Hydrolytic Deamination of 5-Methylcytosine in Protic Medium—A Theoretical Study

Molecular Interactions From the Density Functional Theory for Chemical Reactivity: The Interaction Energy Between Two-Reagents

Reactivity descriptors indicate where a reagent is most reactive and how it is most likely to react. However, a reaction will only occur when the reagent encounters a suitable reaction partner. Determining whether a pair of reagents is well-matched requires developing reactivity rules that depend on both reagents. This can be achieved using the expression for the minimum-interaction-energy obtained from the density functional reactivity theory. Different terms in this expression will be dominant in different circumstances; depending on which terms control the reactivity, different reactivity indicators will be preferred.

Analysis in silico of chemical reactivity employing the local hyper-softness in some classic aromatic compounds, boron aromatic clusters and all-metal aromatic clusters

In the current work, the authors analyzed and compared the chemical behavior of some (anti)aromatic compounds. The species selected are benzene and cyclobutadiene as the aromatic and antiaromatic classical examples, respectively. Next, the anion Al 4 2 - , which is the first all-metal molecule catalogued as aromatic and its non-metallic isoelectronic analog, B 4 2 - were also analyzed. The antiaromatic clusters Al 4 4 - and B 4 4 - were studied in form of lithium salts. And the end, the non-planar B 12 boron cluster and its isoelectronic analogs ( B 11 Be - and B 11 C + ) were considered for being analyzed under the same criterium. The analysis was realized employing the following descriptors: molecular electrostatic potential and local hyper-softness to get insights concerning local reactivity when facing reagents leading to ionic or covalent interactions. The results show that all the molecules analyzed presented some specific variations in their respective local reactivity despite being labeled as aromatic compounds. This analysis provides a notion that the local reactivity is more based on the nature of the atoms and the molecular geometry than the aromatic character by itself.

Modelling the Anti-Methicillin-Resistant Staphylococcus Aureus (MRSA) Activity of Cannabinoids: A QSAR and Docking Study

Twenty-four cannabinoids active against MRSA SA1199B and XU212 were optimized at WB97XD/6-31G(d,p), and several molecular descriptors were obtained. Using a multiple linear regression method, several mathematical models with statistical significance were obtained. The robustness of the models was validated, employing the leave-one-out cross-validation and Y-scrambling methods. The entire data set was docked against penicillin-binding protein, iso-tyrosyl tRNA synthetase, and DNA gyrase. The most active cannabinoids had high affinity to penicillin-binding protein (PBP), whereas the least active compounds had low affinities for all of the targets. Among the cannabinoid compounds, Cannabinoid 2 was highlighted due to its suitable combination of both antimicrobial activity and higher scoring values against the selected target; therefore, its docking performance was compared to that of oxacillin, a commercial PBP inhibitor. The 2D figures reveal that both compounds hit the protein in the active site with a similar type of molecular interaction, where the hydroxyl groups in the aromatic ring of cannabinoids play a pivotal role in the biological activity. These results provide some evidence that the anti-Staphylococcus aureus activity of these cannabinoids may be related to the inhibition of the PBP protein; besides, the robustness of the models along with the docking and Quantitative Structure–Activity Relationship (QSAR) results allow the proposal of three new compounds; the predicted activity combined with the scoring values against PBP should encourage future synthesis and experimental testing.

A facile one-step fluorescence method for the quantitation of low-content single base deamination impurity in synthetic oligonucleotides

Oligonucleotides are being researched and developed as potential drug candidates for the treatment of a broad spectrum of diseases. The characterization of antisense oligonucleotide (ASO) impurities caused by base mutations (e.g. deamination) which are closely related to the target ASO is a significant analytical challenge. Herein, we describe a novel one-step method, utilizing a strategy that combines fluorescence-ON detection with competitive hybridization, to achieve single base mutation quantitation in extensively modified synthetic ASOs. Given that this method is highly specific and sensitive (LoQ = 4 nM), we envision that it will find utility for screening other impurities as well as sequencing modified oligonucleotides.

