Carboxylic acids as promoters for internucleotide-bond formation via condensation of a nucleoside phosphoramidite and a nucleoside: relationship between the acidity and the activity of the promoter

The relationship between the activity and the acidity of a carboxylic acid as a promoter for condensation of a nucleoside phosphoramidite and a nucleoside was investigated. The investigation revealed that the acid, the pKa value of which in acetonitrile is less than 18, is capable of promoting the condensation reaction, and acid with a pKa value outside of this range does not serve as a promoter. In carboxylic acids serving as promoters, the ones with higher acidity generally show greater activity. In particular, acids with a pKa value less than ca. 16 (measured by a potentiometric method), such as trichloroacetic acid (pKa=10.6), trifluoroacetic acid (pKa=12.7), dichloroacetic acid (pKa=13.2 or 15.8), and 2,4-dinitrobenzoic acid (pKa=16.1), show high levels of activity higher than that of conventionally used 1H-tetrazole. These carboxylic acids generally serve as excellent promoters for both the liquid-phase and the solid-phase synthesis of oligonucleotides via phosphoramidite method.