Nucleophilic Groups Protection of Phosphoramidite for DNA Synthesis

Abstract

Phosphoramidite are the DNA building blocks. For the DNA synthesis to proceed it is necessary to block or protect all the nucleophilic centres not involved in the reaction at each step of the synthesis. The commonly used DNA protecting groups includes; dimethoxytrityl (DMT) which is used to protect the 5'-OH, benzoyl (Bz) is used to protect the exocyclic NH2 groups of adenine and cytosine whilst isobutyryl (Ib) group is used for guanine protection. Thymine does not need protection as it has no exocyclic NH2 groups. The phosphate group is usually protected with the cyanoethyl group, whilst the 3'-OH is protected by virtue of the connection to the controlled pore glass (CPG) solid support. Here, the 2-amino group of the nucleoside, 1 was initially protected as its dimethylformamidine derivative (using N,N-dimethylformamide) which later decomposed into the N-formylamino compound which was never been used before and was found to be suitable for the protection of the exocyclic amino group for DNA synthesis. The 5'-OH group as usual was protected with dimethoxytrityl (DMT) using dimethoxytrityl chloride following which phosphitylation gave the phosphoramidite compound 4. The chemistry involved in the conversion of the dimethylformamidine to N-formylamino compound is presented here.