Pyrimidine Ring Opening in the Unimolecular Dediazoniation of Guanine Diazonium Ion. An Ab Initio Theoretical Study of the Mechanism of Nitrosative Guanosine Deamination

Formation Mechanism of Inter-Crosslink in DNA by Nitrogen Oxides Pollutants through A Diazonium Intermediate

Outdoor air pollution is a mixture of multiple atmospheric pollutants, among which nitrogen oxide (NOx) stands out due to its association with several diseases. NOx reactivity can conduct to DNA damage as severe as interstrand crosslinks (ICL) formation, that in turn is able to block DNA replication and transcription. Experimental studies have suggested that the ICL formation due to NOx is realized through a diazonium intermediate (DI). In this work, we have modeled the DI structure, including a DNA double-strand composed of two base pairs GC/CG, being diazotized as one of the guanine nucleotides. The structural stability of DNA with DI lesion was essayed through 500 ns molecular dynamics simulations. It was found that the DNA structure of the oligonucleotide is stable when the DI is present since the loss of a Guanine–Cytosine hydrogen bond is replaced by the presence of two cation-π interactions. Additionally, we have studied the mechanism of formation of a crosslink between the two guanine nucleobases from the modeled DI by carrying out DFT calculations at the M06-L/DNP+ level of theory. Our results show that the mechanism is thermodynamically favored by a strong stabilization of the ICL product, and the process is kinetically viable since its limiting stage is accessible.

Synthesis of 2'-deoxyoxanosine from 2'-deoxyguanosine, conversion to its phosphoramidite, and incorporation into oxanine-containing oligodeoxynucleotides

Oxanine (Oxa, O) is one of the damaged bases produced from guanine (G) through nitrosative deamination induced by nitric oxide (NO) or nitrous acid (HNO(2)). Large-scale preparation of Oxa-containing oligodeoxynucleotide (Oxa-ODN) with the desired base sequence is a prerequisite for exploring detailed properties of Oxa in DNA. This can be accomplished by incubation of G nucleosides with NaNO(2) in acetic acid buffer (pH 3.5) to produce Oxa nucleosides (e.g., 2'-deoxyoxanosine or dOxo), conversion of dOxo to DMT-dOxo-amidite by tritylation and conventional phosphoramidation, and subsequent synthesis of Oxa-ODN. The presence of Oxa in the synthetic ODN is confirmed by enzymatic digestion. Oxa-ODN is useful for analyzing the biochemical and biophysical properties of Oxa in DNA, which is believed to be involved in NO-induced genotoxicity and cytotoxicity. In addition, since Oxa possesses the carbodiimide-activated carboxylate function (O-acylisourea structure), Oxa-ODN can be used as a functional DNA oligomer that makes covalent cross-linkages with amine or amine-containing biomolecules and amine-modified solid surfaces.

Acetylation of the amino group on guanosine induced by nitric oxide in acetonitrile under aerobic conditions

When nitric oxide was bubbled into acetonitrile under aerobic conditions, the solution showed a cobalt-blue color. Addition of guanosine into the solution generated N2-acetylguanosine as a major product. The result of the reaction using 15N labeled acetonitrile indicated that the nitrogen atom of the acetylated exocyclic amino group on N2-acetylguanosine originated from acetonitrile. We discuss the reaction mechanism for the acylation.

