Adsorption of Adenine, Cytosine, Thymine, and Uracil on Sulfide-Modified Montmorillonite: FT-IR, M?ssbauer and EPR Spectroscopy and X-Ray Diffractometry Studies

In the present work the interactions of nucleic acid bases with and adsorption on clays were studied at two pHs (2.00, 7.00) using different techniques. As shown by Mössbauer and EPR spectroscopies and X-ray diffractometry, the most important finding of this work is that nucleic acid bases penetrate into the interlayer of the clays and oxidize Fe²⁺ to Fe³⁺, thus, this interaction cannot be regarded as a simple physical adsorption. For the two pHs the order of the adsorption of nucleic acid bases on the clays was: adenine????cytosine?>?thymine?>?uracil. The adsorption of adenine and cytosine on clays increased with decreasing of the pH. For unaltered montmorillonite this result could be explained by electrostatic forces between adenine/cytosine positively charged and clay negatively charged. However for montmorillonite modified with Na₂S, probably van der Waals forces also play an important role since both adenine/cytosine and clay were positively charged. FT-IR spectra showed that the interaction between nucleic acid bases and clays was through NH⁺ or NH ₂ ⁺ groups. X-ray diffractograms showed that nucleic acid bases adsorbed on clays were distributed into the interlayer surface, edge sites and external surface functional groups (aluminol, silanol) EPR spectra showed that the intensity of the line g????2 increased probably because the oxidation of Fe²⁺ to Fe³⁺ by nucleic acid bases and intensity of the line g?=?4.1 increased due to the interaction of Fe³⁺ with nucleic acid bases. Mössbauer spectra showed a large decreased on the Fe²⁺ doublet area of the clays due to the reaction of nucleic acid bases with Fe²⁺.     

Synthesis and Studies of 3′-C-Trifluoromethyl-β-D-ribonucleosides Bearing the Five Naturally Occurring Nucleic Acid Bases

Abstract

3′-C-Trifluoromethyl-β-D-ribonucleoside derivatives bearing the five naturally occurring nucleic acid bases have been synthesized. All these derivatives were prepared by glycosylation reactions of purine and pyrimidine bases with a suitable peracylated 3-C-trifluoromethyl ribofuranose precursor. After deprotection, the resulting title nucleoside analogues were tested for their inhibitory properties against the replication of HIV, HBV and several RNA viruses. However, none of these compounds showed significant antiviral activity.     

Polymethylene derivatives of nucleic bases with ω-functional groups: VII. Cytotoxicity in the series of <Emphasis Type="Italic">N</Emphasis>-(2-oxocyclohexyl)-ω-oxoalkyl-substituted purines and pyrimidines

New polymethylene derivatives of the nucleic bases with β-diketo function in the ω-position have been synthesized by alkylation of uracil, thymine, cytosine, hypoxanthine, adenine, and N ²-isobutyryl guanine with 2-(ω-chloroalkanoyl)cyclohexanones. The physicochemical characteristics of compounds synthesized and their effect on tumor K562 and HCT116 cell lines have been studied.     

Effects of Ionizing Radiation on Bacterial DNA-membrane Complexes

THE model proposed by Alper¹ for lethal radiation damage to cells is based on inferential evidence that there are two important sites of damage by ionizing radiation. At one site, damage referred to as type “N” is associated with a low oxygen enhancement ratio (OER) and is probably to nucleic acid, while at the other site, type “O” damage is associated with a considerably higher oxygen enhancement value and is to a non-nucleic acid target. The model demands that the two values of OER are respectively less and greater than that observed for the overall lethal effect. More recently² Alper reviewed further inferential evidence³ that cell membranes are the site of type O damage, though there may be subsequent interaction with the lesions following energy deposition in DNA⁴.     

Radiation-induced decomposition of the purine bases within DNA and related model compounds

This survey focuses on recent developments in the radiation chemistry of purine bases in nucleic acids and related model compounds. Both direct and indirect effects of ionizing radiation are investigated with special emphasis on the structural characterization of the final decomposition products of nucleic acid components. Available assays for monitoring radiation-induced base lesions are critically reviewed.     

