BORANE-AMINE COMPLEXES - VERSATILE REAGENTS IN THE CHEMISTRY OF NUCLEIC ACIDS AND THEIR ANALOGS

A new method for synthesis of N-alkylated nucleosides was developed. Exceptionally mild and selective conversion of N-acyl to the corresponding N-alkyl nucleosides was achieved by reduction with borane-amine complexes. The borane-amine complexes were also used as efficient scavengers of a 4,4′-dimethoxytrityl (DMT) cation. Neutralization of the cation eliminated the boranophosphate group degradation during acidic DMT deprotection and allowed milder acidic conditions for the deprotection.     

The deprotection of Lys(Mtt) revisited.

The selective deprotection of Lys(Mtt)-containing peptidyl resins was successfully monitored by RP-HPLC using very short linear gradients. RP-HPLC analyses of the acidic filtrates also revealed the partial cleavage of the Trt groups and of the peptide-resin bond. The absorbance of the Mtt carbocation at 470 nm is only twice that of the Trt cation. Thus, the UV monitoring at 470 nm seems to be inappropriate, especially at the end of the deprotection, when the Mtt and the Trt levels are comparable.     

Oligonucleotides Containing N7-Cyanoborane-2′-deoxyguanosine

Abstract

For synthesis of N⁷-cyanoborane-containing oligonucleotides, the 5′-DMT protecting group is not a suitable precursor because the boronated nucleoside is incompatible with DMT cations released during deprotection of the oligonucleotide. As an alternative to DMT, we have investigated use of the 5′-Fmoc protecting group. We found that the cyanoborane group is stable during synthesis and deprotection conditions used with Fmoc derivatives.     

Development of a purification procedure for the isolation of nucleosides from urine prior to mass spectrometric analysis

A chromatographic separation of nucleosides from urine has been developed in order to facilitate their mass spectrometric analysis for clinical diagnosis. A number of chromatographic resins were studied in order to develop an effective and efficient purification procedure. The optimized sequential protocol comprises a centrifugation, acidification and neutralization step, followed by application of an affinity chromatographic column and finally further separation on an acidic cation exchange column and a basic anion exchanger. This scheme shows effective clean-up of a standard radiolabelled nucleoside with a recovery of 92.5%, and recovery of nucleosides added to urine samples before extraction showed recoveries of 72-82%.     

Development of a Purification Procedure for the Isolation of Nucleosides from Urine Prior to Mass Spectrometric Analysis

Abstract

A chromatographic separation of nucleosides from urine has been developed in order to facilitate their mass spectrometric analysis for clinical diagnosis. A number of chromatographic resins were studied in order to develop an effective and efficient purification procedure. The optimized sequential protocol comprises a centrifugation, acidification and neutralization step, followed by application of an affinity chromatographic column and finally further separation on an acidic cation exchange column and a basic anion exchanger. This scheme shows effective clean-up of a standard radiolabelled nucleoside with a recovery of 92.5%, and recovery of nucleosides added to urine samples before extraction showed recoveries of 72 – 82%.     

Thiosugars. VIII. Preparation of new 4'-thio-L-lyxo pyrimidine nucleoside analogues

Reaction of 1-O-acetyl-2,3,5-tri-O-benzyl-4-thio-L-lyxofuranose with silylated pyrimidine bases and subsequent deprotection with boron tribromide led to 4'-thio-L-lyxo pyrimidine nucleosides. The 5-bromo-6-methyl derivative was prepared from methyl 2,3,5-tri-O-acetyl-4-thio-L-lyxofuranoside. Deacetylation was performed with sodium methoxide. The anomers were separated by HPLC and their configurations assigned by NMR spectroscopy and X-ray structural analyses. The biological activity of the nucleosides was tested.     

