One-pot TiO2-catalyzed synthesis of nucleic bases and acyclonucleosides from formamide: implications for the origin of life

A novel one-pot TiO2-catalyzed synthesis of nucleobases and acyclonucleosides from formamide is reported. Since formamide can be formed under prebiotic conditions, these reactions have implications for the origin of life. While a number of purine derivatives have been found as products of non-TiO2-catalyzed reactions, important compounds that would not otherwise occur (namely, thymine, 5-hydroxymethyluracil, and acyclonucleosides) are formed in acceptable yields by TiO2-catalyzed reactions. Moreover, TiO2 selectively affects the rates of degradation of nucleobases, as single units and when embedded in polynucleotides.     

Ozonation Of Nucleic Acid Constituents

Ozonation of nucleic constituents in pure water in semi-batch reactor, showed that nucleobases and nucleosides behave in a similar way, regarding ozone consumption and inorganic nitrogen formation. Stoichiometric ratios were found about 1 mole of consumed ozone per mole of oxidized nucleobase and nucleoside, except for adenine and adenosine which presented a stoichiometric ratio near 3 moles per mole. Concerning inorganic nitrogen formation, we noted that the presence of primary amino groups induced ammonia and nitrate formations, but never more than one mole per mole of initial compound. Carbon dioxide and other end-products were released during ozonation of adenine and thymine. GC/MS analyses showed the presence of some simple end-products, such as oxalic acid, urea and carbamic acid. However trioxotriazine (or cyanuric acid) seemed to be an important end-product, issued from a cyclic trimerization of formamide followed by oxidation of carbon-nitrogen double bonds.     

Nucleobase-Derived Nitrones: Synthesis and Antioxidant and Neuroprotective Activities in an In Vitro Model of Ischemia–Reperfusion

Herein, we report the synthesis, antioxidant, and neuroprotective properties of some nucleobase-derived nitrones named 9a–i. The neuroprotective properties of nitrones, 9a–i, were measured against an oxygen-glucose-deprivation in vitro ischemia model using human neuroblastoma SH-SY5Y cells. Our results indicate that nitrones, 9a–i, have better neuroprotective and antioxidant properties than α-phenyl-N-tert-butylnitrone (PBN) and are similar to N-acetyl-L-cysteine (NAC), a well-known antioxidant and neuroprotective agent. The nitrones with the highest neuroprotective capacity were those containing purine nucleobases (nitrones 9f, g, B = adenine, theophylline), followed by nitrones with pyrimidine nucleobases with H or F substituents at the C5 position (nitrones 9a, c). All of these possess EC₅₀ values in the range of 1–6 μM and maximal activities higher than 100%. However, the introduction of a methyl substituent (nitrone 9b, B = thymine) or hard halogen substituents such as Br and Cl (nitrones 9d, e, B = 5-Br and 5-Cl uracil, respectively) worsens the neuroprotective activity of the nitrone with uracil as the nucleobase (9a). The effects on overall metabolic cell capacity were confirmed by results on the high anti-necrotic (EC_50′s ≈ 2–4 μM) and antioxidant (EC_50′s ≈ 0.4–3.5 μM) activities of these compounds on superoxide radical production. In general, all tested nitrones were excellent inhibitors of superoxide radical production in cultured neuroblastoma cells, as well as potent hydroxyl radical scavengers that inhibit in vitro lipid peroxidation, particularly, 9c, f, g, presenting the highest lipoxygenase inhibitory activity among the tested nitrones. Finally, the introduction of two nitrone groups at 9a and 9d (bis-nitronas 9g, i) did not show better neuroprotective effects than their precursor mono-nitrones. These results led us to propose nitrones containing purine (9f, g) and pyrimidine (9a, c) nucleobases as potential therapeutic agents for the treatment of cerebral ischemia and/or neurodegenerative diseases, leading us to further investigate their effects using in vivo models of these pathologies.     