Cations as Mediators of the Adsorption of Nucleic Acids on Clay Surfaces in Prebiotic Environments

Monovalent ([Na⁺] > 10 mM) and divalent ([Ca²⁺], [Mg²⁺] > 1.0 mM) cations induced the precipitationof nucleic acid molecules. In the presence of clay minerals (montmorillonite and kaolinite), there was adsorption instead of precipitation. The cation concentration needed for adsorption depended on both the valence of the cations and the chemical nature of the nucleic acid molecules. Double-stranded nucleic acids needed higher cation concentrations than single-stranded ones to be adsorbed to the same extent on clay. Divalent cations were more efficient than monovalent ones in mediating adsorption. Adsorption to the clay occurred only when both nucleic acids and cations were present. However, once the complexes were formed, the cations could not be removed from the system by washing, indicating that they are directly involved in the association between nucleic acids and mineral surfaces.These observations indicate that cations take part directly in the formation of nucleic acid-clay complexes, acting as a `bridge' between the negative charges on the mineral surface and those of the phosphate groups of the genetic polymer. The relatively low cation concentrations needed for adsorption and the ubiquitous presence of clay minerals in the environment suggest that the adsorption of nucleic acids on mineral surfaces could have taken place in prebiotic habitats. This may have played an important role in the formation and preservation of nucleic acids and/or their precursor polymers.     

The biodegradability of nucleic acid bases adsorbed on inorganic and organic soil components

Summary The biodegradability of nucleic acid bases (guanine, adenine, cytosine, thymine and uracil) adsorbed on montmorillonite, illite, kaolinite, soil, gibbsite, goethite and a fulvic acid (FA)-montmorillonite complex was investigated. Each material was mixed with sand, inoculated with a soil suspension and incubated in a Warburg vessel. Lag periods in O₂ uptake were observed at pH 4 and 6 but not at pH 8. Following the lag periods, adsorbed nucleic acid bases were degraded rapidly at linear rates until these levelled off. The cessation of O₂-uptake was shown to be due to the formation of excessive amounts of gaseous NH₃, which not only inhibited microbial respiration by raising the pH to 8 and higher, but also by killing bacteria and actinomycetes. The rate of biodegradation was found to depend on the type of clay or oxide, the dominant cation and the pH. Contribution No 1181     

Effects of Water and pH on the Oxidative Oligomerization of Chloro an Methoxyphenol by a Montmorillonite Clay

This study focussed on the capacity of a montmorillonite clay to oxidize organic contaminants having activating (methoxyphenol) and deactivating (chlorophenol) substituent groups when pH and water conditions are changing. The amount and strength of Lewis and Br?nsted acidity of the clay was measured using organic indicator and titration methods. Water plays two distinct roles in the oxidation of such contaminants by clays: (1) it neutralizes the clay's Lewis acidity, thereby preventing chlorophenol from getting oxidized in significant yields; (2) it does not successfully compete with methoxyphenol for Lewis acid sites because high dimer yields are observed. The high capacity of Na⁺, Ca²⁺, and Fe³⁺ clays to oxidize phenolic compounds at high pH appears to be caused by phenolates being more reactive than the protonated form. The Lewis and Br?nsted acidity measurement of the various homoionic clays tested help explain the high capacity of the clays to oxidize phenolic compounds at low and high pH and their low capacity at near neutral pH. Finally, the results also clarify the effects of exchangeable cations on the capacity of clays to oxidize organic contaminants.     

The Inhibitory Effects of Low-Dose Ionizing Radiation in IgE-Mediated Allergic Responses

