Efficient Synthesis of 8-Thiosubstituted Guanine Derivatives as Potential Tools for Biochemical and Biological Studies

Abstract

A method for the selective introduction of the N²-(dimethylamino)methylene group into 8-thio-9-(2-hydroxyethoxymethyl)guanine (1) has been developed. The effect of the N²-amidine protection on the S-alkylation of 1 was studied.     

Synthesis of 1,5-Anhydro-D-Mannitol Nucleosides with a Purine Base Moeety

Abstract

D-Mannitol nucleosides with a purine base moiety have been conveniently synthesized strating from 1,5-anhydro-4,6-O-benzylidene-D-glucitol. The 3-OH function of 1,5-anhydro-4,6-O-benzylidene-D-glucitol was selectively protected with t-butyldimethylsilyl group and subsequently converted to the corresponding 0-triflate derivative for the introduction of the nucleobase moietes. These nucleoside derivatives were transformed to 1,5-Anhydro-6-O-MMTr-2-(N⁶-benzoyladenin-9-yl)-2-deoxy-3-O-TBDMS-D-mannitol and 1,5-Anhydro-6-O-MMTr-2-(N²-isobutyryl-guanin-9-yl)-2-deoxy-3-O-TBDMS-D-mannitol, useful as the building blocks for oligonucleotide synthesis. Also, the synthesis of the corresponding fully deprotected anhydrohexitol nucleosides were achieved for evaluation of antiviral activity test.     

Structures and stability of N<Subscript>13</Subscript><Superscript>+</Superscript> and N<Subscript>13</Subscript><Superscript>−</Superscript> clusters

The structures and stabilities of eleven N₁₃ ⁺ and N₁₃ ^– isomers have been investigated with second-order Møller–Plesset (MP2) and density functional theory (DFT) methods. Five N₁₃ ⁺ isomers and six N₁₃ ^– isomers are all reasonable local minima on their potential energy hypersurfaces. The most stable N₁₃ ⁺ cation is structure C-2 with C_2v symmetry, which contains a pentazole ring and two N₄ open chains. It is different from those of the N₇ ⁺ and N₉ ⁺ clusters, but similar to the N₁₁ ⁺ cluster. Meanwhile, the most stable N₁₃ ^– structure A-2 is composed of a pentazole ring and a six-membered ring connected by two nitrogen atoms. It is not only different from those of the N₇ ^– and N₉ ^– clusters, but also from the N₁₁ ^– cluster. The decomposition pathways of structures C-2 and A-2 were investigated at the B3LYP/(aug)-cc-pVDZ level. From the barrier heights of the structures C-2 and A-2 decomposition processes, it is suggested that C-2 is difficult to observe experimentally and A-2 may be observed as a short-lived species. Figure Optimized geometrical parameters of N₁₃ ⁺ isomer C-2      

Oligonucleotides With Purine Nitrogen-7 as Glycosylation Site

Abstract

The synthesis of phosphoramidites (2 and 3) derived from hypoxanthine and isoguanine N⁷-2¹-deoxyribonucleosides is described. Solid-phase synthesis furnishes oligonucleotides containing N⁷-glycosylated purines. New base pairs between purine N⁷- and N9-nucleosides are proposed.     

Aminolysis of 2′-Deoxyinosine Aryl Ethers: Nucleoside Model Studies for the Synthesis of Functionally Tethered Oligonucleotides

Abstract

Several O⁶-aryl-2′-deoxyinosines were synthesized and found to undergo conversion to N⁶-substituted-2′-deoxyadenosines upon treatment with aqueous amines. The kinetics for reaction of these nucleosides with various amines suggests that O⁶-phenyl- and O⁶-(p-nitrophenyl)-2′-deoxyinosine are suitable “convertible nucleoside” precursors for the site-specific introduction of functionally tethered 2′-deoxyadenosines into DNA.     