Towards the rationalization of catalytic activity values by means of local hyper-softness on the catalytic site: a criticism about the use of net electric charges

By means of the Spin-Polarized Conceptual Density Functional Theory (SP-CDFT), three 2,6-bis(imino)pyridine catalysts based on iron(II), used for polymerization of ethylene, were studied. The catalysts differed by the substituent group, bearing either -H, -NO2 or -OCH3. To date, catalytic activity, a purely experimental parameter measuring the mass of polyethylene produced per millimole of iron per time and pressure unit at a fixed temperature, has not been explained in terms of local hyper-softness. The latter is a purely theoretical parameter designed for quantifying electronic effects; it is measured using the metal atom responsible for the coordination process with the monomer (ethylene). Because steric effects are not relevant in these kinds of catalysts and only electronic effects drive the catalytic process, an interesting link is found between catalytic activity and the local hyper-softness condensed on the iron atom by means of four functionals (B3LYP, BP86, B97D, and VSXC). This work demonstrates that the use of local hyper-softness, predicted by the SP-CDFT, is a suitable parameter for explaining order relationships among catalytic activity values, thus quantifying the electronic influence of the substituent group inducing this difference; the use of only net electric charges does not lead to clear conclusions. This finding can aid in estimating catalytic activities leading to a more rational design of new catalysts via computational chemistry.

A new insight into the 5-carboxycytosine and 5-formylcytosine under typical bisulfite conditions: a deamination mechanism study

5-Methylcytosine (5-MeCyt) can be converted to 5-hydroxymethylcytosine (5-hmCyt) in mammalian DNA by the ten-eleven translocation enzymes. The conventional bisulfite sequencing cannot discriminate 5-hmCyt from 5-MeCyt, whereas the oxidation products of 5-hmCyt, 5-carboxycytosine (5-caCyt) and 5-formylcytosine (5-fCyt) enable them to be identified in bisulfite sequencing. This mechanism likely involves the decarboxylation of 5-caCyt and deformylation of 5-fCyt to cytosine (Cyt) before deamination. Another possibility could be a direct bisulfite-induced deamination reaction followed by decarboxylation and deformylation. Here the HSO3(-)-induced direct hydrolytic deamination of 5-caCytN3(+)-SO3(-) (paths A and B) and 5-O(+)fCytN3(+)-SO3(-) (paths C and D) has been explored at the MP2/6-311++G(3df,3pd)//B3LYP/6-311++G(d,p) level. The activation free energy (ΔG(s≠) = 54.16 kJ mol(-1)) of the direct hydrolytic deamination of 5-caCytN3(+)-SO3(-) path A is much lower than the ΔG(s≠) of CytN3(+)-SO3(-) (100.91 kJ mol(-1)) under bisulfite conditions, implying that 5-caCyt may firstly involve a process of deamination. Meanwhile, the ΔG(s≠) (103.84 kJ mol(-1)) of the HSO3(-)-induced direct hydrolytic deamination of 5-O(+)fCytN3(+)-SO3(-) path C is in close proximity to our previous theoretical data for CytN3(+)-SO3(-), indicating that the deamination of 5-fCyt is also likely to occur in the presence of bisulfite. Meanwhile, the HSO3(-)-induced direct hydrolytic deamination of 5-caCytN3(+)-SO3(-) path A and 5-O(+)fCytN3(+)-SO3(-) path C is represented and has been further explored in the presence of one and two water molecules. The results show that both in the gas and aqueous phases, the participation of one and two water molecules makes the HSO3(-)-induced direct hydrolytic deamination of 5-caCytN3(+)-SO3(-) path A unfavorable, whereas the contribution of one and two water molecules facilitates the HSO3(-)-induced direct hydrolytic deamination of 5-O(+)fCytN3(+)-SO3(-) path C.

Is the contribution of cis and trans protonated 5-methylcytosine-SO3(-) isomers equal in the conversion to thymine-SO3(-) under bisulfite conditions? A theoretical perspective

