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

Biochemical Characterization and Mutational Studies of Endonuclease Q from the Hyperthermophilic Euryarchaeon Thermococcus gammatolerans

Endonuclease Q (EndoQ) can effectively cleave DNA containing deaminated base(s), thus providing a potential pathway for repair of deaminated DNA. EndoQ is ubiquitous in some Archaea, especially in Thermococcales, and in a small group of bacteria. Herein, we report biochemical characteristics of EndoQ from the hyperthermophilic euryarchaeon Thermococcus gammatolerans (Tga-EndoQ) and the roles of its six conserved residues in DNA cleavage. The enzyme can cleave uracil-, hypoxanthine-, and AP (apurinic/apyrimidinic) site-containing DNA with varied efficiencies at high temperature, among which uracil-containing DNA is its most preferable substrate. Additionally, the enzyme displays maximum cleavage efficiency at above 70 ^oC and pH 7.0 ∼ 8.0. Furthermore, Tga-EndoQ still retains 85% activity after heated at 100 ^oC for 2 hrs, suggesting that the enzyme is extremely thermostable. Moreover, the Tga-EndoQ activity is independent of a divalent ion and NaCl. Mutational data demonstrate that residues E167 and H195 in Tga-EndoQ are essential for catalysis since the E167A and H195A mutants completely abolish the cleavage activity. Besides, residues S18 and R204 in Tga-EndoQ are involved in catalysis due to the reduced activities observed for the S18A and R204A mutants. Overall, our work has augmented biochemical function of archaeal EndoQ and provided insight into its catalytic mechanism.

Novel SERS-based process analysis for label-free segmented flow screenings

In microfluidic segmented flow processes label-free analytical techniques like surface enhanced Raman spectroscopy (SERS) can reveal the chemical composition of the individual droplet contents. The SERS system developed in this work enables a simple connection to micro segmented flow processes through miniaturization. The concept is based on the parallelization of silver/polyacrylamide composite SERS spots on a carrier plate on which the segments are deposited. The transfer of the segments allows an easy connection to existing flow processes and provides optimal conditions for Raman measurements using miniaturized spectrometers. The preparation of the SERS polymer composite was optimized in terms of the silver content in the polymer matrix to obtain a high SERS signal. The performance and long-term stability of the polymer have been successfully demonstrated. The deamination of adenine with sodium nitrite to hypoxanthine was chosen as a case study to demonstrate the capability of the novel SERS-based process analysis. A sequence of approximately one hundred segments in combination with a gradient of the nitrite concentration (0 to 0.4 mol L-1) was generated at two temperatures. The concentration of adenine and hypoxanthine were determined by using a multivariate calibration model, since the Raman spectra of both substances are overlapping. It was shown that the conversion of adenine is increased with higher nitrite concentration and temperature. A conversion of 35% was obtained at 50 °C and a conversion of 60% at 80 °C, respectively.

The mesophilic archaeon Methanosarcina acetivorans counteracts uracil in DNA with multiple enzymes: EndoQ, ExoIII, and UDG

Cytosine deamination into uracil is one of the most prevalent and pro-mutagenic forms of damage to DNA. Base excision repair is a well-known process of uracil removal in DNA, which is achieved by uracil DNA glycosylase (UDG) that is found in all three domains of life. However, other strategies for uracil removal seem to have been evolved in Archaea. Exonuclease III (ExoIII) from the euryarchaeon Methanothermobacter thermautotrophicus has been described to exhibit endonuclease activity toward uracil-containing DNA. Another uracil-acting protein, endonuclease Q (EndoQ), was recently identified from the euryarchaeon Pyrococcus furiosus. Here, we describe the uracil-counteracting system in the mesophilic euryarchaeon Methanosarcina acetivorans through genomic sequence analyses and biochemical characterizations. Three enzymes, UDG, ExoIII, and EndoQ, from M. acetivorans exhibited uracil cleavage activities in DNA with a distinct range of substrate specificities in vitro, and the transcripts for these three enzymes were detected in the M. acetivorans cells. Thus, this organism appears to conduct uracil repair using at least three distinct pathways. Distribution of the homologs of these uracil-targeting proteins in Archaea showed that this tendency is not restricted to M. acetivorans, but is prevalent and diverse in most Archaea. This work further underscores the importance of uracil-removal systems to maintain genome integrity in Archaea, including 'UDG lacking' organisms.

