Synthesis of morpholine nucleoside triphosphates

Triphosphates of all four ribonucleoside derived morpholine subunits were synthesized and characterized by ¹H and ³¹P NMR, UV and mass spectroscopy.     

Ionic-tag-assisted synthesis of nucleoside triphosphates

We describe an ionic-tag-assisted synthesis of nucleoside triphosphates that combines the advantage of one-pot triphosphate formation and liquid-phase extraction.     

Enzyme-catalyzed synthesis of nucleoside triphosphates from nucleoside monophosphates

Syntheses of adenosine 5′-triphosphate (ATP) from adenosine 5′-monophosphate (AMP) and ribavirin 5′-triphosphate (RTP) from ribavirin 5′-monophosphate (RMP) (1) were performed using enzymes as catalysts. Synthesis of ATP is based on acetyl phosphate as the phosphate donor, and acetate kinase (Bacillus stearothermophilus, EC 2.7.2.1), adenylate kinase (porcine muscle, EC 2.7.4.3), and inorganic pyrophosphatase (yeast, EC 2.6.1.1) as the catalysts. Three reactions on a 150-mmol scale provided ATP as its barium salt in 82% yield and 67% purity. Synthesis of RTP used phosphoenol pyruvate (PEP) as the phosphate donor, and pyruvate kinase (rabbit muscle, EC 2.7.1.40) and adenylate kinase (rabbit muscle) as the catalysts. A gram-scale reaction provided RTP as its barium salt in 93% yield and 97% purity. This work demonstrates the utility of the autoxidationresistant acetate kinase fromB. stearothermophilus, the value of pyrophosphatase in controlling the level of pyrophosphate in the reactions and the ability of adenylate kinase to accept at least one substrate other than a derivative of adenosine.     

Synthesis, DNA polymerase incorporation, and enzymatic phosphate hydrolysis of formamidopyrimidine nucleoside triphosphates

The nucleoside triphosphates of N6-(2-deoxy-alpha,beta-d-erythro-pentofuranosyl)-2,6-diamino-4-hydroxy-5-formamidopyrimidine (Fapy.dGTP) and its C-nucleoside analogue (beta-C-Fapy.dGTP) were synthesized. The lability of the formamide group required that nucleoside triphosphate formation be carried out using an umpolung strategy in which pyrophosphate was activated toward nucleophilic attack. The Klenow fragment of DNA polymerase I from Escherichia coli accepted Fapy.dGTP and beta-C-Fapy.dGTP as substrates much less efficiently than it did dGTP. Subsequent extension of a primer containing either modified nucleotide was less affected compared to when the native nucleotide is present at the 3'-terminus. The specificity constants are sufficiently large that nucleoside triphosphate incorporation could account for the level of Fapy.dG observed in cells if 1% of the dGTP pool is converted to Fapy.dGTP. Similarly, polymerase-mediated introduction of beta-C-Fapy.dG could be useful for incorporating useful amounts of this nonhydrolyzable analogue for use as an inhibitor of base excision repair. The kinetic viability of these processes is enhanced by inefficient hydrolysis of Fapy.dGTP and beta-C-Fapy.dGTP by MutT, the E. coli enzyme that releases pyrophosphate and the corresponding nucleoside monophosphate upon reaction with structurally related nucleoside triphosphates.     

A novel method for the preparation of nucleoside triphosphates from activated nucleoside phosphoramidates

[reaction: see text] A novel method for the preparation of nucleoside triphosphates has been developed. The strategy employs a highly reactive pyrrolidinium phosphoramidate zwitterion intermediate that undergoes efficient coupling with tris(tetra-n-butylammonium) hydrogen pyrophosphate to generate nucleoside triphosphate.     

Glycerol nucleoside triphosphates: synthesis and polymerase substrate activities

[Structure: see text] The synthesis of (S)-glycerol nucleoside triphosphates (gNTPs) and the analysis of their substrate activities for enzymatic polymerization is described. NTPs with simplified carbohydrate backbones such as the tNTPs (alpha-L-threose-NTPs) are polymerase substrates and offer the potential to create non-natural aptamer sequences with simplified backbones through enzymatic means. The acyclic (S)-GNA was modeled after the shortened alpha-threofuranosyl backbone. Here we describe the synthesis of (S)-glycerol NTPs and initial enzymatic testing of this further simplified nucleic acid backbone.     