Production of N 2 O by Ammonia Oxidizing Bacteria at Subfreezing Temperatures as a Model for Assessing the N 2 O Anomalies in the Vostok Ice Core

It was suggested that the abnormally high N ₂ O values found in 130,000–160,000 year-old Vostok ice core samples, characterized by high δ ¹⁵ N and low δ ¹⁸ O values, resulted from in situ microbial N ₂ O production. To substantiate these observations we obtained new geochemical data from the last glacial period and showed the existence of additional small N ₂ O anomalies. To test the hypothesis that microbial metabolism could contribute to these anomalies, we developed protocols for examining the ability of Nitrosomonas cryotolerans cells to produce N ₂ O at subfreezing temperatures. Our results show that these model, frozen cultures produce N ₂ O at temperatures as low as ?32°C.     

An Efficient Synthesis Of Acyclic N7- and N9-Adenine Nucleosides Via Alkylation With Secondary Carbon Electrophiles to Introduce Versatile Functional Groups At the C-1 Position of Acyclic Moiety

The introduction of versatile functional groups, allyl and ester, at the C-1 position of the acyclic chain in acyclic adenine nucleosides was achieved for the first time directly by alkylation of adenine and N⁶-protected adenine. Thus, the C-1′-substituted N⁹-adenine acyclic nucleoside, adenine-9-yl-pent-4-enoic acid ethyl ester (11), was prepared by direct alkylation of adenine with 2-bromopent-4-enoic acid ethyl ester (6), while the corresponding N⁷-regioisomer, 2-[6, (dimethylaminomethyleneamino)-purin-7-yl]-pent-4-enoic acid ethyl ester (10), was obtained in one step by the coupling of N,N-dimethyl-N′- (9H-purin-6-yl)-formamidine (9) with 2-bromopent-4-enoic acid ethyl ester (6). The functional groups, ester and allyl, were converted to the desired hydroxymethyl and hydroxyethyl groups, and subsequently to phosphonomethyl derivatives and corresponding pyrophosphorylphosphonates.     

Synthesis,Molecular Conformation and Activity Against Herpes Simplex Virus of (E)-5-(2-Bromovinyl)-2′-Deoxycytidine Analogs

Analogs of (E)-5-(2-bromovinyl)-2 ′-deoxycytidine (BrVdCyd) (1) by substitution at N⁴ were synthesized to impart resistance against deamination. The anti-HSV-1 activity and solution conformation of these analogs were determined. N⁴-Acetyl-BrVdCyd (2) was a potent inhibitor of HSV-1 replication whereas N⁴-propanoyl-BrVdCyd (3) had good activity and N⁴-Butanoyl-BrVdCyd (4) had only low activity against HSV-1 replication. N⁴-Methyl-BrVdCyd (5) was devoid of activity against HSV-1.     

N6-methyl adenosine in siRNA evades immune response without reducing RNAi activity

Abstract

siRNA is a powerful method to suppress specific gene expression and has recently been utilized for molecular biology as well as medicine. However, introduction of dsRNA stimulates immune-responses as side-effects. In the present study, we utilized N⁶-methyl adenosine, one of the natural modified nucleosides, instead of adenosine in siRNA. When adenosine in the passenger or guide strand of siRNA was completely replaced with N⁶-methyl adenosine, the immune response against siRNA was evaded without any reduction in RNAi activity. This knowledge will promote the medical application of siRNA and enhance our understanding on cellular discrimination of non-self and self dsRNA.     

9-(2-Deoxy-ß-D-xylofuranosyl)adenine and 1-(2-Deoxy-ß-D-xylofuranosyl)thymine: Phosphorylation and Stability

Abstract

Phosphorylation of 1-(2-deoxy-β-D-xylofuranosyl)thymine (1) or 9-(2-deoxy-β-D-xylofuranosyl)adenine (3) with phosphoryl chloride gives the cyclic 3′,5′-phosphates (2 and 4a) but not the 5′-monophosphates 8a or 8b. The latter are obtained by phosphorylation of the 3′-0-benzoylated 2′-deoxy-β-D-xylonucleosides (7a, b) and subsequent base-catalyzed removal of the benzoyl groups. Compound 3, as the parent dA, depurinates in acidic medium, a reaction which is facilitated in the case of the N⁶-benzoyl derivative 9b and reduced after the introduction of an amidine protecting group. N-Glycosylic bond hydrolysis of 2′-deoxy-β-D-xylofuranosyl nucleosides is enhanced by a factor of two compared to 2′-deoxy-β-D-ribofuranosyl nucleosides.     

