Differential reactivity of alpha and beta 2'-deoxyribonucleosides towards protonation and metalation

The reactivity of artificial 2'-deoxyribonucleosides, designed as nucleoside surrogates in metal-mediated base pairs, towards protonation and metalation has been shown to be dependent on the choice of the anomer. The alpha nucleosides comprising the aglycones imidazole, 1,2,4-triazole, benzimidazole and imidazo[4,5-b]pyridine are more basic than the respective beta nucleosides as was shown by a combined experimental and theoretical approach. The DeltapK(a) values observed experimentally are in the range of 0.19+/-0.03 to 0.41+/-0.07 (with the error representing three times the standard deviation of the mean value). An independent confirmation of this differential reactivity was obtained from density functional theory (DFT) calculations using 1,2,4-triazole nucleoside as an example. The result of these calculations is in good agreement with the experimental data (DeltapK(a)=0.16 vs. 0.21+/-0.07). The stability of the respective metal ion complexes of the anomeric 1,2,4-triazole nucleosides follows the same trend as that of the respective protonated nucleosides: Those of the alpha nucleoside are more stable than those of the beta nucleoside (Deltalogbeta(2)=0.6+/-0.2 for the 2:1 complex with Ag(+); Deltalogbeta(1)=0.51+/-0.07 for the 1:1 complex with Hg(2+)). These slightly different reactivities will be useful for fine-tuning the metal-ion binding behavior of oligonucleotides containing metal-mediated base pairs.     

The role of spin in biological processes: O2, NO,nucleobases, nucleosides,nucleotides and Watson–Crick base pairs

The experimental electron affinities of adenine, guanine, cytosine, thymine and uracil have been determined from reduction potentials and negative ion photoelectron spectra. Updated values for purine, pyrimidine and other nitrogen heterocyclics, which have not been measured in the gas phase, are presented. The electron affinity of Watson–Crick guanine–cytosine is estimated empirically. The experimental values are consistent with quantum mechanical semi-empirical multiconfiguration configuration interaction calculations. The bulk hydration energies of the nucleobase anions, 2.34 eV, determined from the experimental data and sequential anion hydration energy difference of about 0.20(5) eV suggest that 10–15 water molecules complete the hydration shell. The electron affinities for the formation of doublet and quartet anions of the nucleobases, nucleosides, nucleotides and Watson–Crick base pairs are calculated. We postulate that low-lying quartet anion states and their spin distribution can and will participate in electron conduction, radiation damage, oxidation damage and repair, strand breakage and protein synthesis.     

Purification of leaf nucleotides and nucleosides on insoluble polyvinylpyrrolidone

Of the 19 nucleotides and nucleosides tested, all were eluted by 1 mM HCl in less than 60 ml from 2 × 6-cm columns of Polyclar AT (an insoluble polyvinylpyrrolidone). Recoveries were good and, with the possible exceptions of ADPG and UDPG, the presence of cotton leaf extract did not decrease recovery of known nucleotides and nucleosides.Passing leaf extracts through Polyclar AT removed most, but not all, of the uv-absorbing impurities that interfere with quantitation of nucleotides and nucleosides. The optimum pH for purification of HClO₄ extracts from leaves of alfalfa, cotton, grape, and orange appeared to be between 2.0 and 3.0. In this pH range Polyclar AT removed from 59 to 91% of the substances in leaf extracts that absorbed at 230 nm and from 93 to 97% of the substances that absorbed at 320 nm.Extraction of leaf extract with isoamyl alcohol was relatively ineffective and extraction with ether was almost completely ineffective in removing uv-absorbing impurities.Because nucleotides and nucleosides quickly pass through a short column of Polyclar AT at pH 3.0 while plant phenols are retained, this procedure provides a simple and rapid method for bulk purification of leaf extracts prior to chromatography and assay of nucleotides and nucleosides.     

