A simple method of the preparation of 2′-O-Methyladenosine Methylation of adenosine with methyl iodide in anhydrous alkaline medium

A simple and effective method of the methylation on the 2′-O position of adenosine is described. Adenosine is treated with CH₃I in an anhydrous alkaline medium at 0°C for 4 h. The major products of this reaction are monomethylated adenosine at either the 2′-O or 3′-O position (total of 64%) and the side products are dimethylated adenosine (2′,3′-O-dimethyladenosi, 21%, and N⁶-2′-O-dimethyladenosine, 11%). The ratio of 2′-O- and 3′-O-methyladenosine has been found to be 8 to 1. Therefore, this reaction preferentially favors the synthesis of 2′-O-methyladenosine. The monomethylated adenosine is isolated from reaction mixture by a silica gel column chromatography. Then the pure 2′-O-methyladenosine can be separated by crystallization in ethanol from the mixture of 2′-O and 3′-O-methylated isomers. The overall yield of 2′-O-methyladenosine is 42%.     

Syntheses of prodrug-type 2′-O-methyldithiomethyl oligonucleotides modified at natural four nucleoside residues and their conversions into natural 2′-hydroxy oligonucleotides under reducing condition

We previously reported that reducing-environment-responsive prodrug-type small interfering RNA (siRNA) bearing 2′-O-methyldithiomethyl (2′-O-MDTM) uridine exhibits efficient knockdown activity and nuclease resistance. In this report, we describe the preparation of 2′-O-MDTM oligonucleotides modified not only at uridine but also at adenosine, guanosine and cytidine residues by post-synthetic modification. Precursor oligonucleotides bearing 2′-O-(2,4,6-trimethoxybenzylthiomethyl) (2′-O-TMBTM) adenosine, guanosine, and cytidine were reacted with dimethyl(methylthio)sulfonium tetrafluoroborate to form 2′-O-MDTM oligonucleotides in the same manner as the oligonucleotide bearing 2′-O-TMBTM uridine. Furthermore, the oligonucleotides bearing 2′-O-MDTM adenosine, guanosine, and cytidine were efficiently converted into corresponding natural 2′-hydroxy oligonucleotides under the cytosol-mimetic reducing condition.     

Control by bacteriophage T4 of two sequential phosphorylations of the alpha subunit of Escherichia coli RNA polymerase

The effect of 2′-O-methylation upon the base-stacking properties of dinucleoside monophosphates has been studied by circular dichroism measurements over the temperature range from ?20 °C to +80 °C at high and at low salt concentration of 13 2′-O-methyl derivatives in neutral aqueous solution. It is found that 2′-O methylation generally enhances the stacking propensity of dinucleoside monophosphates except for the dimers with adenine in the 3′-linked nucleoside, where the converse trend is observed. The influence of 2′-O-methylation upon the base-stacking property of a dimer correlates in part with the effect of a reduction in salt concentration, suggesting that the 2′-O-methyl group effects the stacking by displacing ions from the immediate environment of the dimer as well as by intramolecular steric effects. The dimers which exhibit an enhanced stacking due to the 2′-O-methylation are found in a larger than statistical abundance in yeast transfer RNA, whereas those showing a reduced stacking occur in minor abundance. These observations are discussed in relation to some current views on the role of modified nucleosides in the conformation of ribonucleic acids.     

Synthesis and characterization of modified nucleotides in the 970 hairpin loop of Escherichia coli 16S ribosomal RNA

The synthesis of the 6-O-DPC-2-N-methylguanosine (m²G) nucleoside and the corresponding 5′-O-DMT-2′-O-TOM-protected 6-O-DPC-2-N-methylguanosine phosphoramidite is reported [DPC, diphenyl carbamoyl; DMT, 4,4′-dimethoxytrityl; TOM, [(triisopropylsilyl)oxy]methyl]. The availability of the phosphoramidite allows for syntheses of hairpin RNAs with site-selective incorporation of 2-N-methylguanosine modification. Four 18-nt hairpin RNA analogues representing the 970-loop region (helix 31 or h31; U960–A975) of Escherichia coli 16S rRNA were synthesized with and without modifications in the loop region. Subsequently, stabilities and conformations of the singly and doubly modified RNAs were examined and compared with the corresponding unmodified RNA. Thermodynamic parameters and circular dichroism spectra are presented for the four helix 31 RNA analogues. Surprisingly, methylations in the loop region of helix 31 slightly destabilize the hairpin, which may have subtle effects on ribosome function. The hairpin construct is suitable for future ligand-binding experiments.     