Tautomerism,Protonation, and Ionization of Formycin in Aqueous Solution by the pH Dependence of 13C Chemical Shifts and 13C-1H Coupling Constants

Abstract

Analyses of the pH dependence of ¹³C chemical shifts and ¹³C-¹H coupling constants of formycin in aqueous soluion revealed two pKa′s, at 4.4 and 9.7, corresponding to a protonation at N₄ and an ionization at N₁. The N₄-protonation results in the transfer of a pyrazolo ring hydrogen from N₂ to N₂-At physiological pH, formycin was found to exist as a mixture of N₁H and N₂H tautomers, with the former being predominant (>94%).     

Determination of N6-Threoninocarbonyladenosine,N2, N2-Dimethylguanosine,Pseudouridine and Other Ribonucleosides in Human Breast Milk

Abstract

Seven modified ribonucleosides from degraded tRNA and rRNA were quantified in milk from mothers with preterm infants. The amounts of N⁶-threoninocarbonyladenosine, N², N²-dimethylguanosine and pseudouridine supplied in the milk have been estimated and related to the respective urinary amounts excreted by preterm infants.     

N6-Alkylthiomethyl and N6-Arylthiomethyl Derivatives of Adenosine and Their Cytokinin Activity

Five new derivatives of adenosine, N⁶-[(1-methylethyl)thiomethyl]-(1), N⁶-methyithiomethyl-(2), N⁶-phenylthiomethyl-(3), N⁶-[(3-amino-3-carboxypropyl)thiomethyl]-(4), and N⁶-[(2-amino-2-carboxyethyl)thiomethyl]adenosine (5), were synthesized and their cytokinin activity was tested in the Amaranthus betacyanin assay and the soybean callus growth.

1, 2, and 3 were active in the former assay and all five compounds were active in the latter assay. The activities of the compounds were, however, weaker than those of the reference derivatives, in which Sulfides were replaced by methylenes, N⁶-isopentyl-, N⁶-n-propyl-, N⁶-benzyl-, and N⁶-(5-amino-5-carboxypentyl)adenosine. This fact indicates that the sulfide structure introduced into the N⁶-side chains had the effect of reducing cytokinin activity.     

SYNTHESIS AND BASE PAIRING PROPERTIES OF 9-DEAZAPURINE N7-NUCLEOSIDES IN OLIGONUCLEOTIDE DUPLEXES AND TRIPLEXES

The 9-deazaguanine N⁷-2′-deoxyribofuranoside (3) as well as the bromo and iodo derivatives 4a,b were synthesized and incorporated in oligonculeotide duplexes and triplexes. Their base pairing properties were investigated and compared with those of the parent purine N⁷-2′-deoxyribofuanosides.     

N2-Substituted-2′-deoxyguanosine 5′-Triphosphates as Substrates for E. coli DNA Polymerase I

Abstract

Several N²-alkyl and N²-phenyl 2′-deoxyguanosine 5′-triphosphates and 2-bromo-2′-deoxyinosine 5′-triphosphate were synthesized and tested as substrates for E. coli DNA polymerase I with a template: primer system requiring incorporation of 85 nucleotides. N²-Methyl-dGTP and N²-ethyl-dGTP were found to be efficiently incorporated in place of dGTP to give full length product. N²-n-Hexyl-dGTP supported limited full length synthesis at high concentration, but N²-phenyl- and N²-(p-n-butylphenyl)-dGTP were poor substrates. 2-Bromo-2′-deoxyinosine 5′-triphosphate was a good substrate for pol I, and it was a replacement only for dGTP. Melting temperatures of oligodeoxyribonucleotides containing N²-alkyl-dG residues, annealed to complementary single stranded DNA, were lower than that of the normal oligomer.     