Cytosine (Cyt) can be converted to 5-methylcytosine (5-MeCyt) in CpG sequences of DNA. Conventional bisulfite sequencing can discriminate Cyt from 5-MeCyt, however inappropriate conversion of 5-MeCyt to thymine and a failure to convert Cyt to uracil always occur when Cyt and 5-MeCyt are treated with bisulfite, which would lead to erroneous estimates of DNA methylation densities. Here, the direct hydrolytic deamination of cis (paths A-C) and trans (paths A'-C') 5-MeCytN3(+)-SO3(-) isomers with bisulfite have been explored at the MP2/6-311++G(3df,3pd)//B3LYP/6-311++G(d,p) level. The activation free energies (ΔG(s-a≠)) of the cis and trans 5-MeCytN3(+)-SO3(-) isomers' paths exhibit no obvious differences, implying both isomers may make an equal contribution to the hydrolytic deamination of 5-MeCyt under bisulfite conditions. It is greatly expected that these results could aid experimental scientists to explore new methods to avoid the formation of the deaminated reactants (5-MeCytN3(+)-SO3(-)). Meanwhile, the HSO3(-)-induced direct hydrolytic deamination of cis and trans 5-MeCytN3(+)-SO3(-) isomers is represented by paths A and A', respectively, and has been further explored in the presence of two water molecules. It was found that the contribution of two water molecules renders the HSO3(-)-induced direct hydrolytic deamination of cis and trans 5-MeCytN3(+)-SO3(-) isomers by paths A and A' favourable. In addition, the ΔG(s-a≠) values (85.74-85.34 kJ mol(-1)) of the rate-limiting steps of the two water-mediated paths A and A' are very close to that of the theoretical value for CytN3(+)-SO3(-) (88.18 kJ mol(-1)), implying that the free barrier gap between Cyt and 5-MeCyt is very small under bisulfite conditions. This further suggests that bisulfite sequencing technology may be easily influenced by the external environment.

Genomic methylation patterns in archaeological barley show de-methylation as a time-dependent diagenetic process

Genomic methylation is variable under biotic and abiotic stresses in plants. In particular, viral infection is thought to significantly increase genomic methylation with particularly high activity around transposable elements. Here we present the genomic methylation profiles of grains of archaeological barley (Hordeum vulgare) from several strata from a site in southern Egypt, from the Napatan to the Islamic periods (800 BCE - 1812 CE). One sample tested positive for viral infection and exhibits an unusually high degree of genomic methylation compared to the rest. A decreasing trend in global methylation levels according to deposition date shows in-situ de-methylation of 5-methylcytosine, which can be described as a diagenetic process. This is most likely a deamination mediated de-methylation process and is expected to lead to 5 mC > T base modifications in addition to the C > U modifications due to cytosine deamination, so represents a time-dependent process of DNA diagenesis in ancient DNA.

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

The 5-methylcytosine derivative 5-hydroxymethylcytosine (5hmCyt), which is generated via enzymatic oxidation, is sometimes referred to as the sixth nucleobase due to its widespread presence in the DNA of brain and embryonic stem cells. In this study, we used density functional based methods and reactivity indices from conceptual DFT to explore the mechanism and key features of the hydrolytic deamination of 5hmCyt. The data obtained are used to compare and contrast this deamination reaction with those of other cytosine derivatives. The deamination process for 5hmCyt is similar to the corresponding processes for other unsaturated derivatives in that the amino form is the reactive one and water addition is the rate-limiting step. However, several differences due to the rotameric asymmetry of the current system are also noted.

Hydroxyl-radical-induced oxidation of 5-methylcytosine in isolated and cellular DNA

The methylation and oxidative demethylation of cytosine in CpG dinucleotides plays a critical role in the regulation of genes during cell differentiation, embryogenesis and carcinogenesis. Despite its low abundance, 5-methylcytosine (5mC) is a hotspot for mutations in mammalian cells. Here, we measured five oxidation products of 5mC together with the analogous products of cytosine and thymine in DNA exposed to ionizing radiation in oxygenated aqueous solution. The products can be divided into those that arise from hydroxyl radical (•OH) addition at the 5,6-double bond of 5mC (glycol, hydantoin and imidazolidine products) and those that arise from H-atom abstraction from the methyl group of 5mC including 5-hydroxymethylcytosine (5hmC) and 5-formylcytosine (5fC). Based on the analysis of these products, we show that the total damage at 5mC is about 2-fold greater than that at C in identical sequences. The formation of hydantoin products of 5mC is favored, compared to analogous reactions of thymine and cytosine, which favor the formation of glycol products. The distribution of oxidation products is sequence dependent in specific ODN duplexes. In the case of 5mC, the formation of 5hmC and 5fC represents about half of the total of •OH-induced oxidation products of 5mC. Several products of thymine, cytosine, 5mC, as well as 8-oxo-7,8-dihydroguanine (8oxoG), were also estimated in irradiated cells.