Ammonia elimination from protonated nucleobases and related synthetic substrates

The results are reported of mass-spectrometric studies of the nucleobases adenine 1h (1, R = H), guanine 2h, and cytosine 3h. The protonated nucleobases are generated by electrospray ionization of adenosine 1r (1, R = ribose), guanosine 2r, and deoxycytidine 3d (3, R = deoxyribose) and their fragmentations were studied with tandem mass spectrometry. In contrast to previous EI-MS studies of the nucleobases, NH(3) elimination does present a major path for the fragmentations of the ions [1h + H](+), [2h + H](+), and [3h + H](+). The ion [2h + H - NH(3)](+) also was generated from the acyclic precursor 5-cyanoamino-4-oxomethylene-dihydroimidazole 13h and from the thioether derivative 14h of 2h (NH(2) replaced by MeS). The analyses of the modes of initial fragmentation is supported by density functional theoretical studies. Conjugate acids 15-55 were studied to determine site preferences for the protonations of 1h, 2h, 3h, 13h, and 14h. The proton affinity of the amino group hardly ever is the substrate's best protonation site, and possible mechanisms for NH(3) elimination are discussed in which the amino group serves as the dissociative protonation site. The results provide semi-direct experimental evidence for the existence of the pyrimidine ring-opened cations that we had proposed on the basis of theoretical studies as intermediates in nitrosative nucleobase deamination.

Direct immobilization of DNA oligomers onto the amine-functionalized glass surface for DNA microarray fabrication through the activation-free reaction of oxanine

Oxanine having an O-acylisourea structure was explored to see if its reactivity with amino group is useful in DNA microarray fabrication. By the chemical synthesis, a nucleotide unit of oxanine (Oxa-N) was incorporated into the 5′-end of probe DNA with or without the -(CH₂)_n- spacers (n = 3 and 12) and found to immobilize the probe DNA covalently onto the NH₂-functionalized glass slide by one-pot reaction, producing the high efficiency of the target hybridization. The methylene spacer, particularly the longer one, generated higher efficiency of the target recognition although there was little effect on the amount of the immobilized DNA oligomers. The post-spotting treatment was also carried out under the mild conditions (at 25 or 42°C) and the efficiencies of the immobilization and the target recognition were evaluated similarly, and analogous trends were obtained. It has also been determined under the mild conditions that the humidity and time of the post-spotting treatment, pH of the spotting solution and the synergistic effects with UV-irradiation largely contribute to the desired immobilization and resulting target recognition. Immobilization of DNA oligomer by use of Oxa-N on the NH₂-functionalized surface without any activation step would be employed as one of the advanced methods for generating DNA-conjugated solid surface.

Cytosine catalysis of nitrosative guanine deamination and interstrand cross-link formation

Effects are discussed of the anisotropic DNA environment on nitrosative guanine deamination based on results of an ab initio study of the aggregate 3 formed by guaninediazonium ion 1 and cytosine 2. Within 3, the protonation of 2 by 1 is fast and exothermic and forms 6, an aggregate between betaine 4 (2-diazonium-9H-purin-6-olate) and cytosinium ion 5. Electronic structure analysis of 4 shows that this betaine is not mesoionic; only the negative charge is delocalized in the pi-system while the positive charge resides in the sigma-system. Potential energy surface exploration shows that both dediazoniation and ring-opening of betaine 4 in aggregate 6 are fast and exothermic and lead irreversibly to E-11, the aggregate between (E)-5-cyanoimino-4-oxomethylene-4,5-dihydroimidazole E-10 and 5. The computed pair binding energies for 3, 6, and E-11 greatly exceed the GC pair binding energy. While 1 can be a highly reactive intermediate in reactions of the "free nucleobase" (or its nucleoside and nucleotide), the cyanoimine 10 emerges as the key intermediate in nitrosative guanine deamination in ds-DNA and ds-oligonucleotides. In essence, the complementary nucleobase cytosine provides base catalysis and switches the sequence of deprotonation and dediazoniation. It is argued that this environment-induced switch causes entirely different reaction paths to products as compared to the respective "free nucleobase" chemistry, and the complete consistency is demonstrated of this mechanistic model with all known experimental results. Products might form directly from 10 by addition and ring closure, or their formation might involve water catalysis via 5-cyanoamino-4-imidazolecarboxylic acid 12 and/or 5-carbodiimidyl-4-imidazolecarboxylic acid 13. The pyrimidine ring-opened intermediates 10, 12, and 13 can account for the formations of xanthosine, the pH dependency and the environment dependency of oxanosine formation, the formation of the classical cross-link dG(N(2)())-to-dG(C2), including the known sequence specificity of its formation, and the formation of the structure-isomeric cross-link dG(N1)-to-dG(C2).