Regioselective Synthesis of Indazole N 1‐ and N 2‐(β‐d‐Ribonucleosides)

The regioselective synthesis of 4‐nitroindazole N ¹‐ and N ²‐(β‐d‐ribonucleosides) (8, 9, 1b and 2b) is described. The N ¹‐regioisomers are formed under thermodynamic control of the glycosylation reaction [fusion reaction or Silyl Hilbert‐Johnson glycosylation for 48 h (66%)], while the kinetic control (Silyl Hilbert‐Johnson glycosylation for 5 h) afforded only the N ²‐isomer (64%). The structures of the nucleosides 1b and 2b were assigned by single crystal X‐ray analyses. The 4‐amino‐N ¹‐(β‐d‐ribofuranosyl)‐1H‐indazole (3b) was obtained from the nitro nucleoside 1b by catalytic hydrogenation. Compound 3b shows fluorescence while the 4‐nitroindazole nucleosides 1b and 2b do not possess this property.     

An Efficient Method for the Synthesis of β-d-Ribonucleosides Catalyzed by Metal Iodides

Abstract

Several β-d-ribonucleosides were synthesized in high yields under mild conditions by N-glycosylations of methyl 2,3,5-tri-O-benzoyl-β-d-ribofuranosyl carbonate (1) with trimethylsilylated nucleoside bases in acetonitrile using a catalytic amount of metal iodide such as SnI₂, SbI₃ or TeI₄. A deprotection of N⁶ -benzoyl group of coupling product took place to a considerable extent when N⁶ -benzoyl-N⁶ , N⁹ -bis(trimethylsilyl)adenine was employed as a nucleoside base using SnI₂ or SnCI₂ as a catalyst while it was minimized when SbI₃ or TeI₄ was used. Further, the N-glycosylation of 1 with 7-trimethylsilyltheophylline in the presence of a catalytic amount of metal iodide was more effectively achieved in nitrile solvents other than acetonitrile.

     

Foliar δ15 N patterns are dependent on seasonal and spatial variations as shown in lowland Scottish scrub

Summary

Patterns of foliar δ¹⁵ N can suggest testable hypotheses concerning N use among and within plant species. However, both spatial and time-series sampling is required to establish how the patterns vary within and among species. On a seasonal basis, foliar δ^l5 Nrankings may change among the species compared. When symbiotic N₂-fixers are among the plants sampled, N₂-fixation may be temporally disjunct from the near-0%c, expected foliar δ¹⁵ N, which is usually attributed to N₂-fixation, and the fates of previously fixed N may not be apparent from a net foliar δ¹⁵ N of either soil or plants.     

Interaction of (2′ -5′) and (3′ -5′) Linked 2-Aminoadenylyl-3-aminoadenosines with Polyuridylic Acid

Abstract

2′-5′ and 3′-5′ linked 2-aminoadenylyl-2-aminoadenosines [(2′-5′)n²Apn²A (1) and (3′-5′)n²Apn²A (2)] were synthesized by condensation of 5′-O-monomethoxytrityl-N ² N ⁶-dibenzoyl-2-aminoadenosine and N ²,N ⁶,2′,3′-O-tetrabenzoyl-2-aminoadenosine 5′-phosphate using dicyclohexylcarbodiimide (DCC). The conformational properties of these dimers 1 and 2 were examined by UV, NMR and CD spectroscopy. The results reveal that the 2′-5′-isomer 1 takes a stacked conformation, which contains a larger base-base overlap and is more stable against thermal perturbation with respect to the 3′-5′-isomer 2. Interactions of 1 and 2 with polyuridylic acid (Poly (U)) were also examined by Tm, mixing curves, UV and CD spectra. Both the dinucleoside isomers 1 and 2 formed a complex of 1 : 2 stoichiometry with poly(U), which was much more stable than that of the corresponding ApA isomer