Mechanisms of base substitution mutagenesis in cancer genomes

Cancer genome sequence data provide an invaluable resource for inferring the key mechanisms by which mutations arise in cancer cells, favoring their survival, proliferation and invasiveness. Here we examine recent advances in understanding the molecular mechanisms responsible for the predominant type of genetic alteration found in cancer cells, somatic single base substitutions (SBSs). Cytosine methylation, demethylation and deamination, charge transfer reactions in DNA, DNA replication timing, chromatin status and altered DNA proofreading activities are all now known to contribute to the mechanisms leading to base substitution mutagenesis. We review current hypotheses as to the major processes that give rise to SBSs and evaluate their relative relevance in the light of knowledge acquired from cancer genome sequencing projects and the study of base modifications, DNA repair and lesion bypass. Although gene expression data on APOBEC3B enzymes provide support for a role in cancer mutagenesis through U:G mismatch intermediates, the enzyme preference for single-stranded DNA may limit its activity genome-wide. For SBSs at both CG:CG and YC:GR sites, we outline evidence for a prominent role of damage by charge transfer reactions that follow interactions of the DNA with reactive oxygen species (ROS) and other endogenous or exogenous electron-abstracting molecules.

TET enzymatic oxidation of 5-methylcytosine, 5-hydroxymethylcytosine and 5-formylcytosine

5-Methylcytosine and methylated histones have been considered for a long time as stable epigenetic marks of chromatin involved in gene regulation. This concept has been recently revisited with the detection of large amounts of 5-hydroxymethylcytosine, now considered as the sixth DNA base, in mouse embryonic stem cells, Purkinje neurons and brain tissues. The dioxygenases that belong to the ten eleven translocation (TET) oxygenase family have been shown to initiate the formation of this methyl oxidation product of 5-methylcytosine that is also generated although far less efficiently by radical reactions involving hydroxyl radical and one-electron oxidants. It was found as additional striking data that iterative TET-mediated oxidation of 5-hydroxymethylcytosine gives rise to 5-formylcytosine and 5-carboxylcytosine. This survey focuses on chemical and biochemical aspects of the enzymatic oxidation reactions of 5-methylcytosine that are likely to be involved in active demethylation pathways through the implication of enzymatic deamination of 5-methylcytosine oxidation products and/or several base excision repair enzymes. The high biological relevance of the latter modified bases explains why major efforts have been devoted to the design of a broad range of assays aimed at measuring globally or at the single base resolution, 5-hydroxymethylcytosine and the two other oxidation products in the DNA of cells and tissues. Another critical issue that is addressed in this review article deals with the assessment of the possible role of 5-methylcytosine oxidation products, when present in elevated amounts in cellular DNA, in terms of mutagenesis and interference with key cellular enzymes including DNA and RNA polymerases.

Computational nanochemistry report on the oxicams--conceptual DFT indices and chemical reactivity

A density functional theory study of eight oxicams was carried out in order to determine their global and local reactivities. These types of reactivities were measured by means of global and local reactivity descriptors coming from the conceptual density functional theory. Net electrophilicity as a global reactivity descriptor and local hypersoftness as a local reactivity descriptor were the used tools to distinguish reactivity and selectivity among these oxicams. Globally, isoxicam presents the highest electron donating capacity; meanwhile, the highest electron accepting capacity is exhibited by droxicam. Locally, two oxicams present neither nucleophilic nor electrophilic relevant reactivity in their peripheral pyridine ring, droxicam and tenoxicam, so that their more reactive zones are found on the respective fused rings. Oxicams have been divided into two subgroups in order to facilitate the local analysis of reactivity. One group is characterized because their most important condensed values for local hypersoftnes are well-separated: 4-meloxicam, lornoxicam, meloxicam, and normeloxicam. Meanwhile, the opposite situation is found in droxicam, isoxicam, piroxicam, and tenoxicam. As a whole, the nucleophilic characteristic noticeably predominates in these eight oxicams instead of an electrophilic behavior, thus meaning a greater tendency to donate electrons rather than withdrawing them; a consequence of this behavior implies a favorable interaction with a hypothetical receptor bearing one or more electron acceptor functional groups rather than electron donor functional groups; this would imply a maximization of this interaction from the covalent point of view.

