Cellular dynamics of antisense oligonucleotides and short interfering RNAs.

We aim to compare quantitatively the dynamics of the effectiveness of antisense oligonucleotides (AS ODNs) versus short interfering RNAs (siRNAs) and relate their effectiveness to sequence metrics (e.g., predicted free energy of binding). AS ODNs against a quantitative model target, pd1EGFP (destabilized enhanced GFP [green fluorescent protein]), were selected using our thermodynamic model, and siRNA sequences were designed to be identical to the AS ODN sequences in the antisense strand. We evaluated d1EGFP inhibition in transiently and stably transfected Chinese hamster ovary (CHO) cells over time using flow cytometry. Overall, our results show that the rationally designed AS ODN and siRNA sequences proved effective inhibitors of GFP expression and suggest that certain regions of mRNA may be susceptible to both AS ODNs and siRNAs.