Simultaneous determination of nucleosides and nucleotides in dietary foods and beverages using ion-pairing liquid chromatography–electrospray ionization-mass spectrometry

A method using ion-pairing liquid chromatography–electrospray ionization (ESI)-mass spectrometry (MS) was developed for the simultaneous determination of 23 types of purine or pyrimidine nucleosides and nucleotides in dietary foods and beverages. Dihexylammonium acetate (DHAA) was used as an ion-pairing agent and an ultra performance liquid chromatography (UPLC™) system with a reversed-phase column and a gradient program was employed for the separation of nucleosides and nucleotides. Positive-ion ESI-MS was applied for the detection of nucleosides, and negative-ion ESI-MS was used for nucleotides. Lower limits of quantitation ranged from 0.02 μmol/L (UMP and AMP) to 1.3 μmol/L (CDP). The present method was validated, and sufficient reproducibility and accuracy was obtained for the quantitative measurement of the 23 types of nucleosides and nucleotides. The method was subsequently applied to their determination in a range of Japanese foods and beverages that are considered to contain significant amounts of umami flavor compounds. Because dietary purine nucleosides and nucleotides are known to be related to hyperuricemia and gout, the determination of their concentrations in dietary foods is useful for both evaluating umami flavor and assessing the effects of dietary food on purine metabolism.     

Interactions of the dimethyldiazaperopyrenium dication with nucleic acids. 1. Binding to nucleic acid components and to single-stranded polynucleotides and photocleavage of single-stranded oligonucleotides

The binding of dimethyldiazaperopyrenium dication (1) with nucleosides, nucleotides, and single-stranded polynucleotides has been studied by photophysical methods. It has been shown that 1 may be a potential selective fluorescent probe for A- and/or T-rich polynucleotides. 1 efficiently cleaves oligonucleotides at guanine sites, under illumination with visible light, and therefore may be used as a sequence-specific artificial photonuclease.     

Covalent binding of LTA(4) to nucleosides and nucleotides

Leukotriene A(4) (LTA(4)) is a chemically reactive conjugated triene epoxide that is formed by 5-lipoxygenase and is an intermediate in the formation of the biologically active eicosanoids leukotriene B(4) and leukotriene C(4). The present study was undertaken to determine whether or not LTA(4) could serve as an electrophilic species that nucleosides and nucleotides could attack, ultimately resulting in a covalent adduct. Electrospray ionization mass spectrometry and tandem mass spectrometry were used to study the covalent binding of LTA(4) with uridine, cytidine, adenosine, and guanosine. The reaction with guanosine was found to yield five major and at least six minor adduct species. Reversed phase HPLC and mass spectrometric data suggested that the guanosine attacked LTA(4) either at carbon-12 or carbon-6 with opening the epoxide at carbon-5 to yield a series of adducts characterized by the molecular anion [M-H](-) at m/z 600.3. Reactions of LTA(4) with mixtures of nucleosides and nucleotides revealed that guanine-containing nucleosides were the most reactive toward LTA(4). The facility of the reaction of guanine with LTA(4) raises the possibility that this intermediate of leukotriene biosynthesis formed on or near the cellular nuclear envelope may react with nucleosides and nucleotides present in RNA or DNA.     

Quantitative changes in the content of nucleic acid bases and their derivatives in a culture ofPenicillium sizowi

Acid-soluble (“free”) nucleotides, nucleosides and bases were analyzed in the mycelium and in the culture filtrate of the fungusPenicillium sizowi, using micro-thin-layer chromatography on alumina and densitometry of the zones of the individual components. It was found that the levels of the various components underwent complicated changes, the corresponding curves exhibiting from one to three maxima which occur at different periods of cultivation. It was observed that a substantial amount of nucleotides, nucleosides and bases occurs in the medium as early as at the beginning of the exponential phase of growth. An attempt was made to elucidate some peculiarities of the nucleotide pool ofPenicillium species, using enzymes responsible for the individual transformations of nucleotides, nucleosides and bases.     