Non-Canonical Helical Structure of Nucleic Acids Containing Base-Modified Nucleotides

Chemically modified nucleobases are thought to be important for therapeutic purposes as well as diagnosing genetic diseases and have been widely involved in research fields such as molecular biology and biochemical studies. Many artificially modified nucleobases, such as methyl, halogen, and aryl modifications of purines at the C8 position and pyrimidines at the C5 position, are widely studied for their biological functions. DNA containing these modified nucleobases can form non-canonical helical structures such as Z-DNA, G-quadruplex, i-motif, and triplex. This review summarizes the synthesis of chemically modified nucleotides: (i) methylation, bromination, and arylation of purine at the C8 position and (ii) methylation, bromination, and arylation of pyrimidine at the C5 position. Additionally, we introduce the non-canonical structures of nucleic acids containing these modifications.     

Origin of informational polymers: The concurrent roles of formamide and phosphates

Formamide chemistry provides a unitary system by gathering all of the precursors needed to synthesise pregenetic informational polymers in a single milieu. This is not observed with HCN chemistry. With common catalysts, formamide affords all of the precursor nucleobases, photochemically condenses into acyclonucleosides, favours transphosphorylation and enhances micellar aggregation of surfactants. Also, formamide provides a set of physicochemical conditions that thermodynamically favour the polymeric state of nucleotides over the monomers. In the origin-of-informational-polymers scenario, formamide acts in every step, the least characterised being the set of its reactions with phosphates. On this matter, we report two complementary sets of results: 1) the synthesis of prebiotic precursors from formamide, which are catalysed by soluble and mineral phosphates-we observed the formation of rich mixtures that include uracil, 9H-purine, cytosine, dihydrouracil, hypoxanthine, adenosine, urea, parabanic acid, the amino acid N-formylglycine and the peptide-condensing agent carbodiimide; and 2) the protection of ribo- and deoxyribophosphoester bonds by phosphates. The relevance of these effects with respect to the origin of informational polymers is discussed.     

Ozonation of Selected Molecules Constituting Cellular Matter

Ozonation of purine and pyrimidine bases and of carbohydrates was studies in laboratory experiments. The results showed that nucleobases are much more reactive with molecular ozone in aqueous solution than carbohydrates. Second order rate constants for direct reaction of ozone on purines (adenine and guanine) and on pyrimidines (cytosine, thymine and uracil) ranged from 0.76 × 10³ to 6.8 × 10³ M^-1s^-1at 2°C. The difference of reactivity between these solutes may be attributed to their substituents. As far as carbohydrates are concerned, direct reactions of ozone are very slow k₀₃ ? 0.1 – 0.3 M_-1s_-1 at 20°C, and the results indicated that free radical reactions are predominant in the degradation pathway of carbohydrates by ozone. Some ozonation by-products of monosaccharides (glucose, xylose) and disaccharides (cellobiose) also were identified in this study by means of GC/MS analyses.     

Modification of montmorillonites with thermally stable phosphonium cations and comparison with alkylammonium montmorillonites

Alkylammonium montmorillonites have onset temperature of degradation in the same temperature range used for compounding of thermoplastics, thus, requiring more thermally stable organic cations. In the current study, phosphonium, imidazolium and pyridinium ions differing in their chemical architecture (length of alkyl chains, number of phenyl groups etc.) were exchanged on the surface of montmorillonites. The montmorillonites with two different cation exchange capacities (CECs) were used. The thermal behavior of the modified montmorillonites was analyzed by thermogravimetric analysis. To achieve quantitative insights into the onset of degradation, temperatures to reach 5% and 10% mass loss and peak degradation temperatures were compared. Time to reach 1% mass loss was also calculated in the dynamic TGA. The surfactants used in the study were more thermally stable than the conventional alkylammonium cations due to their delayed onset as well as peak degradation temperatures. The time required to attain certain extent of degradation was also much higher in the case of phosphonium montmorillonites, thus, confirming their better thermal resistance. Though the degradation temperatures as well as profiles of the modified montmorillonites with different CECs were similar, the dynamic TGA revealed better thermal behavior of the higher CEC montmorillonite. The X-ray diffraction studies also concluded that optimal modification of the montmorillonite surface could be attained, thus, confirming the high potential of phosphonium montmorillonites for nanocomposites.     