Ab Initio Study of the SN1Ar and SN2Ar Reactions of Benzenediazonium Ion with Water. On the Conception of “Unimolecular Dediazoniation” in Solvolysis Reactions

The nucleophilic substitution of N2 in benzenediazonium ion 1 by one H2O molecule to form protonated phenol 2 has been studied with ab initio (RHF, MP2, QCISD(T)//MP2) and hybrid density functional (B3LYP) methods. Three mechanisms were considered: (a) the unimolecular process SN1Ar with steps 1 --> Ph+ + N2 and Ph+ + H2O --> 2, (b) the bimolecular process SN2Ar with precoordination 1 + H2O --> 1 x H2O, SN reaction 1 x H2O --> [TS]++ --> 2 x N2 and dissociation of the postcoordination complex 2 x N2 --> 2 + N2, and (c) the direct bimolecular process SN2Ar that bypasses precoordination and involves just the SN reaction 1 + H2O --> [TS]++ --> 2 + N2. The SN2Ar reactions proceed by way of a Cs symmetric SN2Ar transition state structure that is rather loose, contains essentially a phenyl cation weakly bound to N2 and OH2, and is analogous to the transition state structures of front-side nucleophilic replacement at saturated centers. In solvolysis reactions, all of these processes follow first-order kinetics, and the electronic relaxation is essentially the same. It is argued that "unimolecular dediazoniations" have to proceed by way of SN2Ar transition state structures because strict SN1Ar reactions cannot be realized in solvolyses, despite the fact that the Gibbs free energy profile favors the strict SN1Ar process over the SN2Ar reaction by 6.7 kcal/mol. It is further argued that the direct SN2Ar process is the best model for the solvolysis reaction for dynamic reasons, and its Gibbs free energy of activation is 19.3 kcal/mol and remains higher than the SN1Ar value. Even though the SN1Ar and SN2Ar models provide activation enthalpies and SKIE values that closely match the experimental data, the analysis leads us to the unavoidable conclusion that this agreement is fortuitous. While the experiments do show that the solvent effect on the activation energy is about the same for all solvents, they do not show the absence of a solvent effect. The ab initio results presented here suggest that the solvent effect on the direct SN2Ar dediazoniation is approximately 12 kcal/mol, and computation of solvent effects with the isodensity polarized continuum model (IPCM) support this conclusion.

Nitrosative Adenine Deamination: Facile Pyrimidine Ring-Opening in the Dediazoniation of Adeninediazonium Ion

[reaction: see text]. Dediazoniation of adeninediazonium ion, 1, forms the heteroaromatic cation, 2. Ab initio studies at the CCSD(fc)/6-31G**//MP2(full)/6-31G** level now reveal that the cyclic cation 2 is kinetically and thermodynamically unstable with respect to the pyrimidine ring-opened cation, 3. The results suggest that 4-cyano-5-isocyano-imidazole, 4, and 4,5-dicyanoimidazole, 5, might be formed to some extent in nitrosative deaminations of adenine.

Absence of 2'-deoxyoxanosine and presence of abasic sites in DNA exposed to nitric oxide at controlled physiological concentrations