5-alkylvinyl-1,2,4-triazole nucleosides: Synthesis and biological evaluation

Abstract

Some 5-substituted ribavirin analogues have a high antiviral and anticancer activity, but their mechanisms of action are obviously not the same as their parent compound. The SAR studies performed on 3 (5)-substituted 1,2,4-triazole nucleosides have shown a high dependency between the structure of the 3 (5)-substituent and the level of antiviral/anticancer activity. The most active substances of the row contain coplanar with the 1,2,4-triazole ring aromatic substituent which is connected by a rigid ethynyl bond. However, the compounds with the trans-vinyl linker also had antiviral activity. We decided to study the antitumor activity of ribavirin analogues with alkyl/aryl vinyl substituents in the 5th position of the 1,2,4-triazole ring. Protected nucleoside analogues with various 5-alkylvinyl substituents were obtained by Horner-Wadsworth-Emmons reaction from the common precursor and converted to the nucleosides. Arylvinyl nucleosides were synthesised according the reported procedures. All compounds did not show significant antiproliferative activity on several tumour cell lines. Coplanar aromatic motif in the 5-substituent for the anticancer activity manifestation was confirmed.     

Adenosine,but not guanosine,protects vaginal epithelial cells from Trichomonas vaginalis cytotoxicity

Trichomonas vaginalis causes the most common non-viral sexually transmitted disease worldwide. The cytoadherence and cytotoxicity upon the vaginal epithelial cells are crucial for the infection. Extracellular nucleotides are released during cell damage and, along with their nucleosides, can activate purinoceptors. The opposing effects of nucleotides versus nucleosides are regulated by ectonucleotidases. Herein we evaluated the hemolysis and cytolysis induced by T. vaginalis, as well as the extracellular nucleotide hydrolysis along with the effects mediated by nucleotides and nucleosides on cytotoxicity. In addition, the gene expression of purinoceptors in host cells was determined. The hemolysis and cytolysis exerted by all T. vaginalis isolates presented positive Pearson correlation. All T. vaginalis isolates were able to hydrolyze nucleotides, showing higher NTPDase than ecto-5′-nucleotidase activity. The most cytotoxic isolate, TV-LACM6, hydrolyzes ATP, GTP with more efficiency than AMP and GMP. The vaginal epithelial cell line (HMVII) expressed the genes for all subtypes of P1, P2X and P2Y receptors. Finally, when nucleotides and nucleosides were tested, the cytotoxic effect elicited by TV-LACM6 was increased with nucleotides. In contrast, the cytotoxicity was reversed by adenosine in presence of EHNA, but not by guanosine, contributing to the understanding of the purinergic signaling role on T. vaginalis cytotoxicity.     

Interconversion and uptake of nucleotides, nucleosides, and purine bases by the marine bacterium MB22.

Whole cells and isolated membranes of the marine bacterium MB22 converted nucleotides present in the external medium rapidly into nucleosides and then into bases. Nucleosides and purine bases formed were taken up by distinct transport systems. We found a high-affinity common transport system for adenine, guanine, and hypoxanthine, with a Km of 40 nM. This system was inhibited noncompetitively by purine nucleosides. In addition, two transport systems for nucleosides were present: one for guanosine with a Km of 0.8 microM and another one for inosine and adenosine with a Km of 1.4 microM. The nucleoside transport systems exhibited both mixed and noncompetitive inhibition by different nucleosides other than those translocated; purine and pyrimidine bases had no effect. The transport of nucleosides and purine bases was inhibited by dinitrophenol or azide, thus suggesting that transport is energy dependent. Inside the cell all of the substrates were converted mainly into guanosine, xanthine, and uric acid, but also anabolic products, such as nucleotides and nucleic acids, could be found.     

