Chromophoric 5'-O-Silyl protection of N-protected 2'-ACE ribonucleosides for solid-phase RNA synthesis

Recent advances in the understanding of the pivotal roles played by endogenous small RNAs in gene regulation have resulted in a substantial and rapidly growing market for synthetic RNA. 5'-Silyl-2'-ACE chemistry has proven to be a robust and reliable technology for the synthesis of oligoribonucleotides. This unit describes an important improvement to this chemistry, by adding a cycle-to-cycle traceability analogous to that inherent in 5'-dimethoxytrityl-based approaches. This is achieved by first regioselectively introducing a 5'-alkynylsilyl protecting group onto the 2'-ACE-protected nucleosides. The 5'-alkynylsilyl group is then reacted with an azide derivative of the chromophore Disperse Red 1, which enables spectrophotometric interrogation of each coupling step following 5'-deprotection. Finally, the protected nucleosides are elaborated into their 3'-phosphoramidite derivatives for use in solid-phase RNA synthesis.