On the Route to the Photogeneration of Heteroaryl Cations. The Case of Halothiophenes

2-Chloro-, 2-bromo-, and 2-iodothiophenes undergo photochemical dehalogenation via the triplet state. In the presence of suitable π-bond nucleophiles, thienylation occurs with modest yield from chloro and bromo derivatives (via photogenerated triplet 2-thienyl cation). Specific trapping by using oxygen along with computational analysis carried out by means of a density functional method support that, in the case of iodo derivatives, homolytic thienyl-I bond fragmentation occurs first and heteroaryl cations are formed by electron transfer within the triplet radical pair, thus opening an indirect access to such cations.

Computational study on the deamination reaction of adenine with OH−/nH2O (n = 0, 1, 2, 3) and 3H2O

Deamination of adenine is one of several forms of premutagenic lesions occurring in DNA. In the present study, mechanisms for the deamination reaction of adenine with OH−/nH2O (n = 0, 1, 2, 3) and 3H2O were investigated. HF/6-31G(d), B3LYP/6-31G(d), MP2/6-31G(d), and B3LYP/6-31+G(d) levels of theory were employed to search for and optimize all geometries. Energies were calculated at the G3MP2B3 and CBS-QB3 levels of theory. The effect of solvent (water) was computed using the polarizable continuum model (PCM). Intrinsic reaction coordinate (IRC) calculations were performed for all transition states. Five pathways were investigated for the deamination reaction of adenine with OH−/nH2O and 3H2O. The first four pathways (A–D) are initiated by deprotonation at the amino group of adenine by OH−, while pathway E is initiated by tautomerization of adenine. For all pathways the next two steps involve formation of a tetrahedral intermediate followed by dissociation to products via a 1,3-proton shift. Deamination with a single OH− has a high activation barrier (190 kJ mol−1 using the G3MP2B3 level) for the rate-determining step. The addition of one water molecule reduces this barrier by 68 kJ mol−1 at the G3MP2B3 level. Adding additional water molecules decreases the overall activation energy of the reaction, but the effect becomes smaller with each additional water molecule. The most plausible mechanism is pathway E, the deamination reaction of adenine with 3H2O, with an overall G3MP2B3 activation energy of 139 and 137 kJ mol−1 for the gas phase and PCM, respectively. This barrier is lower than that for the deamination with OH−/3H2O by 6 and 2 kJ mol−1 for the gas phase and PCM, respectively.

Polyvinyl pyrrolidone promotes DNA cleavage by a ROS-independent and depurination mechanism

Polyvinyl pyrrolidone polymer (PVP) has been widely applied in biological and medical fields. A few in vitro studies indicated that PVP might cause toxicity. However, the underlying mechanism is poorly understood. In this work, we found that PVP directly induced strand breakages of various DNA molecules, implicating a cleavage activity. Moreover, reactive oxygen species (ROS) scavenging analysis shows that DNA cleavage activity of PVP is not related to ROS-induced oxidation. As revealed by gel electrophoresis and liquid chromatography/mass spectrometry analysis, the major cleavage products of DNA were identified as two purine bases, guanine and adenine, suggesting that PVPs have a novel depurination activity. The selective depurination and DNA cleavage activity of PVPs were further confirmed by studying the interaction of PVP with four nucleosides and four well-designed oligodeoxynucleotides probes containing specific nucleotides. This study may provide insights into PVP-DNA interactions and resultant genotoxicity and may also open a new way for DNA study.

Modeling the dissociative hydrolysis of the natural DNA nucleosides

Two-dimensional PCM-B3LYP/6-31+G(d) potential energy surfaces for the hydrolysis of the four natural 2'-deoxyribonucleosides (2'-deoxyadenosine, 2'-deoxyguanosine, 2'-deoxycytidine, and thymidine) are characterized using a model that includes both implicit (bulk) solvent effects and (three or four) explicit water molecules in the optimization routine. For the first time, the experimentally predicted dissociative (S(N)1) mechanism is found to be favored over the synchronous (S(N)2) pathway for all nucleosides studied. Due to the success of our model in stabilizing the charge-separated intermediates along the S(N)1 pathway, it is proposed that the new model presented here is the smallest system capable of generating the experimentally predicted oxacarbenium cation intermediate. We therefore stress that dissociative mechanisms should be studied with methodologies that account for the (bulk) environment in the optimization routine, where these effects are often only included as a correction to the energy in the current literature. In addition to accounting for charge stabilization through implicit solvation, nucleophile activation and leaving group stabilization should also be explicitly introduced into the model to further stabilize the system. Our work also emphasizes the importance of studying the Gibbs surface, which in some cases provides a better description of chemically important regions of the reaction surface or changes the calculated trend in the magnitude of dissociative barriers. In addition, it is proposed that the methodology presented in this study can be used to calculate uncatalyzed deglycosylation barriers for a range of DNA nucleosides, which when compared to the corresponding enzyme-catalyzed reactions, will allow the prediction of the rate enhancement (barrier reduction) due to the enzyme.

