Specific Measures for Efficient Deprotection

Deprotection involving concentrated ammonia is a critical step in the synthetic cycle. In particular, the use of (fluorescent) dyes linked to oligonucleotides or some other specific modifications is limited due to their lack of stability in the presence of concentrated ammonia solution, which is required for cleavage of the amides. Sometimes an improvement in deprotection yields may be achieved by an increase of reaction temperature from 55°C to 80°C, which reduces reaction time to 60 min [48]. A prerequisite for significantly milder cleavage protocols, however, is a change in protective groups at pyrimidine and purine bases. 

The 2-(acetoxymethyl)benzoyl-protective group (4,5,6) has initially been used in the synthesis of particularly base-labile backbone modifications, such as phosphate methyl esters or methylphosphonates [51, 52], again thymine remains unprotected. Cleavage is achieved by elegant intramolecular reaction within 90 min at room temperature by use of potassium carbonate in dry methanol (Fig. 11). 

Another established method for base protection is the use of dimethylformamidine (dmf) (7, 8, 9) protected phosphoramidites. In this case deprotection is achieved in concentrated ammonia solution at 55 °C within 60 min [53,54], 

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