RNA oligonucleotide synthesis via 5′-silyl-2′-orthoester chemistry

The chemical synthesis of RNA oligonucteotides is a valuable resource far biological research. A new approach for RNA synthesis that is now as reliable and efficient as DNA synthesis methods is described in this report. A 5 ' -O-silyl ether is used in conjunction with acid-labile orthoester protecting groups on the 2 ' -hydroxyls. RNA synthesis proceeds efficiently on commercial synthesizers in high yields. Analysis by anion-exchange HPLC shows that the quality and yields of RNA synthesized with this chemistry are unprecedented. Furthermore, this chemistry enables analysis and purification of stable 2 ' -O-protected RNA. This property serves to minimize possibilities for degradation of the RNA. In addition, it now possible to analyze troublesome sequences, which, when fully 2 ' -O-deprotected, do not easily resolve into one major conformation due to strong secondary structure. When ready for use, the RNA is easily 2 ' -O-deprotected in mild-acidic aqueous buffers in 30 min. This new RNA chemistry has enabled the routine high-quality synthesis of RNA oligonucleotides up to 50 bases in length regardless of sequence or secondary structure. (C) 2001 Academic Press.