Revisiting caffeate's capabilities as a complexation agent to silver cation in mining processes by means of the dual descriptor--a conceptual DFT approach

Caffeic acid (C(9)H(8)O(4)) and its conjugate base C(9)H(7)O(4) (-) (anionic form-known as caffeate) were analyzed computationally through the use of quantum chemistry to assess their intrinsic global and local reactivity using the tools of conceptual density functional theory. The anionic form was found to be better at coordinating the silver cation than caffeic acid thus suggesting the use of caffeate as a complexation agent. The complexation capability of caffeate was compared with that of some of the most common ligand agents used to coordinate silver cations. Local reactivity descriptors allowed identification of the preferred sites on caffeate for silver cation coordination thus generating a plausible silver complex. All silver complexes were analyzed thermodynamically considering interaction energies in both gas and aqueous phases; the complexation free energy in aqueous phase was also determined. These results suggest that more attention be paid to the caffeate anion and its derivatives because this work has shed new light on the behavior of this anion in the recovery of silver cations that could be exploited in silver mining processes in a environmentally friendly way.

THE HYDROLYTIC DEAMINATION MECHANISM OF PROTONATED ADENINE: A DFT STUDY

The hydrolytic deamination mechanism of protonated adenine has been studied using density functional theory method. There are five pathways according to adenine protonated at N1, N3 and N7, respectively. As for the N1 protonated adenine only one pathway has been found, while for N3 and N7 protonated adenine two pathways have been found. Pathway c2 is preferred due to lowest activation free energy barrier of 53.02 kcal/mol. In this pathway, the hydroxyl group of water attacks C6 atom and hydrogen atom attacks N10 atom to produce enol form of protonated hypoxanthine and ammonia, then hydrogen transfer occurs to cause enol-keto tautomerization of protonated hypoxanthine with the assistance of ammonia. Adenine deamination is easier to take place under acidic condition than under neutral condition owing to lower activation energy barrier.

Quantum mechanics study and Monte Carlo simulation on the hydrolytic deamination of 5-methylcytosine glycol

The efficient formation of 5-methylcytosine glycol (mCg) and its facile deamination to thymine glycol (Tg) may account for the prevalent C → T transition mutation found at methylated CpG site (mCpG) in human p53 gene, a hallmark for many types of human tumors. In this work, the hydrolytic deamination of mCg was investigated at the MP2 and B3LYP levels of theory using the 6-311G(d,p) basis set. In the gas phase, three pathways were explored, paths A-C, and it indicates that the direct deamination of mCg with H(2)O by either pathway is unlikely because of the high activation free energies involved in the rate-determining steps, the formation of the tetrahedral intermediate for paths A and B as well as the formation of the Tg tautomer for path C. In aqueous solution, the role of the water molecules in the deamination of mCg with H(2)O was analyzed in two separate parts: the direct participation of one water molecule in the reaction pathway, called the water-assisted mechanism; and the complementary participation of the aqueous solvation. The water-assisted mechanism was carried out for mCg and the cluster of two water molecules by quantum mechanical calculations in the gas phase. This indicates that the presence of the auxiliary water molecule significantly contributes to decreasing all the activation free energies. The bulk solution effect on the water-assisted mechanism was included by free energy perturbation implemented on Monte Carlo simulations, which is found to be substantial and decisive in the deamination mechanism of mCg. In this case, the water-assisted path A is the most plausible mechanism reported for the deamination of mCg, where the calculated activation free energy (22.6 kcal mol(-1) at B3LYP level of theory) agrees well with the experimentally determined activation free energy (24.8 kcal mol(-1)). The main striking results of the present DFT computational study which is in agreement with previous experimental data is the higher rate of deamination displayed by mCg residues with respect to 5-methylcytosine (mC) bases, which supports that the deamination of mCg contributes significantly to the C → T transition mutation at mCpG dinucleotide site.

Mutual relationship between stacking and hydrogen bonding in DNA. Theoretical study of guanine-cytosine, guanine-5-methylcytosine, and their dimers

The mutual relationship between stacking and hydrogen-bonding and the possible influence of stacking in the different behavior of cytosine (C) and 5-methylcytosine (C') in DNA have been studied through complete DFT optimization of different structures of G-C and G-C' dimers (i.e., G-C/C-G and G-C'/C'-G), using four different functionals. Our results show that stacking leads to an increase of the O(6)...H-N(4) hydrogen bond length and to a simultaneous decrease of the N(2)-H...O(2) one, in such a way that both lengths approach each other and, in some cases, an inversion occurs. These results suggest that stacking can be a factor to explain the disparity between theory and experiment on the relative strength of the two lateral hydrogen bonds. Regarding the difference between cytosine and 5-methylcytosine, we have shown that methylation enhances the stacking interactions, mainly due to the increase of polarizability. Methylation also favors the existence of slid structures which can produce local distortions of DNA.