Isolation and purification of flavonoid glucosides from Radix Astragali by high-speed counter-current chromatography

High-speed counter-current chromatography methods, combined with resin chromatography were applied to the separation and purification of flavonoid glycosides from the Chinese medicinal herb, Radix Astragali. Five flavonoid glycosides, namely calycosin-7-O-β-d-glucoside, ononin, (6aR, 11aR)-9,10-dimethoxypterocarpan-3-O-β-d-glucoside, (3R)-2′-hydroxy-3′,4′-dimethoxyisoflavan-7-O-β-d-glucoside and calycosin-7-O-β-d-glucoside-6′′-O-acetate, were obtained. Among them, calycosin-7-O-β-d-glucoside-6′′-O-acetate was preparatively separated from Radix Astragali for the first time. Their structures were identified by ESI–MS, ¹H NMR, ¹³C NMR, and 2D NMR.     

Effective gene silencing activity of prodrug-type 2′-O-methyldithiomethyl siRNA compared with non-prodrug-type 2′-O-methyl siRNA

Small interfering RNAs (siRNAs) are an active agent to induce gene silencing and they have been studied for becoming a biological and therapeutic tool. Various 2′-O-modified RNAs have been extensively studied to improve the nuclease resistance. However, the 2′-O-modified siRNA activities were often decreased by modification, since the bulky 2′-O-modifications inhibit to form a RNA-induced silencing complex (RISC). We developed novel prodrug-type 2′-O-methyldithiomethyl (MDTM) siRNA, which is converted into natural siRNA in an intracellular reducing environment. Prodrug-type 2′-O-MDTM siRNAs modified at the 5′-end side including 5′-end nucleotide and the seed region of the antisense strand exhibited much stronger gene silencing effect than non-prodrug-type 2′-O-methyl (2′-O-Me) siRNAs. Furthermore, the resistances for nuclease digestion of siRNAs were actually enhanced by 2′-O-MDTM modifications. Our results indicate that 2′-O-MDTM modifications improve the stability of siRNA in serum and they are able to be introduced at any positions of siRNA.     

Identification of acylation products in SHAPE chemistry

SHAPE chemistry (selective 2′-hydroxyl acylation analyzed by primer extension) has been developed to specifically target flexible nucleotides (often unpaired nucleotides) independently to their purine or pyrimidine nature for RNA secondary structure determination. However, to the best of our knowledge, the structure of 2′-O-acylation products has never been confirmed by NMR or X-ray data. We have realized the acylation reactions between cNMP and NMIA under SHAPE chemistry conditions and identified the acylation products using standard NMR spectroscopy and LC–MS/MS experiments. For cAMP and cGMP, the major acylation product is the 2′-O-acylated compound (>99%). A trace amount of N-acylated cAMP has also been identified by LC–UV–MS². While for cCMP, the isolated acylation products are composed of 96% of 2′-O-acylated, 4% of N,O-diacylated, and trace amount of N-acylated compounds. In addition, the characterization of the major 2′-O-acylated compound by NMR showed slight differences in the conformation of the acylated sugar between the three cyclic nucleotides. This interesting result should be useful to explain some unexpected reactivity of the SHAPE chemistry.     

Oligo(2′-<Emphasis Type="Italic">O</Emphasis>-methylribonucleotides) and their derivatives: III. 5′-Mono- and 5′-bispyrenyl derivatives of oligo(2′-<Emphasis Type="Italic">O</Emphasis>-methylribonucleotides) and their 3′-modified analogues: Synthesis and properties

5′-Pyrenylmethylphosphamide and 5′-bispyrenylmethylphosphordiamide derivatives of oligo(2′-O-methylribonucleotides) and their analogues with thymidine attached at their 3′-termini by a 3′-3′-phosphodiester internucleotide bond (“inverted” thymidine) were synthesized. The effect of the pyrene residue(s) on the thermal stability of duplexes of the modified oligonucleotides with RNA and DNA was studied. A possibility of detection of hybridization of 5′-mono- and 5′-bispyrenyl derivatives with RNA and DNA targets in solution was demonstrated according to the changes in fluorescence. 5′-Pyrenylphosphamide derivatives of oligo(2′-O-methylribonucleotides) and their inverted analogues were shown to be used as sensitive probes for the detection of single nucleotide polymorphisms in RNA and DNA by the method of thermal duplex denaturation with fluorescence change registration.     

