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Modeling Recursive RNA Interference

Figure 4

Optimization of restoration.

Figures of merit describing restoration efficiency plotted as a function of RNAi efficacy parameter gamma. Pink curve plots the relative restoration ratio R which measures the ratio of restoration relative to the initial level of knockdown. Larger R indicates that gene expression is restored to a level closer to its normal expression level in the absence of any RNAi, as required for switch-off/switch-on experiments [15]. Maximum value of R is 0.25 which occurs for γ = 2, corresponding to a system in which RNAi knocks down gene expression only three-fold. Blue curve plots the normalized absolute restoration Δ which is the reporter level during recursive RNAi minus the reporter level without recursive RNAi, expressed in units normalized by the pre-RNAi expression level of the reporter. Larger values indicate more easily detected restoration. Both curves show a peak, indicating optimal performance, at comparatively low values of gamma.

Figure 4