Figure 3
From: Partition function and base pairing probabilities of RNA heterodimers
Example for the concentration dependency for two mRNA-siRNA binding experiments. In [54], Schubert et al. designed several mRNAs with identical target sites for an siRNA si, which are located in different secondary structures. In variant A, the VR1 straight mRNA, the binding site is unpaired, while in the mutant mRNA VR1 HP5-11, A', only 11 bases remain unpaired. We assume an mRNA concentration of a = 10 nmol/1 for both experiments. Despite the similar binding pattern, the binding energies (ΔF = FAB- FA- FB) differ dramatically. In [54], the authors observed 10% expression for VR1 straight, and 30% expression for the HP5-11 mutant. Our calculation shows that even if siRNA is added in excess, a large fraction of the VR1 HP5-11 mRNA remains unbound.