Sequence analysis of small amounts of nonradioactive oligoribonucleotides containing ribose-methylated nucleosides by a combination of 3H- and 32P-labeling techniques

The oligonucleotides A-G-A-Cm-U and Gm-A-A-Y-A-ψ were used as model compounds to demonstrate how the complete nucleotide sequence of small amounts of nonradioactive oligoribonucleotides (0.2–0.3 nmol) can be derived by a combination of ³H-labeling procedures previously published and a new method for the characterization of 2′-O-methylated nucleosides based on enzymatic ³²P labeling. The newly developed method for the identification of ribose-methylated nucleosides entails ³²P labeling by [γ-³²P]ATP/polynucleotide kinase of the 5′-terminus of a ribonuclease T₂-stable 2′-O-methylated dinucleotide derived from the polyribonucleotide, conversion of the labeled dinucleotide to the ³²P-labeled 2′-O-methylated nucleoside 5′-monophosphate, and identification of the monophosphate by its chromatographic properties on a polyethyleneimine-cellulose thin layer. The novel method is simple, fast, and sensitive and, at present, represents the only way by which ribose-methylated nucleosides can be analyzed in small amounts (0.01 nmol) of nonradioactive oligonculeotides or RNA.     

Flavonoid diversification in different leaf compartments of Primula auricula (Primulaceae)

Populations of Primula auricula L. subsp. auricula from Austrian Alps were studied for flavonoid composition of both farinose exudates and tissue of leaves. The leaf exudate yielded Primula-type flavones, such as unsubstituted flavone and its derivatives, while tissue flavonoids largely consisted of flavonol 3-O-glycosides, based upon kaempferol (3, 4) and isorhamnetin (5–7). Kaempferol 3-O-(2″-O-β-xylopyranosyl-[6″-O-β-xylopyranosyl]-β-glucopyranoside) (3) and isorhamnetin 3-O-(2″-O-β-xylopyranosyl-[6″-O-β-xylopyranosyl]-β-glucopyranoside) (6) are newly reported as natural compounds. Remarkably, two Primula type flavones were also detected in tissues, namely 3′-hydroxyflavone 3′-O-β-glucoside (1) and 3′,4′-dihydroxyflavone 4′-O-β-glucoside (2), of which (1) is reported here for the first time as natural product. All structures were unambiguously identified by NMR and MS data. Earlier reports on the occurrence of 7,2′-dihydroxyflavone 7-O-glucoside (macrophylloside) in this species could not be confirmed. This structure was now shown to correspond to 3′,4′-dihydroxyflavone 4′-O-glucoside (2) by comparison of NMR data. Observed exudate variations might be specific for geographically separated populations. The structural diversification between tissue and exudate flavonoids is assumed to be indicative for different ecological roles in planta.     

An automated procedure for the analysis of methylated nucleosides in nuclear RNA and mRNA.

A commercial high pressure liquid chromatographic system is used for the rapid analysis of 2′-O-methylnucleosides and pyrophosphate-linked methylated termini of nuclear RNAs and mRNAs. Oligonucleotides or RNA samples were enzymatically hydrolyzed to nucleosides and analyzed automatically by cationexchange chromatography in less than 1 hr using a 0.4 m ammonium formate buffer system at 55° c. This method is sufficiently sensitive to detect the N⁷-methylguanosine residue in 0.1 mg of Novikoff ascites hepatoma mRNA and may be used for qualitative or quantitative studies on RNA methylation in vivo or in vitro.     

Site-Specific RNA Cleavage Using Terpyridine·Cu(II)-Linked 2′-O-Methyloligonucleotides

Abstract

2′-Deoxy- and 2′-O-methyl-5′-O-terpyridyl derivatives of adenosine and cytidine were synthesized and used to construct 5′-end-modified oligonucleotides. These antisense agents complexed with Cu(II) exclusively cleaved a complementary RNA oligomer at the site opposite the terpyridine-nucleoside residue. We also found that the terpyridine·Cu(II) moiety stabilizes 2′-O-methyl RNA duplex. These suggest that after RNA hybridization, the terpyridine moiety is close to the RNA strand, presumably in an end capping manner.     