Stereocontrolled Synthesis of Oligo(nucleoside phosphorothioate)s

Encouraging results obtained for modulation of gene expression by antisense oligonucleotides and their analogues have kindled hopes for a new generation of therapeutics against viral infections, cancer, and many other diseases. Among such analogues, oligo(nucleoside phosphorothioate)s (Oligo-S) have generally shown the highest efficacy in inhibiting the biosynthesis of “unwanted” proteins. The first clinical trials of antisense agents are now in progress using Oligo-S against genital warts and acute myeloid leukemia, and tests of Oligo-S against AIDS should follow soon. Nevertheless, their mechanism of action, internalization, cellular trafficking, subcellular localization, and interaction with cellular proteins is still poorly understood. It is assumed a priori that application involves rapid and efficient molecular recognition of target RNA by Oligo-S; however, the effects of the chirality of Oligo-S have so far been unappreciated, because Oligo-S has not yet been synthesized with stereocontrol. Indeed, the diastereomeric composition of Oligo-S has never been determined, primarily because of the lack of appropriate analytical methods. Since each of the diastereomers is a stereochemically unique chemical entity, questions arise as to which diastereomer is responsible for an observed biological response, including positive (curative) or possibly negative (toxic) side effects. In this review we intend provide a perhaps somewhat speculative assessment of the problems associated with the stereo-controlled synthesis of Oligo-S and to discuss the state-of-the-art in this field including strategies that may lead to Oligo-S of predetermined chirality. This article is not intended to discourage researchers from further studies of dia-steromeric mixtures of Oligo-S as potential pharmaceuticals. Throughout the history of medicinal chemistry numerous useful medicines were discovered, developed, and employed without the detailed knowledge of their structure. Indeed, the composition of the vaccines discovered by Pasteur is a subject of vigorous study still today.     

Novel synthesis of nucleoside 5'-phosphoramidates through reaction of nucleoside triphosphates with amines mediated by trimethylsilyl chloride

Reaction of nucleoside triphosphates (NTPs) with amines in pyridine mediated by trimethylsilyl chloride produced nucleoside 5'-phosphoramidates in moderate yields without any preprotection of nucleosides and amino acid methyl esters. The reaction pathway is very similar to the mechanism of the RNA capping reaction, DNA or RNA ligation reaction, and catalysis of hydrolases and nucleases involving the formation of covalent enzyme-NMP (nucleoside 5'-monophosphate) intermediates in biological systems, which could provide a valuable clue for the enzymatic reactions.     

Mechanisms of enzymatic hydrolysis of nucleoside triphosphates by quantum and molecular mechanics

Results of simulation of the mechanism of hydrolysis of adenosine triphosphate and guanosine triphosphate in protein matrices, as well as of deprotonated methyl triphosphate in water clusters by quantum and molecular mechanics with separation of the reaction system into conformationally flexible effective fragments are discussed.     

Synthesis of nucleoside mono- and triphosphates bearing oligopyridine ligands, their incorporation into DNA and complexation with transition metals

Modified nucleoside mono- (dA(R)MPs and dC(R)MPs) and triphosphates (dA(R)TPs and dC(R)TPs) bearing bipyridine or terpyridine ligands attached via acetylene linker were prepared by single-step aqueous-phase Sonogashira cross-coupling of 7-iodo-7-deaza-dAMP or -dATP, and 5-iodo-dCMP or -dCTP with the corresponding bipyridine- or terpyridine-linked acetylenes. The modified dN(R)TPs were successfully incorporated into the oligonucleotides by primer extension experiment (PEX) using different DNA polymerases and the PEX products were used for post-synthetic complexation with Fe(2+).     