Synthesis of carotenoid-cysteine conjugates

Isozeaxanthin under acidic conditions forms an allylic cation which reacts readily with thiol nucleophiles. With N-acetylcysteine as a nucleophile the products obtained are carotenoid-cysteine conjugates in which the amino acid moiety is attached to the carotenoid via sulphur in position 4. The water solubility of the products can be increased by deprotection of the amino group. The antioxidant activity of the products were examined on human liver cells under conditions of hydrogen-peroxide induced oxidative stress.     

Synthesis of nucleoside 3'-thiophosphates in one step procedure.

A mild and efficient one-step method of thiophosphorylation was devised for acid-sensitive nucleosides. The procedure is based on thiophosphorylation of nucleoside magnesium alkoxide by 2-chloro-2-thio-1,3,2-dioxaphospholane. The utility and efficiency of this method combined with deprotection of the resulting cyclic triester were demonstrated by its application to the synthesis of both adenosine 3'- and 5'-thiophosphates. The procedure does not require protection of the exocyclic amino group and can be successfully used for the thiophosphorylation of nucleosides that are unusually sensitive to depurination.     

4,4′-Dimethoxytrityl group derived from secondary alcohols: Are they removed slowly under acidic conditions?

Removal of 4,4'-dimethoxytrityl (DMT) groups from primary and secondary hydroxyl functionality was investigated. It was observed that deblocking of DMT group from secondary hydroxyl group of molecules attached to solid support under acidic conditions occurred relatively slowly compared to primary hydroxyl group. Marginal difference in rate of detritylation was observed between DMT group attached to 5'-hydroxyl group of deoxyribonucleoside and 2'-O-methoxyethylribonucleoside when attached to one kind of support. Removal of DMT from nucleoside attached to OligoPrep solid support was found to be slow.     

Facile synthesis of 1',2'-cis-beta-pyranosyladenine nucleosides

1',2'-cis-beta-Glycosyladenine nucleosides, such as beta-altroside, beta-mannoside, and beta-idoside, were efficiently synthesized from the corresponding 1',2'-trans-beta-6-chloropurine derivatives, beta-glucoside, and beta-galactoside. Nucleophilic substitution of the O-trifluoromethanesulfonyl groups at the C-2' and/or 3' was carried out using tetrabutylammonium acetate or cesium acetate under mild conditions. Subsequent deprotection and amidation afforded the desired compounds, 1',2'-cis-beta-pyranosyladenine nucleosides.     

Stability and cleavage conditions of (2-furyl)-L-alanine-containing peptides

The furyl group of (2-furyl)-L-alanine-containing peptides obtained from Fmoc solid-phase synthesis is partially degraded to several by-products during the final TFA-mediated deprotection in the presence of cation scavengers such as ethanedithiol and propanedithiol. The major by-product corresponds to a bis-dithioacetale formed after acidic hydrolysis of the furyl group. We examined several cleavage conditions and found that cleavage cocktails containing water and triisopropylsilane or 3,6-dioxa-1,8-octanedithiol (DODT) in trifluoroacetic acid are sufficient to minimize the side reaction.     

Synthesis of 2'-deoxy-6,3'-methano-cyclo-pyrimidine nucleosides

The nucleophilic attack of lithiated pyrimidines to a suitably-protected 3-ketosugar, afforded the 3-branched sugar stereospecifically, followed by intramolecular glycosylation to give 6,3'-methano-cyclo-pyrimidine nucleosides. The 2'-deoxygenation was achieved by sequential protection, deprotection and radical reduction.     

Synthesis and DNA binding properties of a new benzo[f]imidazo[1,5b]-isoquinoline-butan-1,2-diol derivative

A benzo[f]imidazo[1,5b]-isoquinoline derivative 4 with a 1,2-butandiol linker was prepared by reaction of a trimethylsilylated 5-naphthylidenehydantoin 3 with a 2,3-dideoxy-D-glycero-pentafuranoside 2 in 22% yield. After deprotection, the resulting compound 5 was converted to a DMT protected phosphoramidite building block 7 for standard DNA synthesis. DNA/DNA, DNA/RNA duplexes with 5 inserted as bulges were destabilized, except when the new amidite was used for the synthesis of a zipping duplex.     