Purification of 5′-O-Trityl-on Oligoribonucleotides. Investigation of Phosphate Migration During Purification and Detritylation.

Abstract

Synthetic oligoribonucleotides (RNA) are efficiently prepared with 2′-O-tert-butyldimethylsilyl nucleoside 3′-O-phosphoramidites with labile base-protection; A_dmf or A_Pac, G_dmf, C_ibu, U. After cleavage from the polystyrene support, the exocyclic amine protecting groups are removed with conc. NH₄OH: ethanol/3:1 by heating at 55°C for 3–5 h. The 2′-O- silyl protecting groups are removed with tetra-n-butylammonium fluoride in THF or more conveniently with neat triethylamine trihydrofluoride. To gain the advantages of increased capacity on reverse phase HPLC and the convenience of cartridge based purification (OPC, Oligonucleotide Purification Cartridge), the 5′ trityl was left on the RNA as the final protecting group to be removed. The mild conditions which are effective for trityl removal are shown to preserve 3′-5′ phosphate linkage integrity in RNA. The absence of phosphate migration is demonstrated by model studies, utilizing N⁴ -isobutyryl-5′-O-DMT-3′-O-TBDMS-2′-O-(2-cyanoethyl-N,N-diisopropylphosphoramidite) as a control monomer and digestion by 3′-5′ selective P1 nuclease and alkaline phosphatase and HPLC analysis. Oligoribonucleotides were analyzed by Microgel capillary electrophoresis, anion-exchange HPLC, and the enzymatic digest/HPLC method.

     

Inhibition of the peptidyl transferase A-site function by 2'-O-aminoacyloligonucleotides

New “non-isomerizable” analogs of the 3′-terminus of AA-tRNA, C-A(2′Phe)H, C-A(2′Phe)Me, C-A(2′H)Phe and C-A(2′Me)Phe, were tested as acceptor substrates of ribosomal peptidyl transferase and inhibitors of the peptidyl transferase A-site function. The 3′-O-AA-derivatives were active acceptors of Ac-Phe in the peptidyl transferase reaction, while the 2′-O-AA-derivatives were completely inactive. Both 2′- and 3′-O-AA-derivatives were potent inhibitors of peptidyl transferase catalyzed Ac-Phe transfer to puromycin. The results indicate that although peptidyl transferase exclusively utilizes 3′-O-esters of tRNA as acceptor substrates, its A-site can also recognize the 3′-terminus of 2′-O-AA-tRNA.     

Flavonoid variation in the liverwort Conocephalum conicum: Evidence for geographic races

The flavonoids of 2 samples of Conocephalum conicum gametophyte tissue have been studied, one from U.S.A. and the other from Germany. Common to both samples were vicenin-2, lucenin-2, the 7-O-glucuronides of apigenin, chrysoeriol and luteolin and the previously unknown 7-O-glucuronide 4′-O-rhamnosides of apigenin, chrysoeriol and luteolin. Additionally the German sample contained the 7,4′-di-O-glucuronides of apigenin and luteolin and a new compound, apigenin 7-O-diglucuronide 4′-O-glucuronide. The North American sample contained, additionally, luteolin 7,3′-di-O-glucuronide, luteolin 7-O-glucuronide 3′,4′-di-O-rhamnoside (a new triglycoside) and 2 further derivatives of luteolin 7-O-glucuronide. Evidence is presented for the existence of geographic faces of C. conicum and for the qualitative invariability of the flavonoid patterns with changing season or environment.     