Hydrophilic interaction chromatography of nucleoside triphosphates with temperature as a separation parameter

Eight deoxynucleoside triphosphates (dNTPs) and nucleoside triphosphates (NTPs): ATP, CTP, GTP, UTP, dATP, dCTP, dGTP and dTTP, were separated with two 15 cm ZIC-pHILIC columns coupled in series, using LC-UV instrumentation. The polymer-based ZIC-pHILIC column gave significantly better separations and peak shape than a silica-based ZIC-HILIC column. Better separations were obtained with isocratic elution as compared to gradient elution. The temperature markedly affected the selectivity and could be used to fine tune separation. The analysis time was also affected by temperature, as lower temperatures surprisingly reduced the retention of the nucleotides. dNTP/NTP standards could be separated in 35 min with a flow rate of 200 μL/min. In Escherichia coli cell culture samples dNTP/NTPs could be selectively separated in 7 0min using a flow rate of 100 μL/min.     

Cross-coupling reactions of unprotected halopurine bases, nucleosides, nucleotides and nucleoside triphosphates with 4-boronophenylalanine in water. Synthesis of (purin-8-yl)- and (purin-6-yl)phenylalanines

An expeditious and highly efficient single-step methodology for the introduction of a phenylalanine moiety into position 8 and 6 of the purine scaffold was developed based on aqueous-phase Pd-catalysed Suzuki-Miyaura cross-coupling reactions of unprotected 4-boronophenylalanine with 8-bromo- or 6-chloropurines. The scope of the methodology was demonstrated by syntheses of unprotected (adenin-8-yl)phenylalanine base, nucleosides, nucleotides and nucleoside triphosphates as well as (purin-6-yl)phenylalanine base and nucleosides. All these products were obtained in high yields and in optically pure form.     

Separation of nucleoside mono-, di- and triphosphates by capillary electrophoresis via cadmium complexation

Summary The CE separation of twelve nucleotides (5′-mono-, di-, triphosphates of adenosine, guanosine, cytidine and uridine) was improved by adding cadmium ion to the ammonium citrate/citric acid buffer (pH 5, ionic strength 100 mM). Cadmium ion acts as a complexing agent for some nucleotides (ATP, CTP, GTP, UTP, GDP). In order to accelerate the separation, the electroosmotic flow was reversed by flushing the fused-silica capillary with 0.2 % aqueous solution of the polycationic surfactant hexadimethrine bromide. A good separation of the twelve nucleotides studied was then achieved on a dynamically coated capillary in less than 5 min by using an ammonium citrate/citric acid buffer (pH 5, ionic strength 100 mM) to which 2 mM cadmium ion has been added. High peak efficiencies were obtained (210 000 theoretical plates) and the resolution between two adjacent peaks was always greater than 1.5.     

Synthesis of enzymatically and chemically non-hydrolyzable analogues of dinucleoside triphosphates Ap(3)A and Gp(3)G.

Dinucleoside polyphosphates are ubiquitous compounds tightly involved in the regulation of a number of key biological processes. Hydrolysis-resistant analogues of Ap(3)A and Gp(3)G, two important members of that family of nucleotides, have been synthesized. P(1),P(2):P(2),P(3)-Bis-methylene diadenosine and diguanosine triphosphates were prepared from O,O-dialkyl methaneselenophosphonates using an original methodology. Whereas the 2-fold addition of the methanephosphonate anion to the activated phosphorus species cannot be performed, multiple condensation of lithiated methaneselenophosphonate with electrophilic trivalent phosphorus compounds is revealed to be very effective. A one-pot condensation/esterification/oxidation sequence involving O,O-dialkyl methaneselenophosphonates provides a highly efficient route to the PCH(2)PCH(2)P backbone. This new development in selenophosphonate chemistry offers a great potential for further regioselective functionalization of polyphosphate mimics.     

Field desorption and fast atom bombardment mass spectrometry of pyridine nucleotides and nucleoside triphosphates

Summary The complete mass spectra of nicotinamide mononucleotide (free acid), -nicotinamide adenine dinucleotide (free acid and lithium salt), dihydronicotinamide adenine dinucleotide (disodium salt), nicotinamide adenine dinucleotide phosphate (disodium salt) and adenosine-5- triphosphate (disodium salt) are introduced. The first comparison of field desorption and fast atom bombardment mass spectrometry of these biologically active phosphates is reported. A critical evaluation of the merits and pitfalls of both soft ionization methods for the investigations of pyridine nucleotides and nucleoside triphosphates is given. In particular, the experimental difficulties for ionic desorption of organic phosphates in FD-MS and the basic problems of chemical noise as well as matrix/substance-interaction in FAB-MS are discussed.

