Method Optimizes Interfering RNA

A new high-throughput method allows researchers to optimize nucleic acids for RNA interference (RNAi), Merck scientists report (J. Am. Chem. Soc., DOI: 10.1021/ja2068774). In RNAi, a double-stranded RNA molecule called small interfering RNA (siRNA) guides an enzyme complex (RISC) to cleave the complementary messenger RNA (mRNA) and prevents its translation into protein. The siRNAs can be improved by chemical modification so they interact more effectively with RISC and the target mRNA. To streamline this optimization, Gabor Butora and coworkers sequentially replaced the natural nucleosides with inosine, a nucleoside containing ribose and hypoxanthine, which acts as a universal base that pairs up with any of the canonical bases. By using inosine, the team can evaluate modifications along the siRNA oligomer and test their effect without having to synthesize modified versions of all four natural nucleosides. To illustrate the methodology they used an siRNA corresponding to part of the human ApoB gene as a test case and found that nucleosides containing 2´-O-benzyl modification would be well tolerated at four positions in the siRNA.