Nitric oxide (NO(*)) is a physiologically important molecule at low concentrations, while high levels have been implicated in the pathophysiology of diseases associated with chronic inflammation, such as cancer. While an extensive study in vitro suggests that oxidative and nitrosative reactions dominate the complicated chemistry of NO(*)-mediated genotoxicity, neither the spectrum of DNA lesions nor their consequences in vivo have been rigorously defined. We have approached this problem with a major effort to define the spectrum of nitrosative DNA lesions produced by NO(*)-derived reactive nitrogen species under biological conditions. Plasmid pUC19 DNA was exposed to steady state concentrations of 1.3 microM NO(*) and 190 microM O(2) (calculated steady state concentrations of 40 fM N(2)O(3) and 3 pM NO(2)(*) in the bulk solution) in a recently developed reactor that avoids the undesired gas phase chemistry of NO(*) and approximates the conditions at sites of inflammation in tissues. The resulting spectrum of nitrosatively induced abasic sites and nucleobase deamination products was defined using plasmid topoisomer analysis and a novel LC/MS assay, respectively. With a limit of detection of 100 fmol and a sensitivity of 6 lesions per 10(7) nt in 50 microg of DNA, the LC/MS analysis revealed that 2'-deoxyxanthosine (dX), 2'-deoxyinosine (dI), and 2'-deoxyuridine (dU) were formed at nearly identical rates (k = 1.2 x 10(5) M(-1) s(-1)) to the extent of approximately 80 lesions per 10(6) nt after 12 h exposure to NO(*) in the reactor. While reactions with HNO(2) resulted in the formation of high levels of 2'-deoxyoxanosine (dO), one of two products arising from deamination of dG, dO, was not detected in 500 microg of DNA exposed to NO(*) in the reactor for up to 24 h (<6 lesions per 10(8) nt). This result leads to the prediction that dO will not be present at significant levels in inflamed tissues. Another important observation was the NO(*)-induced production of abasic sites, which likely arise by nitrosative depurination reactions, to the extent of approximately 10 per 10(6) nt after 12 h of exposure to NO(*) in the reactor. In conjunction with other studies of nitrosatively induced dG-dG cross-links, these results lead to the prediction of the following spectrum of nitrosative DNA lesions in inflamed tissues: approximately 2% dG-dG cross-links, 4-6% abasic sites, and 25-35% each of dX, dI, and dU.

Ab initio calculation of inner-sphere reorganization energies of arenediazonium ion couples

The geometries of a series of substituted arenediazonium cations (p-NO2, p-CN, p-Cl, p-F, p-H, m-CH3, p-CH3, p-OH, p-OCH3, p-NH2) and the corresponding diazenyl radicals were optimized at the HF/6-31G, MP2/6-31G, B3LYP/6-31G, B3LYP/TZP, B3PW91/TZP, and CASSCF/6-31G levels of theory. Inner-sphere reorganization energies for the single electron-transfer reaction between the species were computed from the optimized geometries according to the NCG method and compared to experimental values determined by Doyle et al. All levels of theory predicted a CNN bond angle of 180 degrees in the cation. A bent neutral diazenyl radical was predicted at all levels of theory excepting B3LYP/TZP and B3PW91/TZP for the p-Cl-substituted compound. Inner-sphere reorganization energies determined at the HF, MP2, and CASSCF levels of theory correlated poorly with both experimental results and calculated geometries. Density functional methods correlated best with the experimental values, with B3LYP/6-31G yielding the most promising results, although the ROHF/6-31G survey also showed some promise. B3LYP/6-31G calculations correctly predicted the order of the inner-sphere reorganization energies for the series, excluding the halogen-substituted compounds, with values ranging from 42.8 kcal x mol(-1) for the p-NO2-substituted species to 55.1 kcal x mol(-1) for NH2. The magnitudes of these energies were lower than the experimental by a factor of 2. For the specific cases examined, the closed-shell cation geometries showed the expected geometry about the CNN bond, with variations in the CN and NN bond lengths correlating with the electron-donating/withdrawing capacity of the substituent. As predicted by Doyle et al., a large geometry change was observed upon reduction. The neutral diazenyl radicals showed a nominal CNN bond angle of 120 degrees and variations in the CN and NN bond lengths also correlated with the electron-donating/withdrawing capacity of the substituent. Changes in theta(CNN) and r(CN) both correlated well with calculated lambda(inner). The key parameters influencing inner-sphere reorganization energy were the CN and NN bond lengths and the CNN bond angle. This influence is explained qualitatively via resonance models produced from NRT analysis and is related to the amount of CN double bond character. Based on these observations, B3LYP/6-31G calculations are clearly the most amenable for calculating inner-sphere reorganization energies for the single electron-transfer reaction between cation/neutral arenediazonium ion couples.