Ionizing radiation has different biological effects according to dose and dose rate. In particular, the biological effect of low-dose radiation is unclear. Low-dose whole-body gamma irradiation activates immune responses in several ways. However, the effects and mechanism of low-dose radiation on allergic responses remain poorly understood. Previously, we reported that low-dose ionizing radiation inhibits mediator release in IgE-mediated RBL-2H3 mast cell activation. In this study, to have any physiological relevance, we investigated whether low-dose radiation inhibits allergic responses in activated human mast cells (HMC-1(5C6) and LAD2 cells), mouse models of passive cutaneous anaphylaxis and the late-phase cutaneous response. High-dose radiation induced cell death, but low-dose ionizing radiation of <0.5 Gy did not induce mast cell death. Low-dose ionizing radiation that did not induce cell death significantly suppressed mediator release from human mast cells (HMC-1(5C6) and LAD2 cells) that were activated by antigen-antibody reaction. To determine the inhibitory mechanism of mediator released by low-dose ionizing radiation, we examined the phosphorylation of intracellular signaling molecules such as Lyn, Syk, phospholipase Cγ, and protein kinase C, as well as the intracellular free Ca²⁺ concentration ([Ca²⁺]_i). The phosphorylation of signaling molecules and [Ca²⁺]_i following stimulation of FcεRI receptors was inhibited by low dose ionizing radiation. In agreement with its in vitro effect, ionizing radiation also significantly inhibited inflammatory cells infiltration, cytokine mRNA expression (TNF-α, IL-4, IL-13), and symptoms of passive cutaneous anaphylaxis reaction and the late-phase cutaneous response in anti-dinitrophenyl IgE-sensitized mice. These results indicate that ionizing radiation inhibits both mast cell-mediated immediate- and delayed-type allergic reactions in vivo and in vitro.     

Repair of oxidative DNA damage by amino acids

Guanyl radicals, the product of the removal of a single electron from guanine, are produced in DNA by the direct effect of ionizing radiation. We have produced guanyl radicals in DNA by using the single electron oxidizing agent (SCN)₂^–, itself derived from the indirect effect of ionizing radiation via thiocyanate scavenging of OH. We have examined the reactivity of guanyl radicals in plasmid DNA with the six most easily oxidized amino acids cysteine, cystine, histidine, methionine, tryptophan and tyrosine and also simple ester and amide derivatives of them. Cystine and histidine derivatives are unreactive. Cysteine, methionine, tyrosine and particularly tryptophan derivatives react to repair guanyl radicals in plasmid DNA with rate constants in the region of ~10⁵, 10⁵, 10⁶ and 10⁷ dm³ mol^–1 s^–1, respectively. The implication is that amino acid residues in DNA binding proteins such as histones might be able to repair by an electron transfer reaction the DNA damage produced by the direct effect of ionizing radiation or by other oxidative insults.     

Radioactivity in mushrooms from selected locations in the Bohemian Forest,Czech Republic

¹³⁷Cs is one of the most important radionuclides released in the course of atmospheric nuclear weapon tests and during accidents in nuclear power plants such as that in Chernobyl, Ukraine, or Fukushima, Japan. The aim of this study was to compare ¹³⁷Cs and ⁴⁰K concentrations in particular species of mushrooms from selected locations in the Bohemian Forest (Czech: ?umava), Czech Republic, where a considerable contamination from the Chernobyl accident had been measured in 1986. Samples were collected between June and October 2014. Activities of ¹³⁷Cs and ⁴⁰K per dry mass were measured by means of a semiconductor gamma spectrometer. The ¹³⁷Cs values measured range from below detection limit to 4300?±?20 Bq kg^?1, in the case of ⁴⁰K from 910?±?80 to 4300?±?230 Bq kg^?1. Differences were found between individual locations, due to uneven precipitation in the course of the movement of the radioactive cloud after the Chernobyl accident. There are, however, also differences between individual species of mushrooms from identical locations, which inter alia result from different characteristics of the soil and depths of mycelia. The values measured are compared with established limits and exposures from other radiation sources present in the environment. In general, it can be stated that the values measured are relatively low and the effects on the health of the population are negligible compared to other sources of ionizing radiation.     

<Emphasis Type="Italic">Rhizophagus irregularis</Emphasis> MUCL 41833 can colonize and improve P uptake of <Emphasis Type="Italic">Plantago lanceolata</Emphasis> after exposure to ionizing gamma radiation in root organ culture

Long-lived radionuclides such as ⁹⁰Sr and ¹³⁷Cs can be naturally or accidentally deposited in the upper soil layers where they emit β/γ radiation. Previous studies have shown that arbuscular mycorrhizal fungi (AMF) can accumulate and transfer radionuclides from soil to plant, but there have been no studies on the direct impact of ionizing radiation on AMF. In this study, root organ cultures of the AMF Rhizophagus irregularis MUCL 41833 were exposed to 15.37, 30.35, and 113.03 Gy gamma radiation from a ¹³⁷Cs source. Exposed spores were subsequently inoculated to Plantago lanceolata seedlings in pots, and root colonization and P uptake evaluated. P. lanceolata seedlings inoculated with non-irradiated AMF spores or with spores irradiated with up to 30.35 Gy gamma radiation had similar levels of root colonization. Spores irradiated with 113.03 Gy gamma radiation failed to colonize P. lanceolata roots. P content of plants inoculated with non-irradiated spores or of plants inoculated with spores irradiated with up to 30.35 Gy gamma radiation was higher than in non-mycorrhizal plants or plants inoculated with spores irradiated with 113.03 Gy gamma radiation. These results demonstrate that spores of R. irregularis MUCL 41833 are tolerant to chronic ionizing radiation at high doses.     