微波固相法合成纳米ZnO及其光催化性能研究

以ZnSO4.7H2O,H2C2O4.2H2O为原料,在微波条件下制得前驱体ZnC2O4.2H2O,经洗涤、干燥、焙烧得产品。采用XRD对产物的物相组成、粒度进行分析,结果表明:该产品为粒径15.5 nm的六方晶型的氧化锌。以该氧化锌为催化剂,对亚甲基蓝溶液进行光催化降解。结果发现,经500℃焙烧1.5 h所得的纳米氧化锌其用量为75 mg时,对50 mL质量浓度为5 mg/L的亚甲基蓝溶液的降解效果最好,在紫外灯下降解2 h,降解率可达98%。     

Study of Ribavirin–Nucleic Acids Interaction

The UV–Vis absorption spectra of ribavirin in the absence and presence of calf thymus DNA are presented and discussed in this paper. The molecular structure of ribavirin was investigated by the semiempirical AM1 method, which triggered two polymorphic modifications of the antiviral drug also reported in the literature. Our experimental results point out two types of the binding. The first type involves a non-electrostatic (internal) binding, consisting of the intercalation of drug between the nitrogenous bases of nucleic acid. The second type (an external binding) involves the drug binding to the nucleic acid grooves. In addition, the binding constant of the second process has an order of magnitude greater than the binding constant for the first process, calculated by the Benesi–Hildebrand, Scott, and Scatchard methods, which supposes a 1:1 binding ratio. Also, the interactions of two polymorphic modifications of ribavirin (V₁ and V₂) with nucleic acids by the molecular mechanic and semiempirical AM1 methods were analyzed. The experimental data pointed out that in the ribavirin–nucleic acid complexes, the 1,2,4-triazole-3-carboxamide chromophore is intercalated between the bases of the nucleic acid sequences, the carboxamidic group is set outside of the nucleic acid sequence toward the major groove, and the 2-hydroxymethyl-tetrahydrofuran-3,4-diol fragment is located in the minor groove. In order to stress the sequence specificity of ribavirin, different models of the nucleic acid sequences containing adenine (A), thymine (T), cytosine (C), and guanine (G) in AAAAAA, TTTTTT, CCCCCC, GGGGGG, ATATAT, CGCGCG, ATCGAT, and CGATCG were used. The theoretical results outline the differences in the contributions of the electrostatic and van der Waals interactions to the total binding energy and the preference of ribavirin for the binding at the sequences of nucleic acids containing adenine and thymine bases.     

Improved sensitivity and selectivity of uric acid voltammetric sensing with mechanically grinded carbon/graphite electrodes

Determination of uric acid (UA) levels in body fluids is important for diagnostics and prevention of severe metabolic disorders. Electrochemical determination of the UA relies on an oxidation signal measurable at different carbon-based electrodes. Improvement of the UA electrochemical sensing has usually been attained via various modifications of the electrode surfaces. In this paper we show that a strong enhancement of the UA oxidation signal can be reached by a simple mechanical grinding of the surfaces of glassy carbon or edge plane-oriented pyrolytic graphite electrodes with SiC particles of an optimum size 15 μm. In contrast to fine polished electrodes (finally with 1-μm particles), the grinded ones exhibited an excellent separation of oxidation signals of ascorbic acid, dopamine (representing most important natural interferents in UA determination), xanthine and hypoxanthine (precursors of UA in purine catabolism), making it possible to detect these substances in a mixture. Enhancement of UA and dopamine (DA) oxidation signals at the grinded electrodes allowed their easy detection at nanomolar levels in up to 10⁴-fold excesses of ascorbic acid. Due to a strong adsorption at the electrode surface, nanomolar concentrations of UA and DA can be determined by ex situ voltammetry. Similarly strong enhancement of oxidation signals was observed for purine nucleobases, guanine and adenine. The grinded electrodes have been tested in analysis of real clinical samples of human serum or urine. An excellent agreement between electrochemical and routine biochemical determination of UA in the biological samples is demonstrated.     

