Review Article

Variables and Strategies in Development of Therapeutic Post-Transcriptional Gene Silencing Agents

Figure 4

Secondary and tertiary structure as a limiting variable in PTGS efficacy. Energy diagrams are presented for both the target mRNA and the PTGS agent. The folded target mRNA has a site targeted for annealing which is buried in secondary or tertiary structure. The rate of unfolding of this region is determined by the activation energy required for conformational transition that leads to accessibility of the annealing platform. For the folded target RNA to be accessible it must present a single-stranded annealing platform(s) at its surface to allow annealing with the PTGS agent upon intermolecular collision. Buried regions of the RNA that are targeted must wait at physiological temperatures for relaxation of secondary and tertiary structure in order to present an annealing platform. Many regions are expected to never be exposed. The Arrhenius rate provides an estimate of how long it takes for a single-stranded platform to emerge at physiological temperature (310°K = 37°C) and is dependent upon the activation energy (Ea) of the transition. Likewise, any internal secondary structure of the PTGS agent itself can prevent annealing to target or slow catalysis and impact efficacy. Melting of inhibitory secondary or tertiary structure in the PTGS agent then can allow exposure of the antisense flanks to support annealing to the target mRNA.
531380.fig.004