The Synthesis of Novel Regioisomeric Ring-Expanded Xanthine Nucleosides Containing The 5:7-Fused Imidazo[4,5-e][1,2,4]Triazepine Ring System

Abstract

The syntheses of novel regioisomeric ring-expanded purine nucleosides containing the imidazo[4,5-e][1,2,4]triazepine nucleus are reported. The glycosylation of the heterocycle 3,4,6,7-tetrahydroimidazo[4,5-e][1,2,4]triazepine-5,8-dione (2a) by the stannic chloride procedure gave nucleosides 3 and 4, with the sugar moiety attached at the 7-and 3-positions of the heterocycle, respectively. On the other hand, the mercuric cyanide procedure for glycosylation of 2a yielded nucleosides 4 and 5, with the sugar attached at the 1-position in the latter. In either procedure, 4 was the minor isomer and was obtained only in trace amounts. While debenzoylation of 3 and 5 provided the respective parent nucleosides 8 and 10, that of 4 resulted in ring-opening to produce 9. Attempted enzymic glycosylation of 2a with purine nucleoside phosphorylase failed to yield any nucleoside product.     

Synthesis of 1,2,4-triazole C-nucleosides from hydrazonyl chlorides and nitriles

A series of 1,3-diaryl-5-(2,3,5-tri-O-benzoyl-beta-D-ribofuranosyl)-1H-1,2,4-triazole nucleosides (3a-f) were synthesized via the intermolecular cyclization of hydrazonyl chlorides with peracylated ribofuranosyl cyanide catalyzed by Yb(OTf)3 or AgNO3, respectively. Similarly, the 1,2,4-triazole of glucopyranosyl C-nucleosides 5a,b were prepared from the hydrazonyl chlorides and the nitrile 4. Alternatively, the 1,2,4-triazole N-nucleoside 8 was obtained from cyclization of the unsymmetrical bis[alpha-(4-methoxyphenyl)aminobenzylidene]-hydrazine with peracylated 1-amino-D-manno-pentitol.     

The pitfalls of molecular phylogeny based on four species,as illustrated by the Cetacea/Artiodactyla relationships

We study the reliability of phylogeny based on four taxa, when the internal, ancestral, branch is short. Such a quartet approach has been broadly used for inferring phylogenetic patterns. The question of branching pattern between the suborders Ruminantia and Suiformes (order Artiodactyla) and the order Cetacea is chosen as an example. All the combinations of four taxa were generated by taking on and only one species per group under study (three ingroups and one outgroup). Using real sequences, the analysis of these combinations demonstrates that the quartet approach is seriously misleading. Using both maximum parsimony and distance methods, it is possible to find a quartet of species which provided a high bootstrap proportion for each of the three possible unrooted trees. With the same set of sequences, we used all the available species simultaneously to construct a molecular phylogeny. This approach proved much more reliable than the quartet approach. When the number of informative sites is rather low, the branching patterns are not supported through bootstrap analysis, preventing us from false inference due to the lack of information. The reliable resolution of the phylogenetic relationships among Ruminantia, Suiformes, and Cetacea will therefore require a large number of nucleotides, such as the complete mitochondrial genomes of at least 30 species.     

Preparation of cyclic nucleotide antisera with thyroglobulin-cyclic nucleotide conjugates

Antisera to cyclic AMP and cyclic GMP were obtained by immunizing rabbits with antigens prepared by conjugating the 2'0-succinyl derivative of the cyclic nucleotides to thyroglobulin. The cyclic nucleotide-thyroglobulin conjugates were injected intradermally into multiple sites on the backs of the animals. This immunization procedure resulted in the production of antiserum in four of five animals capable of binding at a final serum dilution of greater than 1:10,000, 20% of the corresponding iodinated cyclic nucleotide derivative added. The antisera were also highly specific. The antiserum for cyclic AMP had a 2500-fold or greater relative affinity for cyclic AMP than other nucleotides or nucleosides, while that for cyclic GMP had a 5000-fold or greater affinity for 2'0 acetylated nucleotides or nucleosides except for acetylated cyclic IMP. The obstacles to measuring cyclic nucleotides, particularly cyclic GMP, in tissues were also overcome by refining and simplifying the methods for iodination, purification and assay. Furthermore, a "disequilibrium" incubation was developed as an alternative to the acetylation method to increase the sensitivity of the radioimmunoassay. Thus, the levels of both cyclic GMP and cyclic AMP can be determined rapidly and easily in the same tissue sample.     