Clay-Nucleic Acid Complexes: Characteristics and Implications for the Preservation of Genetic Material in Primeval Habitats

The equilibrium adsorption of three nucleic acids: chromosomal DNA, supercoiled plasmid DNA, and 25S rRNA, on the clay minerals, montmorillonite (M) and kaolinite (K), were studied. Adsorption of the nucleic acid on the clays was rapid and maximal after 90 min of contact time. Chromosomal DNA was adsorbed to a greater extent than plasmid DNA and RNA, and the adsorption was also greater on M than on K. Adsorption isotherms were of the L type, and a plateau was reached with all the complexes, with the exception of chromosomal DNA adsorbed on M. To determine where nucleic acids are adsorbed on clay minerals and the nature of the interaction, complexes were studied by X-ray diffraction (X-RD), electron microscopy, and Fourier transform infrared (FT-IR) spectroscopy. X-RD showed that nucleic acids did not penetrate the clay, indicating that the adsorption occurred primarily on the external surfaces of clay particles, as also suggested by electron microscopy observations. FT-IR spectra of clay-tightly bound nucleic acid complexes showed absorption bands that indicate a variation of the nucleic acids status as a consequence of their adsorption on clay. Data obtained suggested that the formation of clay-nucleic acid complex could have an important role in the preservation of genetic material in primeval habitats.     

The Purification and Characterization of Gemini Particles from Abutilon Mosaic Virus Infected Malvaceae

Gemini particles were purified from Abutilon Mosaic Virus infected Abutilon sellovianum, Sida micrantha and Malva parviflora. They sediment with 82 S, possess a density of 1.30 g/cm³ in Cs₂SO₄ and a nucleic acid percentage of 18 % calculated from ultra-violett spectrometry. Their proteins are separated in SDS-PAGE into two components of 28 000 and 27 000 mol. wt. Their nucleic acid consists of single-stranded circular DNA with length distribution maxima of 2 800, 2 500 and 1 300 bases for the circular molecules and 2 050, 1 850, and 1 300 bases for the correspondmg linear molecules.     

The Role of Structural Water in the Formation of Nucleotide Mispairs

Abstract

The results of NMR investigation of the double-helical nucleic acid fragments containing A · C, C · U, m⁶G · U and m⁶G · G mispairs can be explained on the assumption that the bases in such pairs being in usual tautomeric forms are linked via water bridges. A computer analysis of intermolecular interactions in the systems containing two bases and one or two water molecules shows that these pairs correspond to the energy minima. The formation of pairs with water bridges can be considered an intermediate step in mutagenesis caused by some spontaneous errors arising during nucleic acid biosynthesis as well in mutagenesis induced by alkylating agents.     

Polymethylene derivatives of nucleic bases bearing ω-functional groups: IX—An unusual reaction of methyl 2-thiocyano-5-chloropentanoate with uracyl and thymine

Although the search of inhibitors of the key enzymes of HIV replication has remained a topical and intensively studied topic over the last several decades, potential inhibitors of the enzymes bearing thiocyano groups have been little studied. In this work, we tried to synthesize polymethylene derivatives of nucleic bases bearing thiocyano groups at the ω-position of the polymethylene chain. The reaction of new alkylating reagents, methyl α-thiocyano-ω-chloroalkanoates, with nucleic bases led to a complicated and barely separated product mixture. The only exceptions were the reactions of uracil or thymine with methyl 2-thiocyano- 2-chloropentanoate, in which 2-(N ¹-uracilyl or -thyminyl)tetrahydrothiophene-2-carboxylates were isolated in 45–50% yields. The potential mechanism of the reaction is discussed.     

