcal/mol) compares favorably to previous MP2/6-31G (23.4 kcal/mol) results and a debated experiment (21.0 kcal/mol).     

H-bonding patterns in the platinated guanine-cytosine base pair and guanine-cytosine-guanine-cytosine base tetrad: an electron density deformation analysis and AIM study

The atoms in molecule theory (AIM) and electronic structure analysis are applied together to investigate H-bonding patterns in metalated nucleobase complexes. The influence of Pt on the intra GC base pair H-bonding has been found to reduce intra base pair H-bonding of N4(C)...O6(G) in the platinated GC pair and GCGC tetrad. The relaxation of geometry constrains in metalated nucleobases is found to be decisively important in the formation of novel molecular architectures from nucleobases and metal entities. The incorporation of the platinum in the GCGC tetrad benefits the formation of the unique CH...N (H5(C)...N1(G)) hydrogen bond pattern in the tetrad by offering improved geometric constraints rather than through changing the electronic properties around the H5(C) and N1(G) sites. Platination at the N7 of guanine reduces the deprotonation energy considerably.     

Effect of nucleobase sequence on the proton-transfer reaction and stability of the guanine-cytosine base pair radical anion

The formation of base pair radical anions is closely related to many fascinating research fields in biology and chemistry such as radiation damage to DNA and electron transport in DNA. However, the relevant knowledge so far mainly comes from studies on isolated base pair radical anions, and their behavior in the DNA environment is less understood. In this study, we focus on how the nucleobase sequence affects the properties of the guanine-cytosine (GC) base pair radical anion. The energetic barrier and reaction energy for the proton transfer along the N(1)(G)-H···N(3)(C) hydrogen bond and the stability of GC˙(-) (i.e., electron affinity of GC) embedded in different sequences of base-pair trimer were evaluated using density functional theory. The computational results demonstrated that the presence of neighboring base pairs has an important influence on the behavior of GC˙(-) in the gas phase. The excess electron was found to be localized on the embedded GC and the charge leakage to neighboring base pairs was very minor in all of the investigated sequences. Accordingly, the sequence behavior of the proton-transfer reaction and the stability of GC˙(-) is chiefly governed by electrostatic interactions with adjacent base pairs. However, the effect of base stacking, due to its electrostatic nature, is severely screened upon hydration, and thus, the sequence dependence of the properties of GC˙(-) in aqueous environment becomes relatively weak and less than that observed in the gas phase. The effect of geometry relaxation associated with neighboring base pairs as well as the possibility of proton transfer along the N(2)(G)-H···O(2)(C) channel have also been investigated. The implications of the present findings to the electron transport and radiation damage of DNA are discussed.     

Double-proton transfer in adenine-thymine and guanine-cytosine base pairs. A post-Hartree-Fock ab initio study

The results of a comprehensive study on the double-proton transfer in Adenine-Thymine (AT) and Guanine-Cytosine (GC) base pairs at room temperature in gas phase and with the inclusion of environmental effects are obtained. The double-proton-transfer process has been investigated in the AT and GC base pairs at the B3LYP/6-31G(d) and MP2/6-31G(d) levels of theory. It has been predicted that the hydrogen-bonded bases possess nonplanar geometries due to sp3 hybridization of nitrogen atoms and because of the soft intermolecular vibrations in the molecular complexes. An analysis of the energetic parameters of the local minima suggests that rare AT base pair conformation is not populated due to the shallowness of this minimum, which completely disappears from the Gibbs free energy surface. The stabilization of canonic or rare forms of the DNA bases by water molecules and metal cations has been predicted by calculating the optimal configuration of charges (using differential product/transition state stabilization approach) followed by calculations of the interactions between the base pair and a water/sodium cation.     

Triplet (pi,pi) reactivity of the guanine-cytosine DNA base pair: benign deactivation versus double tautomerization via intermolecular hydrogen transfer

Ab initio computations (CASSCF/6-31G* supported by CAS-PT2 single-point calculations) are used to study the reactivity of the triplet excited state of the guanine-cytosine DNA base pair. When the triplet excitation is centered on cytosine there is a competition between benign deactivation to the ground state and a hydrogen transfer route that can trigger double tautomerization. The calculated barriers favor the benign deactivation, but this route goes through a singlet/triplet intersystem crossing with small spin-orbit coupling. Therefore, the potentially mutagenic, double tautomerization route cannot be ruled out completely, and the two paths are probably an alternative to the well-known cytidine photodimerization reaction.     

