Large Scale Synthesis

The most commonly used dA-CE Phosphoramidite containing benzoyl protecting groups suffers substantial degradation by depurination after excessive exposure to acids like TCA. At the same time, the depurination resistant dA monomer, protected with diethylformamidine (def), is essentially stable to depurination during the same exposure to TCA. The def-dA monomer is fully compatible with regular deprotection procedures. Dmf-dG is also a depurination resistant CE Phosphoramidite with the isobutyryl group of the original monomer replaced with dimethylformamidine (dmf). Although depurination does occur in regular oligonucleotide synthesis, the degradation is at an extremely low level. However in certain other circumstances, depurination may become more significant, such as synthesis of long oligos, chip-based synthesis, and large-scale synthesis

The most common side reaction during deprotection of oligonucleotides on a large scale is the alkylation of dT residues by acrylonitrile, formed by ß-elimination of the cyanoethyl phosphate protecting groups, to generate N3-cyanoethyl-dT.

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  1. Nucleoside deoxythymidine Remove This Item
  2. Sugar Type Deoxyribose Remove This Item
  • N3-Cyanoethyl-dT
    N3-Cyanoethyl-dT (10-1531)
    Catalog #: 10-1531
    Formal Name: 5'-Dimethoxytrityl-N3-(2-cyanoethyl)-2'-deoxyThymidine,3'-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite
 
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