Studies on the t-butyldimethylsilyl group as 2'-O-protection in oligoribonucleotide synthesis via the H-phosphonate approach

Abstract

Two model compounds, 1 and 2, have been studied to test the stability of the t-butyldimethylsilyl (t-BDMSi) group towards conditions used during chemical synthesis of RNA fragments by the H-phosphonate approach. When 1 was treated with anhydrous acid for 16 h both the H-phosphonate diester and the t-BDMSi group remained intact. Removal of the t-BDMSi group from 2 with 1.0 M tetrabutylammonium fluoride (TBAF -3H20) in THF was complete within 4 h and neither concomitant cleavage nor migration of the phosphodiester linkage could be detected even after 24 h. The dimer 2 was not completely stable towards concentrated aqueous ammonia and both loss of the t-BDMSi group and concomitant cleavage of the phosphodiester linkage occurred upon prolonged treatment. These reactions were substantialy suppressed in ethanol containing ammonia solutions, however to alleviate this problem during oligoribonucleotide synthesis, more labile protecting groups for heterocyclic bases would be desired. In conclusion, these studies indicate that 2 -O-t-BDMSi can be considered as a convenient and safe protecting group, which should secure synthesis of oligoribonucleotides with exclusively 3'-5' internucleotidic linkages.

Advances in the Synthesis of Oligonucleotides by the Phosphoramidite Approach

“…Stawinski et ai.435, 439 have indeed shown that the 2'-O-TBDMS group in 230 was cleaved by concentrated ammonium hydroxide at 55 °C at a rate of 27% after 8 h and 65% after 24 h. The internucleotidic phosphodiester cleavage resulting from this loss occurred at a rate of 2.7% after 8 h and 23% after 24 h. 435,439 u…”

“…The final removal of the 2'-O-TBDMS group from 230 with tetra-n-butylammonium fluoride occurred smoothly within 4 h without cleavage or isomerization of the phosphodiester linkage. 435,439 In an effort to reduce the damage caused to the 2'-O-TBDMS group by ammonium hydroxide during the removal of the aglycone protecting groups, Wu et a/. 229 and Chaix et a/.228,312 reported the solid-phase synthesis of oligoribonucleotides via N-phenoxyacetylated 2'-O-TBDMS ribonucleoside phosphoramidites.…”

NMR structure of a 4 × 4 nucleotide RNA internal loop from an R2 retrotransposon: Identification of a three purine–purine sheared pair motif and comparison to MC-SYM predictions

“…The phosphoramidites and CPG support were bought from Glen Research or Proligo. For each 1-mmol synthesis, the base-protecting groups and CPG support were removed by incubating in 2 mL of 3:1 (v/v) ammonia/ethanol solution at 55°C overnight (Stawinski et al 1988). The solid support was removed by filtration and the filtrate was lyophilized.…”

Stability of a 2′‐O‐(Carbamoylmethyl)adenosine‐Containing Dinucleotide

“…Addition of 1 % water to the methanolic ammonia (Figure 2, g) also did not cause formation of 5, which suggests that these conditions are robust and not particularly sensitive to moisture. Two other sets of conditions that are sometimes used for deprotection of oligonucleotides at room temperature also did not cause formation of 5; 25 % ethylenediamine in ethanol (Figure 2, i) and a mixture of concentrated aqueous ammo-nia (32 %) and ethanol (3:1) [24] (Figure 2, j). In summary, these studies clearly show substantial degradation of the carbamoylmethyl group to the carboxymethyl derivative under standard conditions used for deprotection in oligonucleotide synthesis (concentrated aqueous ammonia at 55°C), whereas under the other tested conditions the carbamoylmethyl moiety remained intact.…”