Effects of protein inhibitors and auxin on nucleic Acid metabolism in peanut cotyledons

The accumulation of labeled phosphorus into newly synthesized nucleic acids or peanut cotyledon slices incubated with chloramphenicol, puromycin, or 2,4-dichlorophenoxyacetic acid (2,4-D) was reduced. Promotion of nucleic acid synthesis was not noted by any of these chemicals. Chloramphenicol completely inhibited the synthesis of the DNA-RNA fraction at 1.25 × 10⁻³ m while soluble and ribosomal RNA was inhibited by 70% and 80%, respectively. At the same concentration messenger RNA was inhibited by only 40%. These effects suggest that chloramphenicol inhibit nucleic acid synthesis in peanut cotyledons in a differential manner. Similar results were noted for DNA at low concentrations of 2,4-D. However, at high concentrations of 2,4-D, DNA as well as RNA fractions were inhibited in a similar manner at a given concentration. Puromycin did not differentially inhibit nucleic acid synthesis except at 2 × 10⁻³ m where DNA was least inhibited.     

Potential and structure controlled interfacial behavior of uracil derivatives

The adsorption and related interfacial behavior of uracil, various methylated uracil derivatives, uridine, uridine-5'-monophosphate and uridine-3'5'-cyclic monophosphate has been studied by surface electrochemical measurements at a mercury electrode. All uracil derivatives exhibit an initial "dilute" adsorption region where the virtually flat uracil residue is absorbed flat on the electrode surface. In the case of uracil and its methylated derivatives the area occupied by one molecule is about 60-70 A2. Uracil, thymine and 1,5-dimethyluracil exhibit a second adsorption region where they rearrange on the surface and adopt a perpendicular orientation and occupy about 40 A2 per molecule. In this perpendicular orientation the uracils are bound to the electrode through the N(3)-H or perhaps N(1)-H functions in a manner similar to their Watson-Crick bonding in nucleic acids. When in the perpendicular orientation the adsorbed molecules undergo extensive stacking (association) interactions, again similar to those observed between adjacent bases in nucleic acids. The ability of a uracil derivative to undergo a surface reorientation is critically dependent on electrode potential, bulk-solution concentration and molecular structure.     

Theoretical Study of the TiO2 and MgO Surface Acidity and the Adsorption of Acids and Bases

We present ab-initio periodic Hartree–Fock calculations (crystal program) of small molecules on TiO₂ and MgO. The adsorption of the molecules may be molecular or dissociative. This depends on their acid and basic properties in the gas phase. For the molecular adsorption, the molecules are adsorbed as bases on Ti(+IV) sites, the adsorption energies correlate with the proton affinities. The dissociations on the surface correlate with the gas phase cleavages: thus, the dissociation of MeOH leads to a preferential basic cleavage (the fragment HO– is adsorbed on a Ti⁺⁴ ion and the fragment Me⁺ is adsorbed on a O²– ion of the oxide). The opposite result is obtained with MeSH. Another important factor is the adsorbate–adsorbate interaction: favorable cases are a sequence of H-bonds for the hydroxyl groups resulting from the water dissociation and the mode of adsorption for the ammonium ions. Lateral interactions also force the adsorbed CO₂ molecules to bend over the surface so that their mutual orientation resembles the geometry of the CO₂ dimer. With respect to water adsorption, MgO appears to be a basic oxide. As experimentally observed, NH₃ adsorbs preferentially on TiO₂ and CO₂ on MgO. However, this difference of reactivity should not be expressed in terms of acid vs. basic behaviour but in terms of hard and soft acidity. The MgO surface is a 'soft' acidic surface that reacts preferentially with the soft base, CO₂.     

The thermodynamic effects of exposing nucleic acid bases to water: solubility measurements in water and organic solvents

In order to examine the thermodynamic effects of exposing nucleic acid bases to water, we have measured the solubility of adenine, cytosine, and uracil in water and in organic solvents as a function of temperature. Transfer of a nucleic acid base from an organic environment into water is characterized by positive values for ΔH and for ΔS. We conclude from this result that the overall interaction between nucleic acid bases and water cannot be hydrophobic. If the effect we observe represents structure breaking in water by nucleic acid bases, this process would account for a major portion of the large, positive melting entropy of DNA, and would also contribute substantially to the melting enthalpy.