Figure 1.

The stability of transitional nucleation correlated with the target binding affinity of RNAi. (A) The transitional nucleation (ΔG[2:6]) is prerequisite to initiate functional miRNA-like target interaction, in which a small RNA loaded into Ago was geometrically tilted (based on Ago–miRNA structure studies), represented as a model (see Supplementary Figure S1). Of note, base pairing in position 6, named pivot, critically functions as transition to triggering RNAi. (B) Considering free energy of transitional nucleation, −ΔG[2:6] was used to denominate number of target sites (seed or total) in Ago HITS-CLIP data from mouse brain, compared with the expression level of cognate miRNAs (log₂[Ago–miRNA]_family) by calculating the correlation coefficient (R²), of which values were indicated in the table. (C–D) R² was further improved by considering free energy of transitional nucleation (ΔG[2:6]_avr). (E–H) The same analyses used in panels C–D except applied to Ago HITS-CLIP data from 293S cells (E–F) or human hearts (G–H).