Oligonucleotide synthesis yield

The protected nucleoside-3-phosphoramidite monomer units such as 671 are used in the solid-phase oligonucleotide synthesis. In the 60mer synthesis, 104 allylic protective groups are removed in almost 100% overall yield by the single Pd-catalyze reaction with formic acid and BuNH2[432], N,(9-protection of uridine derivatives was carried out under pha.se-transfer conditions[433]. 

Palladium-mediated (Sonogashira) coupling [332] of 5-iodouracil with alkynes can be performed under mild reaction conditions, and is compatible with the supports, linkers, and protective groups used in solid-phase oligonucleotide synthesis (Entries 12 and 13, Table 15.28). This coupling reaction has been used to prepare modified oligonucleotides on polystyrene and on CPG. The reaction of halopyrimidines with amines to yield aminopyrimidines is discussed in Section 10.1.2. 

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