A Toxoplasma gondii Oxopurine Transporter Binds Nucleobases and Nucleosides Using Different Binding Modes

Toxoplasma gondii is unable to synthesize purines de novo, instead salvages them from its environment, inside the host cell, for which they need high affinity carriers. Here, we report the expression of a T. gondii Equilibrative Nucleoside Transporter, Tg244440, in a Trypanosoma brucei strain from which nucleobase transporters have been deleted. Tg244440 transported hypoxanthine and guanine with similar affinity (K_m ~1 µM), while inosine and guanosine displayed K_i values of 4.05 and 3.30 µM, respectively. Low affinity was observed for adenosine, adenine, and pyrimidines, classifying Tg244440 as a high affinity oxopurine transporter. Purine analogues were used to probe the substrate-transporter binding interactions, culminating in quantitative models showing different binding modes for oxopurine bases, oxopurine nucleosides, and adenosine. Hypoxanthine and guanine interacted through protonated N1 and N9, and through unprotonated N3 and N7 of the purine ring, whereas inosine and guanosine mostly employed the ribose hydroxy groups for binding, in addition to N1H of the nucleobase. Conversely, the ribose moiety of adenosine barely made any contribution to binding. Tg244440 is the first gene identified to encode a high affinity oxopurine transporter in T. gondii and, to the best of our knowledge, the first purine transporter to employ different binding modes for nucleosides and nucleobases.     

Preparation and biodegradation of clay composites of PLA

PurposePerspective applications of nanocomposites in biomedical applications are investigated in this work by producing intercalated dispersions of clays into a biodegradable polymer matrix. Poly(lactic acid) (PLA) was selected being produced from renewable resources and approved by the Food and Drug Administration for medical use.In order to improve PLA mechanical properties and to accelerate its degradation, different layered silicate nanoclays are added: montmorillonites and fluorohectorites, without or with organic modifiers. Preparation, characterization, mechanical properties and biodegradation in blood plasma are evaluated.ResultsNew biodegradable materials were obtained, with improved mechanical properties (Young modulus, Peak stress and Strain at break) and with increased degradation rate (weight loss and lactic acid release).     

莫来石纤维增强SiO_2气凝胶隔热材料的制备工艺研究

以正硅酸乙酯(TEOS)为硅源,氢氟酸(HF)为催化剂,采用溶胶-凝胶法及超临界干燥技术制备了莫来石纤维增强S iO2气凝胶隔热材料,研究了HF催化剂、溶剂等制备因素对溶胶-凝胶过程的影响。结果表明,加入HF可以大大加快凝胶化过程,使凝胶时间从几小时缩短至几分钟;溶剂EtOH对凝胶化过程有明显的抑制作用,凝胶时间随其用量的增加而增加;H2O对凝胶化过程的影响比较复杂,凝胶时间随其用量的增加先减后增,转折点处水硅摩尔比为5∶1;气凝胶制备过程中加入甲酰胺可以调节凝胶内部网络结构,防止干燥时由于应力不均而开裂或破裂;适宜的原料配比(摩尔比)为:TEOS∶H2O∶HF∶EtOH∶甲酰胺=1∶(4~6)∶(0.05~0.1)∶(3~6)∶(0.3~0.5)。     

Effect of the Si/Al ratio on the structure and surface properties of silica-alumina-pillared clays