Single- and double-proton-transfer in the aggregate between cytosine and guaninediazonium ion

[formula: see text] The structure of "guaninediazonium ion" in its aggregate with cytosine has been explored with ab initio and density functional methods. The hydrogen-bonded aggregate between cytosine and guaninediazonium ion, 1, is a stable minimum, 3. While the isolated enol tautomer of guaninediazonium ion, 2, is significantly more stable than 1, the tautomeric aggregate 4 that results from double-proton-transfer in 3 is almost isoenergetic with 3. Most interesting and entirely unexpected is the finding that neither 3 nor 4 is predicted to be the thermodynamically predominant structure. Instead, single-proton-transfer to cytosine results in the most stable cytosinium-guaninediazo complex, 5.

Efficient nitroso group transfer from N-nitrosoindoles to nucleotides and 2'-deoxyguanosine at physiological pH. A new pathway for N-nitrosocompounds to exert genotoxicity

The endogenous formation of N-nitrosoindoles is of concern since humans are exposed to a variety of naturally occurring and synthetic indolic compounds. As part of a study to evaluate the genotoxicity of N-nitrosoindoles, the reactions of three model compounds with purine nucleotides and 2'-deoxyguanosine at physiological pH were investigated. The profiles of reaction products were identical for each of the N-nitrosoindoles and three distinct pathways of reaction could be discerned. These pathways were: (i) depurination to the corresponding purine bases, (ii) deamination, coupled with depurination, to give hypoxanthine and xanthine, and (iii) formation of the novel nucleotide 2'-deoxyoxanosine monophosphate and its corresponding depurination product oxanine in reactions with 2'-deoxyguanosine monophosphate. 2'-Deoxyoxanosine and oxanine were observed in reactions with 2'-deoxyguanosine. Further studies showed that formation of all of these products could be rationalized by an initial transnitrosation step. These results suggest that, in contrast to many other genotoxic N-nitrosocompounds which are known to alkylate DNA, the genotoxicity of N-nitrosoindoles is likely to arise through transfer of the nitroso group to nucleophilic sites on the purine bases. All of the products resulting from transnitrosation by N-nitrosoindoles are potentially mutagenic. These findings reveal a new pathway for N-nitrosocompounds to exert genotoxicity.

sigma-Dative and pi-Backdative Phenyl Cation-Dinitrogen Interactions and Opposing Sign Reaction Constants in Dual Substituent Parameter Relations

For the overwhelming number of reactions studied with dual substituent parameter treatments, the ratio of the reaction constants rho(R)/rho(F) = lambda is positive and close to unity. Dediazoniations are prominent representatives of the very few unusual reactions for which dual substituent parameter (DSP) relations yield reaction constants of opposing sign. To understand this exceptional behavior, we have studied with ab initio methods the energetic, structural, and electronic relaxations along the unimolecular, linear dediazoniation path of benzenediazonium ions X-1 to form phenyl cation X-2 in detail for the parent system and two important derivatives (X = H, NH(2), NO(2)). The results support the electron density based model that describes CN bonding in X-1 by synergistic sigma-dative N --> C and C --> N pi-backdative bonding. The analysis provides a theoretical basis for the interpretation of the opposing sign DSP relationship and, in addition, furnishes details about the electronic structure that cannot be deduced from physical-organic studies alone. Polarizations in the sigma-frames critically affect structures (Q values) and electronic structures (populations), and consistent explanations of structural and energetic relaxations in the course of the dediazoniation reactions require their explicit consideration. The classical tool of pi-electron pushing does not suffice to provide a correct account of the electronic structures. In particular, the analysis resolves the apparent paradox that the amino group can function as an electron donor even though it is negatively charged. If sigma-polarizations dominate in cases where they counteract pi-effects, it would seem reasonable to assume that they also are of comparable magnitude where sigma- and pi-effects act in concert. In the later case, explanations based on pi-polarizations might therefore seem consistent but they might lack a physical basis.