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Felddesorptions- und Fast Atom Bombardment-Massenspektrometrie von Pyridin-Nucleotiden und Nucleosid-Triphosphaten

Zusammenfassung Erstmals werden die kompletten Massenspektren von Nicotinamid-Mononucleotid (freie Säure), -Nicotinamid-Adenin-Dinucleotid (freie Säure und Lithiumsalz), Dihydronicotinamid-Adenine-Dinucleotid (Dinatriumsalz), Nicotinamid-Adenin-Dinucleotidphosphat (Dinatriumsalz) und Adenosin-5-triphosphat (Dinatriumsalz) vorgestellt. Über einen ersten Vergleich der Felddesorptions- und Fast Atom Bombardment-Massenspektrometrie von diesen biologisch aktiven Phosphaten wird berichtet. Eine kritische Wertung der Vor- und Nachteile der beiden schonenden Ionisierungsverfahren für die Untersuchungen von Pyridin-Nucleotiden und Nucleosid-Triphosphaten wird gegeben. Insbesondere werden die experimentellen Schwierigkeiten der ionischen Desorption von organischen Phosphaten bei der FD-MS und die grundsätzlichen Probleme des chemischen Untergrundes sowie der Matrix/Substanz-Wechselwirkung bei FAB-MS angesprochen.

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Mass Spectrometry of Nucleotides, VIII. — For Part VII see Reference [1]     

Synthesis of nucleoside tetraphosphates and dinucleoside pentaphosphates from nucleoside phosphoropiperidates via the activation of P(V)-N bond

A novel and efficient method for the preparation of nucleoside 5’-tetraphosphates has been developed by coupling nucleoside 5’-phosphoropiperidates with triphosphate reagent in the presence of 4,5-dicyanoimidazole(DCI) activator.Further coupling of the nucleoside 5’-tetraphosphates with nucleoside 5’-phosphoropiperidates via the P(V)-N activation strategy provided a reliable synthetic method for both symmetrical and asymmetrical dinucleoside pentaphosphates.     

Ferrocenylethynyl derivatives of nucleoside triphosphates: synthesis, incorporation, electrochemistry, and bioanalytical applications

Modified dATP (2'-deoxyadenosine-5'-triphosphate) and dUTP (2'-deoxyuridine-5'-triphosphate) bearing ferrocene (Fc) labels linked via a conjugate acetylene spacer were prepared by single-step aqueous-phase cross-coupling reactions of 7-iodo-7-deaza-dATP or 5-iodo-dUTP with ethynylferrocene. The Fc-labeled dNTPs were good substrates for DNA polymerases and were efficiently incorporated to DNA by primer extension (PEX). Electrochemical analysis of the 2'-deoxyribonucleoside triphosphates (dNTPs) and PEX products revealed significant differences in redox potentials of the Fc label bound either to U or to 7-deazaA and between isolated dNTPs and conjugates incorporated to DNA. Prospective bioanalytical applications are outlined.     

A highly selective and sensitive fluorescence sensing system for distinction between diphosphate and nucleoside triphosphates

Among the numerous chemosensors available for diphosphate (P(2)O(7)(4-), PPi) and nucleoside triphosphates (NTPs), only a few can distinguish between PPi and NTPs. Hence, very few bioanalytical applications based on such selective chemosensors have been realized. We have developed a new fluorescence sensing system for distinction between PPi and NTPs based on the combination of two sensors, a binuclear Zn(II) complex (1·2Zn) and boronic acid (BA), in which one chemosensor (1·2Zn) shows signal changes depending on the PPi (or NTP) concentration, and the other (BA) blocks the signal change caused by NTPs; this system enables the distinction of PPi from NTPs and is sensitive to nanomolar concentrations of PPi. The new sensing system has been successfully used for the direct quantification of RNA polymerase activity.