In the present work, the synthesis of silica-alumina-pillared montmorillonites and their structure are studied. Hydroxy-silico-aluminum oligocations have been obtained by treating previously synthesised aluminum polycations with Si(OC₂H₅)₄. Several Si/Al ratios (0, 0.5, 1, and 2) have been used to prepare pillared clays with various microporous accessibility and acidic properties. The study of the fractal dimensions of the solids shows that their surface becomes more heterogeneous after pillaring. The acidity of alumina- and silica-alumina-pillared montmorillonites is mainly of the Lewis type, and the nature of the acid sites detected by pyridine adsorption seems to be independent of the Si/Al ratio. These results are supported by the product distribution obtained in the 1-butanol dehydration reaction.     

Fluorescence properties of 8-(2-pyridyl)guanine "2PyG" as compared to 2-aminopurine in DNA

Because of their environment-sensitive fluorescence quantum yields, base analogues such as 2-aminopurine (2AP), 6-methylisoxanthopterin (6-MI), and 3-methylisoxanthopterin (3-MI) are widely used in nucleic-acid folding and catalysis assays. Emissions from these guanine mimics are quenched by base-stacking interactions and collisions with purine residues. Fluorescent base analogues that remain highly emissive in folded nucleic acids can provide sensitive means to differentiate DNA/RNA structures by participating in energy transfer from proximal ensembles of unmodified nucleobases. The development of new, highly emissive guanine mimics capable of proper base stacking and base-pairing interactions is an important prerequisite to this approach. Here we report a comparison of the most commonly used probe, 2-aminopurine (2AP), to 8-(2-pyridyl)-2'-deoxyguanosine (2PyG). The photophysical properties of these purine derivatives are very different. 2PyG exhibits enhanced fluorescence quantum yields upon its incorporation into folded nucleic acids--approximately 50-fold brighter fluorescence intensity than 2AP in the context of duplex DNA. Due to its bright fluorescence and compatibility with proper DNA folding, 2PyG can be used to accurately quantify energy-transfer efficiencies, whereas 2AP is much less sensitive to structure-specific trends in energy transfer. When using nucleoside monomers, Stern-Volmer plots of 2AP fluorescence revealed upward curvature of F(0) /F upon titration of guanosine monophoshate (GMP), whereas 2PyG exhibited unusual downward curvature of F(0) /F that resulted in a recovery of fluorescence at high GMP concentrations. These results are consistent with the trends observed for 2PyG- and 2AP-containing oligonucleotides, and furthermore suggest that solutions containing high concentrations of GMP can, in some ways, mimic the high local nucleobase densities of folded nucleic acids.     

On the Origin of the Canonical Nucleobases: An Assessment of Selection Pressures across Chemical and Early Biological Evolution

The native bases of RNA and DNA are prominent examples of the narrow selection of organic molecules upon which life is based. How did nature “decide” upon these specific heterocycles? Evidence suggests that many types of heterocycles could have been present on the early Earth. It is therefore likely that the contemporary composition of nucleobases is a result of multiple selection pressures that operated during early chemical and biological evolution. The persistence of the fittest heterocycles in the prebiotic environment towards, for example, hydrolytic and photochemical assaults, may have given some nucleobases a selective advantage for incorporation into the first informational polymers. The prebiotic formation of polymeric nucleic acids employing the native bases remains, however, a challenging problem to reconcile. Hypotheses have proposed that the emerging RNA world may have included many types of nucleobases. This is supported by the extensive utilization of non-canonical nucleobases in extant RNA and the resemblance of many of the modified bases to heterocycles generated in simulated prebiotic chemistry experiments. Selection pressures in the RNA world could have therefore narrowed the composition of the nucleic acid bases. Two such selection pressures may have been related to genetic fidelity and duplex stability. Considering these possible selection criteria, the native bases along with other related heterocycles seem to exhibit a certain level of fitness. We end by discussing the strength of the N-glycosidic bond as a potential fitness parameter in the early DNA world, which may have played a part in the refinement of the alphabetic bases.     

