Chemically Stabilized Phenylboranylidene Groups Having a Dimethoxytrityl Group as a Colorimetrically Detectable Protecting Group Designed forcis-1,2-Diol Functions of Ribonucleosides in the Solid-Phase Synthesis of m₂^2,2G^5‘ppT

Abstract

To not only improve the inherently poor stability of the phenylboranylidene group as a protecting group of the 2',3'-cis-diol function of ribonucleosides but also introduce a colorimetrically detectable function into its mother structure, various 2-[(dialkylamino)methyl]phenylboronic acid derivatives having a [(4,4'-dimethoxytrityl)oxy]methyl group were synthesized. The reaction of uridine with these substituted phenylboronic acid derivatives gave the corresponding 2',3'-O-phenylboranylideneuridine derivatives. The stability of these phenylboranylidene groups was examined. As a result, it was shown that the steric hindrance around the amino group greatly influenced the stability of the 2-substituted phenylboranylidene groups. The 2-aminomethyl-5-[[(4,4'-dimethoxytrityl)oxy]methyl]phenylboranylidene group was the most stable. Its 2-dimethylamino counterpart, the 2-[(dimethylamino)methyl]-5-[[(4,4'-dimethoxytrityl)oxy]methyl]phenylboranylidene group, was the second most stable. When the most and second stable protecting groups were applied to the synthesis of m(2)(2,2)G(5)(')ppT on controlled pore glass, the second stable protecting group showed the best result. The use of this DMTr-containing protecting group enabled us to estimate colorimetrically the amount of the m(2)(2,2)G residue that was incorporated into the reactive site of the pT-loaded CPG resin.

Selective Enzymatic Demethylation of N2,N2‐Dimethylguanosine in RNA and Its Application in High‐Throughput tRNA Sequencing

“…Several methods have been reported for preparing m 2 G and m 2 2 G derivatives but the most straightforward one used a “one‐step” reductive amination reaction to methylate the exocyclic amine directly . We attempted to combine the reductive amination with Beigelman's protecting strategy to synthesize both phosphoramidites 7 a and 7 b at the same time.…”

Boron and nucleic acid chemistries: merging the best of both worlds

“…Since the pioneering work of Yurkevich et al, 80 the use of boronic acids as 2 0 ,3 0 -dihydroxyl protecting groups for ribonucleosides has been widely developed. [81][82][83][84] In 2005, Sekine et al reported the supported synthesis of a diMe GppdT dimer (19) in which the 5 0 position of each nucleotide is connected by a pyrophosphate bridge (Fig. 11).…”

“…11). 83 The key step of the synthesis is the coupling of a supported 2 0 ,3 0 -boronoprotected activated guanine (20) with a thymidine monophosphate (21). After deprotection using 1% TFA in dichloromethane and cleavage from the support, dimer 19 was obtained in 49% isolated yield.…”

Selective Protection of Secondary Alcohols by Using Formic Acid as a Mild and Efficient Deprotection Reagent for Primary tert-Butyldimethylsilyl Ethers

“…Numerous investigations have been made to achieve selective deprotection of primary TBDMS ethers. Various acids including HCl, 5 HF, 6 acetic acid, 7,8 CSA, 9 toluenesulfonic acid (TsOH), 10 and trifluoroacetic acid (TFA) 11 have been investigated. Smith and Liu used 1% HCl in ethanol to selectively deprotect primary TBDMS ethers while performing the total synthesis of discodermolide.…”