Straightforward synthesis of 3′-deoxy-3′,4′-didehydronucleoside-5′-aldehydes via 2′,3′-O-orthoester group elimination: a simple route to 3′,4′-didehydronucleosides

Straightforward, high-yielding syntheses of 3′-deoxy-3′,4′-didehydronucleoside-5′-aldehydes and 3′-deoxy-3′,4′-didehydronucleosides starting from 2′,3′-O-orthoester derivatives of ribonucleosides are described.     

Concise and efficient synthesis of 3′-O-triphosphates of 2′-deoxyadenosine and 2′-deoxycytidine

We describe concise and efficient synthesis of 2′-deoxyadenosine-3′-O-triphosphate (2′-d-3′-ATP) and 2′-deoxycytidine-3′-O-triphosphate (2′-d-3′-CTP) which are well known for their various biological applications. One-pot synthetic methodology was used to convert N⁶-Benzoyl-5′-O-levulinoyl-2′-deoxyadenosine into N⁶-Benzoyl-5′-O-levulinoyl-2′-deoxyadenosine-3′-O-triphosphate in 72% yield. One-step concurrent deprotection of N⁶-Benzoyl and 5′-O-levulinoyl groups using concentrated aqueous ammonia resulted in 2′-d-3′-ATP in 75% yield. The same synthetic strategy was successfully employed to convert N⁴-Benzoyl-5′-O-levulinoyl-2′-deoxycytidine into 2′-d-3′-CTP in 66% yield.     

General method for the synthesis of 2′-O-carboranyl-nucleosides

The carboranyl cage is a new modifying entity for nucleosides, DNA oligonucleotides, and other biomolecules. Herein, the first reliable method for the synthesis of nucleosides modified with a carborane cluster at the 2′-position is described.     

3′-Amino-5′-carboxymethyl-3′,5′-dideoxy nucleosides for the synthesis of fully amide-linked RNA mimics

A convenient protocol is developed for the synthesis of 3′-[N-(fluorenylmethoxycarbonyl)-amino]-5′-carboxymethyl derivatives of all four natural ribonucleosides from cheap chiral pool compound glucose. Synthesis of fully amide-linked RNA analogues of small oligonucleotides containing, for the first time, all four nucleoside amino acids using standard solid phase Fmoc-chemistry is described.     

A novel entry to 2′-O-aminopropyl modified nucleosides amenable for further modifications

2′-O-aminopropyl modified 4,6-difluoro-substituted benzimidazole nucleosides were synthesized in a two-step synthesis via Michael reaction and a Raney-nickel catalyzed reduction in high yields. These building blocks were used as a starting point for the conjugation of different carboxylic acids to enhance the lipophilicity or cationic character of oligonucleotides when used in biological assays or medical applications.     

A concise synthesis of 4′-O-methyl honokiol

A concise and protecting group free synthesis of the naturally occurring neolignan 4′-O-methyl honokiol is developed. The key biaryl bond is constructed by 1,2-addition of an aryl Grignard reagent to a dienone followed by rearrangement.     

Chemical synthesis of bioactive siRNA in solution phase by using 2-(azidomethyl)benzoyl as 3′-hydroxyl group protecting group

A protecting group AZMB was introduced to ribonucleosides 3′-hydroxyl group to facilitate solution phase synthesis of siRNA. The protection and cleavage reaction were carried out in mild conditions, that is protection by acyl chloride and cleavage by triphenylphosphine. The synthesized siRNA showed good biological activity to suppress targeted superoxide dismutase gene expression.     

Synthesis of 2′-O,3′-O bicyclic adenosine analogues using ring closing metathesis

The synthesis of 2′-O,3′-O bicyclic adenosine derivatives is presented as the first examples of a new family of 13-membered ring bicyclic nucleoside analogues. Cyclisation was achieved through ring closing metathesis (RCM) on a diene intermediate using Grubbs’ catalyst. The Z and E isomers were purified and characterised.     

A new convenient synthesis of aroyl cyanides via the formation of cyanohydrin nitrate intermediates

The treatment of α-bromoarylacetonitriles with AgNO₃ generates cyanohydrin nitrate intermediates, which easily eliminate nitrous acid with the formation of carbonyl bond to afford aroyl cyanides in good to high yields.     

The 2‐Cyano‐2,2‐dimethylethanimine‐N‐oxymethyl Group for the 2′‐Hydroxyl Protection of Ribonucleosides in the Solid‐Phase Synthesis of RNA Sequences

The reaction of 2‐cyano‐2‐methyl propanal with 2′‐O‐aminooxymethylribonucleosides leads to stable and yet reversible 2′‐O‐(2‐cyano‐2,2‐dimethylethanimine‐N‐oxymethyl)ribonucleosides. Following N‐protection of the nucleobases, 5′‐dimethoxytritylation and 3′‐phosphitylation, the resulting 2′‐protected ribonucleoside phosphoramidite monomers are employed in the solid‐phase synthesis of three chimeric RNA sequences, each differing in their ratios of purine/pyrimidine. When the activation of phosphoramidite monomers is performed in the presence of 5‐benzylthio‐1H‐tetrazole, coupling efficiencies averaging 99 % are obtained within 180 s. Upon completion of the RNA‐chain assemblies, removal of the nucleobase and phosphate protecting groups and release of the sequences from the solid support are carried out under standard basic conditions, whereas the cleavage of 2′‐O‐(2‐cyano‐2,2‐dimethylethanimine‐N‐oxymethyl) protective groups is effected (without releasing RNA alkylating side‐products) by treatment with tetra‐n‐butylammonium fluoride (0.5 m) in dry DMSO over a period of 24–48 h at 55 °C. Characterization of the fully deprotected RNA sequences by polyacrylamide gel electrophoresis (PAGE), enzymatic hydrolysis, and matrix‐assisted laser desorption/ionization (MALDI) mass spectrometry confirmed the identity and quality of these sequences. Thus, the use of 2′‐O‐aminooxymethylribonucleosides in the design of new 2′‐hydroxyl protecting groups is a powerful approach to the development of a straightforward, efficient, and cost‐effective method for the chemical synthesis of high‐quality RNA sequences in the framework of RNA interference applications.     