Structural Basis for The Recognition of Deaminated Nucleobases by An Archaeal DNA Polymerase

With increasing temperature, nucleobases in DNA become increasingly damaged by hydrolysis of exocyclic amines. The most prominent damage includes the conversion of cytosine to uracil and adenine to hypoxanthine. These damages are mutagenic and put the integrity of the genome at risk if not repaired appropriately. Several archaea live at elevated temperatures and thus, are exposed to a higher risk of deamination. Earlier studies have shown that DNA polymerases of archaea have the property of sensing deaminated nucleobases in the DNA template and thereby stalling the DNA synthesis during DNA replication providing another layer of DNA damage recognition and repair. However, the structural basis of uracil and hypoxanthine sensing by archaeal B-family DNA polymerases is sparse. Here we report on three new crystal structures of the archaeal B-family DNA polymerase from Thermococcus kodakarensis (KOD) DNA polymerase in complex with primer and template strands that have extended single stranded DNA template 5’-overhangs. These overhangs contain either the canonical nucleobases as well as uracil or hypoxanthine, respectively, and provide unprecedented structural insights into their recognition by archaeal B-family DNA polymerases.     

Fatty acid desaturation by mammary gland microsomes from lactating mice

Microsomal fractions obtained from lactating mouse mammary glands catalyze the desaturation of myristic, palmitic, and stearic acids in the presence of adenosine 5′-triphosphate, coenzyme A, and nicotinamide adenine dinucleotide, reduced form. The products of this reaction are the corresponding monoenoic fatty acids, myristoleic, palmitoleic, and oleic acids respectively. Desaturase, activity was greater with stearate as substrate than with either palmitate or myristate. Palmitate was desaturated at a rate ca. 50% greater than that of myristate. Although both nicotinamide adenine dinucleotide, reduced form and nicotinamide adenine dinucleotide phosphate, reduced form served as electron donors, the former was superior in this regard. Desaturase activity was not influenced by the addition of glycerol 3-phosphate to the incubation medium. However, the presence of this compound did affect the type of lipid formed. In the absence of the added glyceride-glycerol precursor, the major products were phospholipids, whereas in its presence they were triglycerides.     

含氨基螯合纤维的制备 Ⅰ．前驱纤维的制备

将N-乙烯基甲酰胺(NVF)与丙烯腈(AN)的共聚物溶液进行湿法纺丝,制备了含氨基螯合纤维的前驱纤维。研究了凝固条件、纺丝工艺、后处理条件对纤维的结构和性能的影响。结果表明:凝固浴中二甲基甲酰胺溶剂质量分数为20％,湿热拉伸倍数3．0、干热拉伸倍数3．5,纤维断裂强度达3．5 cN／dtex。扫描电镜观察表明纤维为圆形多孔断面,具有较高的孔隙率,适合于制备高效的螯合纤维。     

Hydrothermal Treatment of Carboxy‐methyl Cellulose Salt: Formation and Decomposition of Furans,Pentenes and Benzenes

Carboxymethyl cellulose salt as a model compound was treated hydrothermally to understand the degradation and formation of several chemicals (furfural, 5‐(hydroxymethyl)‐furancarboxaldehyde, and benzene derivatives) that might be interesting as platform chemicals or fuels. To realize a manageable control, closed quartz capillaries were chosen as reactor. Experiments were conducted at temperatures from 250 (subcritical water) to 450 °C (supercritical water) and reaction times from 1 to 60 min. By studying the gas chromatography‐mass spectrometry analysis results of the liquid products, their formation and degradation were detected. It was observed that certain substances only appear for several minutes and are then degraded, while for others the concentration increases at lower rate and keeps stable even for long reaction times. The formation of several benzoic structures from a non‐ring‐structured precursor showed that different reaction mechanisms are involved. Different reaction temperatures showed good correlation to the formation rate of several substances.