Synthesis of Nucleoside 3′-Thiophosphates in One Step Procedure

Abstract

A mild and efficient one-step method of thiophosphorylation was devised for acid-sensitive nucleosides. The procedure is based on thiophosphorylation of nucleoside magnesium alkoxide by 2-chloro-2-thio-1,3,2-dioxaphospholane. The utility and efficiency of this method combined with deprotection of the resulting cyclic triester were demonstrated by its application to the synthesis of both adenosine 3′- and 5′-thiophosphates. The procedure does not require protection of the exocyclic amino group and can be successfully used for the thiophosphorylation of nucleosides that are unusually sensitive to depurination.     

Synthesis of 2'-O-deuteriomethyl ribonucleosides Gm-d3, Am-d3, Um-d3 and Cm-d3.

The synthesis of 2'-O-deuteriomethyl ribonucleosides by iodomethane-d3 (99.5 + atom % D) deuteriomethylation of 3',5'-O-tetra(isopropyldisiloxane)-diyl nucleosides, followed by deprotection, is described.     

Preparation of oligodeoxynucleotide 5'-triphosphates using solid support approach

We report a synthetic procedure for conversion of oligonucleotides to their 5'-triphosphate derivatives with moderate yield. The oligonucleotides were synthesized on solid support using standard phosphoramidite protocols. The DMT protection group was removed and the 5'-OH was phosphitylated using 2-chloro-4H-1,3,2-benzodioxaphosphorin-4-one followed by reaction with tributyammonium pyrophosphate and iodine oxidation. After subsequent removal from support and complete deprotection, the products were isolated by anion-exchange HPLC chromatography. Structures of several 5'-triphosphate derivatives have been proven by phosphorus NMR, Mass-spectrometry and by HPLC comparison with authentic samples.     

A mild and quantitative procedure for the removal of nucleoside alkoxycarbonyl groups using pig liver esterase or Candida antarctica B lipase

A set of eight mono-, di-, tri- and tetraalkoxycarbonylated nucleosides was tested in order to assess their enzymatic hydrolysis. All the alkoxycarbonyl groups of the assayed substrates, from both carbonate and carbamate functions, were quantitatively hydrolysed using pig liver esterase (PLE) at pH 7 and 60 °C, regardless of the nucleoside base. Quantitative full alkoxycarbonyl groups removal was also reached by Candida antarctica B lipase (CAL B) under mild conditions, but in this case, longer reaction times were required. Thus, PLE appears as an useful catalyst for the mild and quantitative deprotection of nucleoside carbonates and carbamates in the synthesis of modified nucleosides.     

Ultrafast Cleavage and Deprotection of Oligonucleotides Synthesis and Use of CAc Derivatives

Abstract

We have investigated the use of alkylamines as fast cleavage and deprotection reagents for the solid phase synthesis of oligonucleotides and found methylamine/ammonium hydroxide (or methylamine) as an efficient reagent. The transamination side product formed with the commonly used dC^bz has been eliminated by the use of dC^Ac phosphoramidite. This system has successfully been used in the synthesis of oligonucleotides and oligonucleoside phosphorothioates. DMT dC^Ac hydrogen phosphonate and DMT ribo C^Ac-2′-O Me phosphoramidite also have been prepared and used in the synthesis of oligonucleotides.     

New methodology for the synthesis of 2'(3')-O-aminoacyl oligoribonucleotides related to the 3'-terminus of aa-tRNA

A new synthetic approach to the title compounds is reported. It is based on the phosphotriester methodology and uses a unique combination of protecting groups (Fmoc and Ph for the aglycons; DMT, CPTr and Mthp for the carbohydrate hydroxy functions; 2-CIPh for the phosphodiester bonds; BPOC for amino acid). This enables selective deprotection of the blocked oligonucleotide intermediates in two steps (oximate and acid treatments) to yield the 2'(3')-O-aminoacyl oligoribonucleotides suitable for biochemical investigations.