A Safe and Practical Procedure for Global Deprotection of Oligoribonucleotides

Abstract

We report a practical global deprotection of RNA 2'-O-tert-butyldimethylsilyl (TBS) ethers using commercially available aqueous NH(4)F. The procedure is applicable to both 96-well plate format and large-scale production of RNA. This improved procedure provides a safe, mild, and cost-effective alternative to highly hazardous Et(3)N x 3 HF, a reagent commonly used in the routine synthesis of RNA.

A Stereocontrolled Synthesis of a Phosphorothioate Cyclic Dinucleotide-Based STING Agonist

“…Final deprotection using triethylamine trihydrogen fluoride (Et 3 N·3HF) provided clean conversion to BMT-390025; however, difficulties associated with the workup and purification of the resulting triethylammonium salt contributed to significant product loss. Optimal conditions using the readily available and less toxic ammonium fluoride resulted in complete deprotection after heating in anhydrous MeOH overnight . SFC purification conditions were developed using “matched” counterion ammonium acetate as the mobile phase, and direct injection of the final deprotection solution led to an efficient final purification delivering the target compound in 60% yield.…”

Safe Deprotection Strategy for the Tert‐Butyldimethylsilyl (TBS) Group During RNA Synthesis

“…One major concern during 2′− O desilylation is a side reaction involving phosphoryl migration, which could result in unintended 2′–5′ linked product; these concerns are addressed by subjecting dimer sequences rUrU and rUOmeU to the NH 4 F and KF desilylation conditions, respectively. Desilylation of rUrU using NH 4 F and desilylation of rUOMeU using KF do not result in phosphoryl migration as confirmed by 1 H NMR trace analysis (Zewge et al, ).…”

“…This study was initiated with a desire to develop alternative desilylating technology and avoid or reduce the use of TEA•3HF as a commonly used reagent in our laboratories. Various fluoride sources and Lewis acids have been investigated (Zewge et al, 2010). The use of acidic reagents for desilylation was not effective for oligoribonucleotides (detrityla-tion and decomposition of RNA was detected via HPLC & LC/MS).…”

Modified nucleotides may have enhanced early RNA catalysis

“…Standard and modified RNA oligonucleotides were synthesized in house via standard phosphoramidite methods using 2′-tert-Butyldimethylsilyl (TBDMS) protecting groups (61) on an ABI 3900 automated synthesizer using commercial reagents [rA(Bz) and rG(iBu) from Thermo Scientific, rC(Ac) and rU(CE) from Bioautomation, and 2′-OMe-rU from Proligo] and 2′-OMe-Bn-dU phosphoramidite, which was synthesized from 2′-OMe-rU (Proligo) as described previously (62). After initial cleavage and base deprotection with t-butyl amine:methanol:water (1:1:2) overnight at 37°C, deprotection of the 2′-O-TBDMS ethers was accomplished using an ammonium fluoride/ dimethylsulfoxide scheme (63).…”