Effects of protonation on proton transfer processes in Watson–Crick adenine–thymine base pair

Intermolecular proton transfer processes in the Watson and Crick adenine–thymine neutral and protonated base pairs have been studied using the density functional theory (DFT) with the non-local hybrid B3LYP density functional. Protonated systems subject to study are those resulting from protonation at the main basic sites of the base pair model, namely N₇ and N₃ of adenine and O₂^′ and O₄^′ of thymine. Protonation of adenine induces a strengthening by about 4–5 kcal/mol of the base pair and does not significantly modify the double proton transfer energy profile obtained for the unprotonated system. On the other hand, protonation at the O₄^′ and O₂^′ thymine moiety causes thymine’s N₃ proton to spontaneously transfer to adenine while non-transferred minima disappear at this level of theory. The different behaviour between protonated adenine– thymine and protonated guanine–cytosine is discussed. Electronic Supplementary Material The online version of this article (doi:) contains supplementary material, which is available to authorized users. Contribution to the Fernando Bernardi Memorial Issue.     

Microhydration of the guanine-cytosine (GC) base pair in the neutral and anionic radical states: a density functional study

A density functional study of the effects of microhydration on the guanine-cytosine (GC) base pair and its anion radical is presented. Geometries of the GC base pair in the presence of 6 and 11 water molecules were fully optimized in the neutral (GC-nH2O) and anion radical [(GC-nH2O)*-] (n = 6 and 11) states using the B3LYP method and the 6-31+G** basis set. Further, vibrational frequency analysis at the same level of theory (B3LYP/6-31+G**) was also performed to ensure the existence of local minima in these hydrated structures. It was found that water molecules surrounding the GC base pair have significant effects on the geometry of the GC base pair and promote nonplanarity in the GC base pair. The calculated structures were found to be in good agreement with those observed experimentally and obtained in molecular dynamics (MD) simulation studies. The water molecules in neutral GC-nH2O complexes lie near the ring plane of the GC base pair where they undergo hydrogen bonding with both GC and each other. However, in the GC anion radical complexes (GC-nH2O, n = 6, 11), the water molecules are displaced substantially from the GC ring plane. For GC-11H2O*-, a water molecule is hydrogen-bonded with the C6 atom of the cytosine base. We found that the hydration shell initially destabilizes the GC base pair toward electron capture as a transient anion. Energetically unstable diffuse states in the hydration shell are suggested to provide an intermediate state for the excess electron before molecular reorganization of the water molecules and the base pair results in a stable anion formation. The singly occupied molecular orbital (SOMO) in the anion radical complexes clearly shows that an excess electron localizes into a pi orbital of cytosine. The zero-point-energy (ZPE-) corrected adiabatic electron affinities (AEAs) of the GC-6H2O and GC-11H2O complexes, at the B3LYP/6-31+G** level of theory, were found to be 0.74 and 0.95 eV, respectively. However, the incorporation of bulk water as a solvent using the polarized continuum model (PCM) increases the EAs of these complexes to 1.77 eV.     

Excited-state proton transfer and ion pair formation in a Cinchona organocatalyst

The excited-state proton transfer and subsequent intramolecular ion pair formation of a cupreidine-derived Cinchona organocatalyst () were studied in THF-water mixtures using picosecond time-resolved fluorescence together with global analysis. Full spectral and kinetic characterization of all the fluorescent species allowed us to monitor the 3-step process for the ion pair dissociation. In the first step, proton transfer occurs through a water "wire" from the 6-hydroxyquinoline unit (excited-state acid) to the covalently bonded basic quinuclidine moiety, resulting in a hydrogen bonded ion pair. This was confirmed by the observed kinetic isotope effect in the presence of heavy water. In the second step, the formed ions are further solvated by a few solvent molecules, producing the solvent separated ion pair. Finally, a fully solvated ion pair is formed. The 5-exponential global model derived from the reaction scheme describes the experimental data very well.     

Marked variations of dissociation energy and H-bond character of the guanine-cytosine base pair induced by one-electron oxidation and Li+ cation coupling

The variation of dissociation energy and H-bond character of the G-C cation and the Li-GC cation have been investigated by employing density functional theory (B3LYP) with the 6-31+G* basis set. The one-electron oxidation and the coupling of Li(+) to the guanine-cytosine base pair can strengthen the interaction between guanine and cytosine. The interaction of the cation Li(+) with guanine is attractive and is attributed to the polarization of the H-bonds between G-C that enhances G-C interaction. The cooperativity of the three H-bonds in the GC and Li-GC cations is different from that in the neutral GC base pair. The proton-transfer process between N(1) of the guanine and N(3) of the cytosine can occur in the GC cation and the Li-GC cation. The geometries of the transition state are out of plane, especially for the transition state of the Li-GC cation. The analysis of the activation energy for the proton-transfer process shows that the GC(+) before and after proton transfer can exist simultaneously in the gas phase, but for the Li-GC(+) system, the Li-GC(+) without proton transfer is the dominating species in the gas phase.     

