Dimethoxytrityl protective group removal

In step 1 of each oligonucleotide-synthesis cycle the 5 -terminal 4,4 -dimethoxytrityl protecting group is removed with trichloroacetic acid, and the support is washed with acetonitrile to prevent dctritylation of the next incoming phosphoramidite. The 4,4 -dimethoxy-... 

J. I. Asakura, M. J. Robins, Y. Asaka, and T. H. Kim, Removal of acetal, silyl, and 4, 4 -dimethoxytrityl protecting groups from hydroxyl functions of carbohydrates and nucleosides with clay in aqueous methanol, J. Org. Chem., 61 (1996) 9026-9027. 

The 5 -0-dimethoxytrityl protecting group is removed by treatment of the reaction mixture with 3% dichloroacetic acid in dichloromethane. 

The synthetic scheme typically involves chain-extending addition of protected mononucleotides to a nucleoside bound covalentiy at the 3 -hydroxyl to an inert siUca-based soHd support, such as controlled pore glass (Fig. 11). The initial base-protected 5 -O-dimethoxytrityl (DMT) deoxynucleoside is linked to the soHd support via the reaction of a siUca-bound amino-silane and the -nitrophenylester of the 3 -succinylated nucleoside, yielding a 3 -terminal nucleoside attached to the soHd support (1) (Fig. 11). Chain elongation requites the removal of the 5 -DMT protecting group. 

Step 2 The second step is removal of the DMT protecting group by treatment with dichloroacetic acid in CH2CI . The reaction occurs by an S -l mechanism and proceeds rapidly because of the stability of the tertiary, benzylic dimethoxytrityl cation. 

The dimethoxytrityl ester protecting group is now removed by treatment with mild acid (CCI3CO2H), which is insufficiently reactive to hydrolyse the amide protection of bases, or the cyanoethyl protection of the phosphate. The coupling cycle can now be repeated using a phosphoramidite derivative of the next appropriate nucleoside. The sequences will be continued as necessary until the desired oligonucleotide is obtained. 

It then remains to remove protecting groups and release the product from the support. All of these tasks, except for the removal of the dimethoxytrityl group, are achieved by use of a single deprotection reagent, aqueous base (ammonia). The cyanoethyl groups are lost from the phosphates by base-catalysed elimination, and amide protection of the bases is removed by base-catalysed hydrolysis. The latter process also achieves hydrolysis of the succinate ester link to the support. 

Bis(hydroxymethyl)phosphonic acid esters that incorporated thymine were employed as a backbone to prepare short oligonucleotide chains. This chain was prepared by condensation of the bis(4,4 -dimethoxytrityl) protected phosphonic acid and iV or N -(2-hydroxyethyl)thymine in the presence of l-(2-mesitylenesul-fonyl)-3-nitro-l,2,4-triazole or by an Appel reaction with or N -(2-aminoethyl)thymine (89a-h). Selective removal of one DMT-group and phos-phitylation yielded the building blocks for solid supported synthesis of the short oligomers by the phosphoramidite approach. Holy has reported the synthesis of 8-amino and 8-substituted amino derivatives of acyclic purine nucleotide analogues. The 8-amino, 8-methylamino- and 8-dimethylamino-adenine and -guanine analogues of iV-(2-phosphonomethoxyethyl) and (S)-iV-(3-hydroxy-2-phosphono-methoxy-propyl) derivatives of purines (90a-i), were prepared by... 

RNA Synthesis. - Methods for the synthesis of RNA are now routine but less efficient than DNA synthesis. The most popular phosphoramidite reagents employ acyl protecting groups for the exocyclic amino functions of the nucleosides, dimethoxytrityl for the 5 -hydroxyl function and 2 -0-tert-butyldimethyl-silyl (tBDMS) for the 2 -hydroxyl function. The silyl protecting group is usually removed by treatment with IM TBAF or ti iethylamine.3HF. Acidic deprotection conditions have also been developed for removal of tBDMS groups. ... 

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