Optimization and characterization of light activated RNA interference

We have previously shown that the introduction of photo‐labile di‐methoxy nitro phenyl ethyl (DMNPE) groups into small interfering RNAs allows for the toggling of RNA interference with light. Modified siRNAs are either partially or completely blocked from reducing gene expression until they are irradiated. After irradiation, the now‐deprotected siRNAs exert an RNA interference effect that is similar to native siRNAs. The focus of this work is the further characterization of this phenomenon. We demonstrate, via ESI‐MS, that the kinetics of deprotection of siRNA closely parallel the kinetics of RNA interference itself; Shorter periods of light activated deprotection lead to less RNA interference effect, and is paralleled by a reduced release of native siRNA as detected vi ESI‐MS. The ability to finely and continuously vary gene expression through variations in light exposure should be a useful tool for examining the effects of intermediate phenotypes. In addition we present further refinements to nucleic acid species that exert light activated RNA interference. Specifically we examine non‐siRNA nucleic acids, new photo‐labile groups and new techniques for controlling their points of modification.