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.

Adenine synthesis in interstellar space: mechanisms of prebiotic pyrimidine-ring formation of monocyclic HCN-pentamers

The question whether the nucleobases can be synthesized in interstellar space is of fundamental significance in considerations of the origin of life. Adenine is formally the HCN pentamer, and experiments have demonstrated that adenine is formed under certain conditions by HCN pentamerization in gas, liquid, and condensed phases. Most mechanistic proposals invoke the intermediacy of the HCN tetramer AICN (4), and it is thought that adenine synthesis is completed by addition of the 5(th) HCN to 4 to form amidine 5 and subsequent pyrimidine cyclization. In this context, we have been studying the mechanism for prebiotic pyrimidine-ring formation of monocyclic HCN-pentamers with ab initio electronic structure theory. The calculations model gas phase chemistry, and the results primarily inform discussions of adenine synthesis in interstellar space. Purine formation requires tautomerization of 5 to the conjugated amidine 6 (via hydrogen-tunneling, thermally with H(+) -catalysis, or by photolysis) or to keteneimine 7 (by photolysis). It was found that 5-(N'-formamidinyl)-1H-imidazole-4-carbonitrile (6) can serve as a substrate for proton-catalyzed purine formation under photolytic conditions and N-(4-(iminomethylene)-1H-imidazol-5(4H)-ylidene)formamidine (7) can serve as a substrate for uncatalyzed purine formation under photolytic conditions. The absence of any sizeable activation barrier for the cyclization of 7 to the (Z)-imino form of 9H-adenine (Z)-2 is quite remarkable, and it is this feature that allows for the formation of the purine skeleton from 7 without any further activation.

NO-dependent modifications of nucleic acids

This review is devoted to chemical transformations of nucleic acids and their components under the action of nitrogen oxide metabolites. The deamination reaction of bases is discussed in the context of possible competing transformations of its intermediates (nitrosamines, diazonium cations, diazotates, triazenes, and diazoanhydrides) and mechanisms of crosslink formation with proteins and nucleic acids. The oxidation and nitration of bases by NO2 is considered together with the possibility of radical transfer to domains from the base stacks in DNA. Reduction of redox potentials of bases as a result of stacking interactions explains the possibility of their reactions within nucleic acids with the oxidants whose redox potential is insufficient for the effective reactions with mononucleotides. Modifications of nucleic acids with peroxynitrite derivatives are discussed in the context of the effect of the DNA primary structure and the modification products formed on the reactivity of single bases. The possibility of reduction of nitro groups within modified bases to amino derivatives and their subsequent diazotation is considered. The substitution of oxoguanine for nitroguanine residues may result; the reductive diazotation can lead to undamaged guanine. The intermediate modified bases, e.g., 8-aminoguanine and 8-diazoguanine, were shown to participate in noncanonical base pairing, including the formation of more stable bonds with two bases, which is characteristic of the DNA Z-form. A higher sensitivity of RNA in comparison with DNA to NO-dependent modifications (NODMs) is predicted on the basis of the contribution of medium microheterogeneity and the known mechanisms of nitrosylation and nitration. The possible biological consequences of nucleic acids NODMs are briefly considered. It is shown that the NODMs under the action of nitrogen oxide metabolites generated by macrophages and similar cells in inflammations or infections should lead to a sharp increase in the number of mutations in the case of RNA-containing viruses. As a result, the defense mechanisms of the host organism may contribute to the appearance of new, including more dangerous, variants of infecting viruses.

