Fully 2'-deoxy-2'-fluoro substituted nucleic acids induce RNA interference in mammalian cell culture

RNA interference is a phenomenon in which RNA molecules elicit potent and sequence-specific post-transcriptional gene silencing. Recent studies have shown that small interfering RNA containing pyrimidine 2'-fluoro modifications elicit RNAi. In this study, we demonstrate that fully-2'-fluorinated nucleic acids can be generated for RNAi studies through either custom solid-phase synthesis or in vitro transcription using a mutated polymerase and fluorinated nucleoside triphosphates. Single-stranded and hybridized fully-2'-fluorinated nucleic acids were subjected to a ribonuclease to assess their resistance to digestion. Duplex siFNA and antisense fully-2'-fluorinated nucleic acids were evaluated for their ability to knockdown green fluorescent protein expression in mammalian cell culture. Based on the results, fully-2'-fluorinated nucleic acids can be successfully generated, and fully-2'-fluorinated nucleic acids products show superior resistance to digestion over native RNA. Melt curve analysis suggests that transcribed fully-2'-fluorinated nucleic acids may contain base miscoding errors or early termination products. Small interfering fluoronucleic acid can induce RNAi and the silencing efficiency is nearly equivalent to the unmodified small interfering RNA species. Silencing from antisense fully-2'-fluorinated nucleic acids was greatly reduced relative to the duplex form. The lack of silencing activity from single-stranded fully-2'-fluorinated nucleic acids, combined with reverse transcription polymerase chain reaction data showing that mRNA decreases following siFNA treatment, suggests that knockdown from siFNA is likely enzymatically driven as opposed to simple translational arrest.