Figure 2
Close relationship between efficacy of miRNA-mediated gene silencing and combinatorial thermodynamic stabilities in the seed-target duplex and the 5′ terminal miRNA duplex.
(a) Correlation between miRNA-mediated gene-silencing activity (relative luciferase activity) and the calculated Tm2–8 of the protein-free seed duplex. The set of luciferase activities compromised by miRNA-mediated gene silencing at 5 nM miRNA concentration was obtained from Figure 1. Tm2–8 value of the protein-free seed region was calculated using the nearest neighbor method. Relative luciferase activity and calculated Tm2–8 showed little, if any, correlation with each other and had a coefficient of −0.50 (p ≤ 0.05). (b) The luciferase activity compromised by miRNA-mediated gene silencing at 5 nM miRNA concentration showed little, if any, correlation with calculated miTm1–5 (r = 0.50, p ≤ 0.05). (d) Correlation between the calculated Tm values in the seed region (positions 2–8) and 5′ terminal region (positions 1–5). The calculated Tm2–8 and the calculated miTm1–5 showed no correlation with each other and had a coefficient of 0.14 (p > 0.05). (d) Correlation between miRNA-mediated gene-silencing activity and the calculated Tm2–8 − 0.53 × miTm1–5 value. Relative luciferase activity and calculated Tm2–8 − 0.53 × miTm1–5 were highly negatively correlated with each other and had a coefficient of −0.79 (p ≤ 0.01).
