Proton-block strategy for the synthesis of oligodeoxynucleotides without base protection, capping reaction, and P-N bond cleavage reaction

A new N-unprotected phosphoramidite method called the "proton-block" approach was developed for the chemical synthesis of oligodeoxynucleotides based on the hitherto simplest and rational principle of acid-base reactions. This concept involves protection of the nucleobases of deoxycytidine and deoxyadenosine with "protons" to convert them to unreactive protonated bases during condensation by use of promoters having pK(a) values lower than 2.8. This strategy was applied to the synthesis of d[CpT] and d[ApT] to check the side reactions associated with the base residues. In this "proton-block" method, 5-nitrobenzimidazolium triflate (NBT) was found to be the best promoter, and THF was superior to CH3CN as the solvent so that the concomitant detritylation due to the inherent acidity of the promoter could be greatly suppressed. Application of this strategy to the solid-phase synthesis gave d[CpT], d[ApT], d[ApA], d[CpC], and d[GpT] as almost single peaks in HPLC analysis. Similarly, d[ApApApT] and d[CpCpCpT] were successfully synthesized without significant side reactions. Finally, d[CpCpCpCpCpCpT] and d[ApApApApApApT] were obtained as the main products. In the case of a longer oligomer, d[CpApGpTpCpApGpTpCpApGPT], a mixed solvent of CH3CN-N-methylpyrrolidone (1:1, v/v) was superior to THF so that the desired oligodeoxynucleotide could be isolated in a satisfactory yield. These results suggest that DNA synthesis can be carried out simply by using the protonated bases at the oligomer level not only without base protection but also without the capping reaction and the posttreatment of branched chains with MeOH-benzimidazolium triflate that previously was requisite. It is concluded that most of the reactions and solvent effects involved in this strategy can be explained in terms of simple acid-base reactions. Some problems associated with the previous posttreatment are also discussed with our own results.