Synthesis and in vitro activities of a new antiviral duplex drug linking Zidovudine (AZT) and Foscarnet (PFA) via an octadecylglycerol residue

To prepare a new antiviral duplex drug linking Zidovudine (AZT) and Foscarnet (PFA) via a lipophilic octadecylglycerol residue we condensed 1-O-4-monomethoxytrityl-3-O-octadecyl-sn-glycerol-2-hydrogenphosphonate obtained from 3-O-octadecyl-sn-glycerol with AZT by the phosphonate method. The purified condensation product was de-tritylated resulting in 3′-azido-3′-deoxythymidylyl-(5′ → 2-O)-3-O-octadecyl-sn-glycerol, followed by treatment with (ethoxycarbonyl)phosphoric dichloride. The resulting 3′-azido-3′-deoxy-thymidylyl-(5′ → 2)-3-O-octadecyl-sn-glycerol-1-O-(ethoxycarbonyl)phosphonate was purified by preparative RP-18 column chromatography. The antiviral duplex drug 3′-azido-3′-deoxythymidylyl-(5′ → 2-O)-3-O-octadecyl-sn-glycerol-1-O-phosphonoformate trisodium salt (AZT–lipid–PFA) was obtained after alkaline cleavage of the phosphonoformate ethylester residue. The overall yield of the five step synthesis performed at gram scale was about 30%. According to a supposed pathway AZT–lipid–PFA could be cleaved to yield a mixture of different antiviral compounds such as AZT, AZT-5′-monophosphate, octadecylglycerol–AZT, PFA and octadecylglycerol–PFA, possibly producing additive and/or synergistic antiviral effects. In vitro studies showed that the duplex drug exhibits antiviral activities against HIV and especially against drug-resistant strains and clinical isolates of HSV and HCMV. The E₅₀ values of AZT–lipid–PFA against HIV ranged between 170 and 200 nM. The half-maximal inhibitory doses (IC₅₀) against highly acyclovir (ACV)-resistant HSV isolates determined by a plaque reduction assay ranged between 1.87 and 4.59 μM. Using ganciclovir (GCV)-sensitive, GCV resistant and drug cross-resistant HCMV strains the IC₅₀-values of AZT–lipid–PFA were between 2.78 and 1.18 μM. With regard to PFA, the IC₅₀-value of AZT–lipid–PFA determined on a multi-drug-resistant HCMV strain was about 90-fold lower than that of PFA, demonstrating the superior antiviral effect of the duplex-drug.     

3′,6′-anhydro-6-O-corynomycoloyl trehalose: Synthesis and identification as the impurity in synthetic cord factor preparations

Acylation of 2,3,4,2′,3′,4′-hexa-O-benzyl-6,6′-di-O-methanesulphonyl-α-α-trehalose (1) with a reduced amount of potassium corynomycolate yielded a mixture which consisted mainly of 2,3,4,2′,3′,4′-hexa-O-benzyl-6-O-corynomycoloyl-6′-O-methanesulphonyl-α,α-trehalose (2). Catalytic hydrogenolysis of 2 gave the mono-mesylate 4 which was converted into 3′,6′-anhydro-6-O-corynomycoloyl-α,α-trehalose (5) but treatment with sodium hydride. The structure of 5 was studied by mass-spectroscopy. Compound 5 was found to be identical with the byproduct obtained in the acylation of 6,6′-di-O-p-toluenesulphonyl-α,α-trehalose with potassium corynomycolate.     

CHIMERIC RNA WITH MODIFIED BACKBONES: ALTERNATING METHYLENE(METHYLIMINO) LINKED PHOSPHODIESTER BACKBONE OLIGONUCLEOTIDES WITH 2′-OH AND 2′-OMe GROUPS

Synthesis of a novel ribo-MMI dimer with 2′-OH and 2′-OMe in 5′- and 3′-nucleosides, respectively is presented. The synthesis was accomplished by reductive coupling of 3′-deoxy-3′-C-formyluridine and 2′-O-methyl-5′-O-methylaminouridine via a thioacetal as the key intermediate for the top part of the dimer. Incorporation of ribo- MMI dimers into oligonucleotides increased binding affinity for target RNA.     

A rapid procedure to determine the content of 2'-O-methylation in RNA by homochromatography

The content of 2′-O-methylated dinucleotides from 17 S rRNA of yeast and 18 S rRNAs of chicken cells and Novikoff rat cells was determined by a new procedure using homochromatography. The procedure is simple and can be used to compare the extent of 2′-O-methylation simultaneously in various RNAs. It was of interest that 18 S rRNAs of chicken and rat have two times more 2′-O-methylated dinucleotides as compared to yeast 17 S rRNA.