Scientific Publications by FDA Staff

Chemistry 2013 Apr 2;19(14):4623-32

The 2-Cyano-2,2-dimethylethanimine-N-oxymethyl Group for the 2'-Hydroxyl Protection of Ribonucleosides in the Solid-Phase Synthesis of RNA Sequences.

Cieslak J, Ausin C, Grajkowski A, Beaucage SL

The reaction of 2-cyano-2-methyl propanal with 2'-O-aminooxymethylribonucleosides leads to stable and yet reversible 2'-O-(2-cyano-2,2-dimethylethanimine-N-oxymethyl)ribonucleosides. Following N-protection of the nucleobases, 5'-dimethoxytritylation and 3'-phosphitylation, the resulting 2'-protected ribonucleoside phosphoramidite monomers are employed in the solid-phase synthesis of three chimeric RNA sequences, each differing in their ratios of purine/pyrimidine. When the activation of phosphoramidite monomers is performed in the presence of 5-benzylthio-1H-tetrazole, coupling efficiencies averaging 99 % are obtained within 180 s. Upon completion of the RNA-chain assemblies, removal of the nucleobase and phosphate protecting groups and release of the sequences from the solid support are carried out under standard basic conditions, whereas the cleavage of 2'-O-(2-cyano-2,2-dimethylethanimine-N-oxymethyl) protective groups is effected (without releasing RNA alkylating side-products) by treatment with tetra-n-butylammonium fluoride (0.5 m) in dry DMSO over a period of 24-48 h at 55 degrees C. Characterization of the fully deprotected RNA sequences by polyacrylamide gel electrophoresis (PAGE), enzymatic hydrolysis, and matrix-assisted laser desorption/ionization (MALDI) mass spectrometry confirmed the identity and quality of these sequences. Thus, the use of 2'-O-aminooxymethylribonucleosides in the design of new 2'-hydroxyl protecting groups is a powerful approach to the development of a straightforward, efficient, and cost-effective method for the chemical synthesis of high-quality RNA sequences in the framework of RNA interference applications.