Oligonucleotide Synthesis Using Ionic Liquids as Soluble Supports

Abstract

The continuing evolution of the methodology for the solution-phase synthesis of oligonucleotides using soluble ionic tags as handles for easy purification is described. This methodology may provide a more cost efficient route for the large scale synthesis of oligonucleotides.

Applications of Mechanochemistry for the Synthesis of DNA on Ionic Liquid Supports

“…This property would allow for the separation of ionic species incorporating [NTf2] -from excess nucleoside phosphoramidites by simple precipitation following addition of diethyl ether or tert-butyl methyl ether (TBME). Although hydrophilic anions such as tetrafluoroborate ([BF4] -) have previously been utilised for oligonucleotide synthesis, [25][26][27] these [BF4] --derived ionic liquids are undesirable for large scale synthesis, as they are hydrophilic and may accumulate unacceptable water contents. Such ionic liquids have been shown to react with phosphorous-derived reagents, 32 and when combined to water may contribute to the degradation of the valuable phosphoramidite reagents used in oligomerisation of nucleotides.…”

“…In this context, the imidazolium cations have proved to be useful counter ions for the formation of diionic species used in the synthesis of oligomers. [25][26][27] Thus, we envisioned that a [C2mim][NTf2]-derived nucleoside would allow for an efficient dimer formation by phosphoramidite-based coupling, followed by oxidation and a purification of the bound-dinucleotide by precipitation using either diethyl ether or TBME. Key to this approach is the hydrophobicity of the conjugated material imparted by the [NTf2] -anion.…”

“…In oligonucleotide synthesis, the first nucleoside is attached to the support via a dicarboxylic acid, such as a 3'-Osuccinyl linking group. 5,6,14,[25][26][27] This is generally achieved by coupling the acid at the 3'-end of the nucleoside via an ester linkage. This synthesis often uses pyridine, 36 Mechanochemical coupling between succinic anhydride and DMT-dT in the presence of DMAP was studied first (Table 1).…”

“…21,22 In that context, ionic liquids have been successfully used for the synthesis of oligopeptides 23 and oligosaccharides, 24 although concern was expressed as to whether the technique could be applied to long and complex oligomers. Such ionic liquid-based oligomerisation methodologies were later adapted for oligonucleotide synthesis by the Damha group, who used N-methylimidazolium tetrafluoroborate ionic liquids to synthesise both oligodeoxyribonucleotides 25,26 and oligoribonucleotides. 27 Use of this ionic liquid support was advantageous in allowing purification of the supported oligomer by precipitation from ethyl acetate (EtOAc) and diethyl ether, after quenching excess nucleoside phosphoramidites with ethanol or tert-butanol.…”

Applications of Mechanochemistry for the Synthesis of DNA on Ionic Liquid Supports

“…[23,24] In that context, ionic liquids have been successfully used for the synthesis of oligopeptides [25] and oligosaccharides, [26] although some concern was expressed as to whether the technique could be applied to long and complex oligomers due to the changing solubility properties as the oligomer grows. Such ionic liquid-based oligomerisation methodologies were later adapted for oligonucleotide synthesis by the Damha group, who used N-methylimidazolium tetrafluoroborate ionic liquids to synthesise both oligodeoxyribonucleotides [27,28] and oligoribonucleotides. [29] Use of this ionic liquid support was advantageous in allowing purification of the supported oligomer by precipitation from EtOAc and diethyl ether, after quenching excess nucleoside phosphoramidites with ethanol or tert-butanol.…”