Theoretical investigation of the hydrogen atom transfer in the hydrated A-T base pair

The hydrated A-T base pair has been studied in order to understand the structural modifications and their electronic rearrangements induced by the movement of the hydrogen atoms in the H-bonds. The comparison of these results with that of the nonhydrated system can explain the role of the H-bonds of the water molecules in this system. Two naïve schemes have been considered, one where the hydrogen bonds of the water molecules are only indirectly involved in the hydrogen atoms transfer between the bases and another where the water molecules are directly involved in this transfer. The results support the idea that the real mechanisms are more complexes than these schemes. Some new stable structures of the A-T(H₂O)₂ and the A-T(H₂O)₄ systems have been found and the mechanisms of their generations have been analysed.     

Influence of Mg(2+) on the guanine-cytosine tautomeric equilibrium: simulations of the induced intermolecular proton transfer

Metallic ions are essential for stabilizing the nucleic acid structure, and are also involved in the majority of RNA and DNA biological functions. However, at large concentrations metals may play an opposite role by promoting alterations in the genetic code (mutagenicity). To contribute to the understanding of this effect, theoretical tools are used to investigate the influence of the magnesium dication on the guanine-cytosine (GC) base pair structure and stability. To this end, a fully hydrated Mg(2+) cation is inserted in two models: an isolated GC base pair, and a more realistic DNA model corresponding to a hydrated double-stranded trimer. Calculations performed with a hybrid ONIOM approach reveal that the Mg(2+) cation coordination to the GC base pair alters drastically the natural tautomeric equilibria in DNA by promoting single proton transfer. Nevertheless, the generated rare tautomer will have a limited impact on the total spontaneous mutation due to the low back-reaction barrier allowing a quick return to the canonical form. Additionally, it is demonstrated that the major effects of biological environment arise from the hydration and stacking influence, whereas the impact of phosphate groups is minor.     

Double proton transfer and charge transfer transitions in hydrogen-bonded systems: formic acid dimer

The barriers for double proton transfer in the ground and lowest Π-Π^* and Π-Π^* excited states of the formic acid dimer have been calculated within a modified INDO scheme. Analysis of the nature of the excited electronic states, with emphasis on charge-transfer transitions, has been performed. The results indicate a lower barrier in the excited Π-Π^* states than in the ground state.     

Selective conformer detection of short-lived base pair tautomers: A computational study of the unusual guanine-cytosine pairs using ultrafast resonance Raman spectroscopy

Base pair mismatch has been regarded as the main source of DNA point mutations, where minor short-lived tautomers were usually involved. However, the detection and characterization of these unnatural species pose challenges to existing techniques. Here, by using systematic structural and ultrafast resonance Raman (RR) spectral analysis for the four possible conformers of guanine-cytosine base pairs, the prominent marker Raman bands were identified. We found that the hydrogen bonding vibrational region from 2300 cm⁻¹ to 3700 cm⁻¹ is ideal for the identification of these short live species. The marker bands provide direct evidence for the existence of the tautomer species, thus offering an effective strategy to detect the short-lived minor species. Ultrafast resonance Raman spectroscopy would be a powerful tool to provide direct evidence of critical dynamical details of complex systems involving protonation or tautomerization.     

Ultrafast excited-state deactivation and energy transfer in guanine-cytosine DNA double helices

The DNA double helix poly(dGdC).poly(dGdC) is studied by fluorescence upconversion spectroscopy with femtosecond resolution. It is shown that the excited-state relaxation of the duplex is faster than that of the monomeric components dGMP and dCMP. This contrasts with the behavior of duplexes composed exclusively of adenine-thymine base pairs, for which an overall lengthening of the fluorescence lifetimes with respect to that of an equimolar mixture of dAMP and TMP was reported previously. Despite the difference in the excited-state deactivation rate between the two types of duplexes, the signature of ultrafast energy transfer is present in both of them. It is attested by the decrease of fluorescence anisotropy decay of the duplexes on the subpicosecond time scale, where molecular motions are inhibited, and is corroborated by the fact that their steady-state fluorescence spectra do not change with the excitation wavelength. Energy transfer involves excited states delocalized over at least two bases, whose existence is revealed by the UV absorption spectrum of the duplex, clearly different from that of an equimolar spectrum of dGMP and dCMP.     

Excited state proton transfer is not involved in the ultrafast deactivation of Guanine-Cytosine pair in solution

Different derivatives of Guanine (G) and Cytosine (C), which sterically enforce the Watson-Crick (WC) conformer, have been studied in CHCl(3) by means of broad-band transient absorption spectroscopy. Our experiments rule out the involvement of an Excited State Proton Transfer (ESPT), which dominates the excited state decay of GC in the gas phase. Instead, the ultrafast dynamics via internal conversion occurs in a polar environment mainly by relaxation in the monomer moieties. Time-dependent density functional theory (TD-DFT) calculations in solution indeed indicate that population transfer from the bright excited states toward the charge transfer state is not effective in CHCl(3) and a noticeable energy barrier is associated with the ESPT reaction. ESPT is therefore not expected to be a main deactivation route for GC pairs within DNA.