The field of therapeutic oligonucleotides has rebounded due to the development of small interfering RNAs (siRNAs). An upsurge is taking place in industry and academia alike, owing to the fact that applications of siRNA in life science research are of outstanding importance in their own right. A key feature of siRNAs is the reprogramming of a complex cellular mechanism, originally evolved to control gene expression. Reprogramming by siRNA includes redirecting catalytic RNase activity to a target mRNA of choice. Despite impressive advances in pharmaceutical chemistry, biology, and technology, the efficiency of different siRNAs, once delivered into the cell, is still variable. Moreover, most of the delivered siRNA material does not reach its final destination in the catalytic complex intact. Conjugation of siRNA to dyes that form donor-acceptor pairs in fluorescence resonance energy transfer (FRET), allows tracing the distribution of intact siRNA during nanoscale formulation and across the various subcellular compartments. Intact siRNAs performs a movement into the nucleus and out again, before being subject to degradation, which leads to perinuclear accumulation of siRNA debris. We are currently characterizing differential distribution patterns of siRNAs from different formulations, with various chemical modifications, and of distinct biological activity. An important aspect of such therapeutic oligonucleotides are their immunostimulant activities. Tracing the degradation of siRNA in cells: Using microinjection of FRET-labeled siRNAs, we can trace minute amounts of intact siRNA inside cells, in order to study pharmacological aspects of intracellular distribution. The labeling is also suitable to monitor in real-time the incorporation of siRNAs in liposomal formulations in very small batch sizes. This work has raised substantial interest in the field.