The P‐Stereocontrolled Synthesis of PO/PS‐Chimeric Oligonucleotides by Incorporation of Dinucleoside Phosphorothioates Bearing an O‐4‐Nitrophenyl Phosphorothioate Protecting Group

Abstract

The synthesis of protected model dinucleoside (3',5')‐O‐aryl phosphorothioates, their separation into pure diastereomers, and their successful incorporation into oligonucleotides followed by stereospecific deprotection of the O‐aryl phosphorothioate function with oximate ion (inversion) enables the preparation of chimeric PO/PS‐oligonucleotides with a predetermined sense of P‐chirality at each internucleotide phosphorothioate position. The absolute configuration at the phosphorus of the internucleotide O‐aryl phosphorothioate in “dimeric building blocks” has been assigned. The 3'‐terminal SP‐phosphorothioate linkages effectively protect such chimeric constructs from degradation by human plasma exonuclease (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005)

Solid-Phase Synthesis of Stereoregular Oligodeoxyribonucleoside Phosphorothioates Using Bicyclic Oxazaphospholidine Derivatives as Monomer Units

“…The mechanism of inversion process at the phosphorus atoms of tricoordinate organophosphorus compounds has not been fully clarified. − In particular, little is known about the mechanism of the inversion process of phosphorus-containing chiral heterocyclic compounds, despite the fact that these compounds have been widely used to synthesize optically pure organophosphorus compounds such as phosphine-based ligands and biologically active compounds. ,,− ,, It has been reported that nucleophilic species (e.g., amines, water, Cl − ) and acids (e.g., amine hydrochlorides) accelerate the inversion process, and their repetitive nucleophilic attacks to the phosphorus atom are proposed to be involved. , However, it cannot rationalize the fact that the inversion is also accelerated in the case that the nucleophilic species and the leaving group at the phosphorus atom are different from each other. In addition, CMPT consisting of less nucleophilic components also accelerated the epimerization of the oxazaphospholidines as above.…”

“…However, access to stereoregular PS-ODNs is still severely limited despite the considerable efforts by many research groups. − Currently, these ODNs are available via the oxathiaphospholane method, ,− in which nucleoside 3′- O -(2-thio-1,3,2-oxathiaphospholane) derivatives are used as monomers, though the method has some drawbacks, such as the time-consuming chromatographic isolation of the diastereopure monomers from ca. 1:1 mixtures of diastereomers, relatively low efficiency of the internucleotidic bond formation under strongly basic conditions, and requirement of another set of four nucleoside 3′- O -(2-oxo-1,3,2-oxathiaphospholane) monomers for the synthesis of stereoregular phosphate/phosphorothioate chimeric ODNs (PO/PS-chimeric ODNs) due to the incompatibility of the method with the conventional phosphoramidite method…”

Chirality matters: stereo-defined phosphorothioate linkages at the termini of small interfering RNAs improve pharmacology in vivo

“…Recently, there has been progress toward efficient synthesis and purification of stereo-defined PS oligonucleotides ( 29 , 30 ). A variety of protocols that yield stereo-defined PS linkages in oligonucleotides have been described such as the H -phosphonate method ( 31 ), use of chiral PS dinucleotide building blocks ( 32 ), use of chiral phosphoramidites with the oxazaphospholidine approach ( 26 , 29 , 30 , 33–35 ), and use of a tricyclic P(III) chiral auxiliary ( 36 ). More recently P(V) chemistry has been elegantly used to synthesize chiral phosphorothioates using limonene precursors ( 37 ).…”

Chemoselective Activation of Nucleoside 3‘-O-Methylphosphonothioates with 1,3,5-Triazinyl Morpholinium Salts

“…We found, however, that instead of the expected ester 10 ( 31 P NMR δ 29.09, 29.12 ppm, diastereomeric ratio ca. 1:1, observed about 5%), the corresponding dithymidyl (3′,3′)-pyrophosphonate (12) [ 31 P NMR δ 24.85, 24.98, 25.1 ppm, 1:2:1 ratio, 85%)] was observed as the foremost product. Pyrophosphonate 12 was, most probably, produced in reaction of the active ester 10 with methylphosphonic acid 11.…”

“…9 Some of these coupling reagents and their analogues have also been used previously in the phosphorylation of several alcohols and amines. 10 Recently, we also demonstrated that both P III and P V compounds can be efficiently activated with 1,2,4 triazoles 11 or N-hydroxybenzotriazoles 12 in the esterification of methylphosphonates or phosphorothioates.…”