Chemical carcinogens in non-enzymatic cytosine deamination: 3-isocyanatoacrylonitrile

Uracil has long been known as the main product of nitrosative cytosine deamination in aqueous solution. Recent mechanistic studies of cytosinediazonium ion suggest that the cation formed by its dediazoniation can ring-open to N-protonated (Z,s-cis)-3-isocyanatoacrylonitrile 7. Stereochemical preferences are discussed of the 3-isocyanatoacrylonitriles (Z,s-cis)-10, (E,s-cis)-11, (Z,s-trans)-12, and (E,s-trans)-13. The electronic structures of 7 and 10-13 have been analyzed and a rationale is provided for the thermodynamic preference for (Z,s-cis)-10. It is shown that s-cis/s-trans-interconversion occurs via C-N rotation-inversion paths with barriers below 3 kcal mol(-1). The proton affinities of 3-isocyanatoacrylonitrile 10 and water are nearly identical and, thus, 3-isocyanatoacrylonitriles can and should be formed in aqueous media from 7 along with 3-aminoacrylonitriles 9. The results highlight the relevance of the chemistry of 3-isocyanatoacrylonitriles for the understanding of the chemical toxicology of nitrosation of the nucleobase cytosine.

Nitrosative cytosine deamination. An exploration of the chemistry emanating from deamination with pyrimidine ring-opening

A discussion of nitrosative deamination of cytosine 1 is presented that argues for the formation of 6 by diazotization of 1 to cytosinediazonium ion 2 and its electrostatic complex 3, dediazoniation to 4 <--> 5, and amide-bond cleavage to 6. The reaction channels available to 6 include hydrolytic deglycation to 3-isocyanatoacrylonitrile 7, water addition to carbamic acid 9 with the possibility for re-closure to uracil 13, water addition to carbamic acid 9, and decarboxylation to 3-aminoacrylonitrile 10. With a view to the instability of the carbamic acid 9, the carbamate models ethyl (Z)-2-cyanovinylcarbamate 14 and (Z)-2-cyano-1-tert-butylvinylcarbamate 20 were studied. Acid-catalyzed hydrolysis of 14 leads to 2-amino-carbonylphenylcarbamate 15, and its cyclization yields the benzo-fused uracil quinazoline-2,4-dione 16. In contrast to the aromatic system 14, acid-catalyzed cyclization cannot compete with oligomerization in the case of 20, and 5-tert-butyluracil 22 is accessible only with base-catalysis. It is shown that 23, the parent of 10, also easily polymerizes. The experimental results provide a rationale as to why 9, 10, and 12 would have escaped detection in in vitro studies: they would have oligomerized. In contrast to the in vitro experiments, the oligomerizations of 9, 10, or 12 clearly are not relevant in vivo because of low monomer concentrations. With the exclusion of recyclization and of oligomerization in vivo, attention thus needs to focus on (Z)-3-aminoacrylonitrile 10 as the most likely deamination product of cytosine aside from uracil.

Effect of Added Nucleophilic Species on the Rate of Primary Amino Acid Nitrosation

The rate of primary amino acid nitrosation, both with and without the addition of nucleophilic species, has been studied using stopped-flow spectrophotometry. The rate of nitrosation in the presence of strong nucleophilic species such as thiocyanate and thiourea was shown to be much faster than nitrosation without the addition of a nucleophile. Rate constants were determined at 25 degrees C for reaction of the amino acids alanine, glycine, and valine with five common nitrosating agents. For the nitrosating agents nitrosyl chloride, nitrosyl bromide, and dinitrogen trioxide the rate of reaction was observed to approach the predicted encounter-controlled limit. However, for nitrosyl thiocyanate and S-nitrosothiourea nitrosation was found to be reaction-controlled. In the reaction-controlled regime, rate constants were found to increase with increasing electrophilic strength of the nitrosating agent, as measured by the parameter En, with a slope indicative of a product-like transition state. Activation energies were also measured, being around 10-30 kJ mol-1 for encounter-controlled rate constants, and 30-50 kJ mol-1 for reaction-controlled rate constants. Our results are discussed in the context of in vivo amino acid nitrosation, where it is proposed that the rate of nitrosation may be considerably greater than currently thought, due to the presence of nucleophilic species.

Amino Effect on the Protonation of β-Aminoacrylonitrile

The protonation of acrylonitrile (1) and of Z- and E-3-aminoacrylonitrile (5 and 9) was studied with the Gaussian-2 method. Ammoniumacrylonitrile ion formation is not important. Nitrilium ion formation is preferred in all cases, and the proton affinities are about 80 kJ/mol higher for aminoacrylonitrile. Remarkably, it is found that C2-protonation of 3-aminoacrylonitriles to form iminium ions can compete with nitrilium ion formation. Beta-aminoacrylonitriles thus show propinquity to both acrylonitriles and enamines, and mechanistic and toxicological implications are discussed.

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.