Convenient synthesis of N-isobutyryl-2′-O-methyl guanosine by efficient alkylation of O-trimethylsilylethyl-3′,5′-di-tert-butylsilanediyl guanosine

We present a novel route for the synthesis of N²-isobutyryl-2′-O-methyl guanosine, introducing 3′,5′-di-tert-butylsilyl and O⁶-trimethylsilylethyl groups as efficient protections during the 2′-O-methylation step with NaH/CH₃I. These protections were then removed simultaneously in a single step with TBAF. The eight-step synthesis is easy to perform, employing convenient commercially available reagents; crude mixtures are of satisfying purity, so only three chromatography purifications were required. Title compound was obtained in 25% overall yield from guanosine.     

Chemical synthesis of an artificially branched hairpin ribozyme variant with RNA cleavage activity

Due to the development in the field of RNA synthesis over the past decade of years, preparation of RNA oligonucleotides longer than 50 nucleotides is possible today. In this report, we describe the chemical preparation of a branched RNA molecule with RNA cleavage activity consisting of 81 nucleotides. It is derived from the hairpin ribozyme, a small catalytic RNA occurring in nature. The hairpin ribozyme consists of two separately folded domains (loop A and loop B domain), which can be joined in a number of different ways without loss of activity. In the construct presented here, 2′-deoxy-N4-(6-hydroxyhexyl)-5-methylcytidine was introduced to connect the loop B domain with the loop A domain via an artificial branch. The synthesized branched RNA is able to catalyze the cleavage of a number of suitable substrates. Compared with the corresponding non-branched reverse-joined ribozyme it cleaves its substrates only 5-fold slower. Surprisingly, no ligation activity could be detected.     

Water promoted one-pot synthesis of 2′-aminobenzothiazolomethyl naphthols and 5-(2′-aminobenzothiazolomethyl)-6-hydroxyquinolines

A novel one-pot, three-component condensation reaction of an aldehyde, 2-aminobenzothiazole and 2-naphthol or 6-hydroxyquinoline in water to give 2′-aminobenzothiazolomethyl naphthols or 5-(2′-aminobenzothiazolomethyl)-6-hydroxyquinolines in high yields at 90 °C without using any catalyst, is described.     

Scalable synthesis of substituted 2,7-dimethyl-9-phenylxanthen-9-ol (DMPx-OH): useful for the preparation of crystalline 5′-O-DMPx-protected nucleosides

A convenient single-step synthesis of several 2,7-dimethyl-9-phenylxanthen-9-ol (DMPx-OH) analogs has been accomplished using a Friedel-Crafts reaction. Treatment of various DMPx-OH with unprotected 2′-O-methoxyethyl-ribonucleosides (MOE) in the presence of B(C₆F₅)_3, as a Lewis Acid catalyst, furnished 5′-O-protected derivatives of 2′-MOE-ribonucleosides in good yields. The deprotection of the DMPx groups was accomplished by acid hydrolysis under very mild conditions. Among the five DMPx analogs synthesized, the 2,7-dimethyl-9-(4-nitrophenyl)xanthene-9-yl group furnished crystalline products enabling non-chromatographic isolation of 5′-O-protetced nucleosides.     

On the design of polymeric 5′-O-ester prodrugs of 3′-azido-2′,3′-dideoxythymidine (AZT)

A new 5′-O-AZT prodrug was synthesized by conjugating 3′-azido-2′,3′-dideoxythymidine (AZT) with poly(oxyethylene H-phosphonate) at room temperature under Atherton-Todd reaction conditions. The acute toxicity of poly(5′-O-AZT-oxyethylene phosphate) was reduced significantly in comparison with non-immobilized AZT.     

Highly diastereoselective synthesis of spiro[cyclopropane-1,3′-indolin]-2′-ones via catalyst-free cyclopropanation using ethyl diazoacetate

Substituted 3-methyleneindolin-2-ones were efficiently cyclopropanated with ethyl diazoacetate to yield spiro[cyclopropane-1,3′-indolin]-2′-ones in a catalyst-free and highly diastereoselective reaction in a mixture of ethanol–acetonitrile (1:1 v/v) as solvent.     

An unexpected methyl group migration during on-column Stille derivatization of RNA

Postsynthetic Stille cross-coupling for functionalization of oligonucleotides on solid support was applied on iodo modified RNA utilizing different protecting group strategies. As result, the otherwise very successful ACE [bis(acetoxyethyloxy)-methyl orthoester] chemistry was found to be limited since methylated side-products formed as was investigated via enzymatic degradation of RNA and various monomer model reactions. Enzymatic digestion of poly uridine sequences revealed presence of considerable amounts of N³-methylated uridine derivatives due to migration of methyl as phosphate protecting group used in ACE strategy. Monomer test reactions mimicking conditions on RNA clearly indicated an enhanced methylation effect correlated to the Stille coupling procedure.     

Regioselective 2′-O-debenzoylation of 2',3'-di-O-benzoyl threose nucleosides

A simple and convenient procedure for the regioselective 2′-O-debenzoylation of 2',3'-di-O-benzoyl threose nucleosides has been achieved successfully affording 3′-O-benzoyl threose nucleosides, which are useful starting material synthons for the synthesis of modified threose nucleosides for different purposes.