Synthesis of 5-Mercaptocytosine Nucleosides and Nucleotides

Abstract

The synthesis of a series of new nucleosides and nucleotides, including ribo-, 2-deoxyribo- and arabinofuranosides of 5-sulfur-substituted cytosines, is described. The synthetic methods employed involve 5-thiolation of the appropriate cytosine or 5-bromocytosine nucleosides and nucleotides, or alternatively, 4-thiation followed by amination of the corresponding protected 5-(S-benzyl)mercaptouracil nucleosides and subsequent deblocking with sodium and liquid ammonia.     

Synthesis of (2'S)- and (2'R)-2'-deoxy-2'-[(2-methoxyethoxy)amino] pyrimidine nucleosides and oligonucleotides

Syntheses of specified 2'-modified nucleosides were achieved: a) via oximation of the 5',3'-blocked 2'-oxocytidine, followed by reduction, or b) by intramolecular nucleophilic addition of 3'-(2-methoxyethoxy)carbamate to the 2'-position with opening of O(2),2'-anhydrouridine. For the first time, 3'-phosphoroamidites of these 2'-modified nucleosides were successfully incorporated into oligonucleotides by solid-phase synthesis. Incorporation of 2'-modified nucleotides into oligodeoxyribonucleotides had a negative effect on the duplex T(m) values with the DNA or RNA complements. Nevertheless, modified nucleotides have shown good target recognition; the (S)-isomer binds preferably to RNA and the (R)-isomer to DNA. Both modified nucleosides significantly increased nuclease resistance of the oligodeoxyribonucleotides.     

Use of automated chromatography on the amino acid analyzer with lithium citrate buffers to separate nucleic acid bases, nucleosides, nucleotides and their precursors

A simple and sensitive method has been developed to separate nucleic acid bases, nucleosides, nucleotides and their precursors by automated chromatography using the amino acid analyzer with lithium citrate buffers. The method is sensitive to a concentration of 5 nmol, linear in the range of 5--100 nmol, and resolves almost all the bases, nucleosides, nucleotides and their precursors of physiologic importance.     

Functionalization of pyrimidine and purine nucleosides at C4 and C6: C-nucleophilic substitution of their C4- and C6-(1,2,4-triazol-1-yl) derivatives

A study of C-nucleophilic substitution at the C4-position on pyrimidine and C6-position on 2'-deoxyguanosine to produce novel nucleosides is presented with the spectroscopic properties of their respective substitution products. C4-(1,2,4-triazol-1-yl) pyrimidine nucleosides 1 were treated with nitroalkanes, malononitrile, acetylacetone, ethyl nitroacetate, acetoacetate and cyanoacetate at 100 degrees C in dioxane in the presence of DBU resulting in the production of novel nucleosides 2-11. To explore the application of this methodology to purine chemistry, this approach was used to produce novel analogs from 2'-deoxyguanosine. We found that the triazolo derivative 12 undergoes C-nucleophilic substitution with nitromethane, malononitrile, acetylacetone, ethyl nitroacetate and cyanoacetate in the presence of potassium carbonate (K2CO3) in DMF at 100 degrees C to give novel nucleosides 13-17.     

Metabolic pool of purine compounds in erythrocytes of mice during growth of transplanted tumors

The pattern of purine derivatives was studied in the erythrocytes of C3HA and ICR mice during Hepatoma 22 and Ehrlich ascites tumor cells growth. Host erythrocytes purine nucleotides, nucleosides and bases were affected by the implanted tumors. The results indicated that the host erythrocytes markedly concentrated adenine and guanine nucleotides on the 5th and 11th-12th day of tumor growth. By contrast, content of nucleosides and bases were sharply decreased during the log growth phase (5th day) with the restoring of these precursors within the 11th-12th day (plateau phase). These observations indicate that aspects of the purine compounds metabolism in host erythrocytes are linked with tumor development.