Figure 2.

Knockdown Activity Modeled by Duplex Melting Temperature and 3-mer Motifs in the Gap Region

(A and B) Knockdown activity in HeLa cells as a function of temperatures of melting (T_m) measured from absorbance melting curves for all the 256 gapmers targeting region A (A) and the 256 gapmers targeting region B (B). Gray area indicates T_m range for the top 10% most active gapmers. Vertical dashed line indicates midpoint of this T_m range, and horizontal dashed line indicates cutoff for the top 10% most active gapmers. (C) Effect sizes of 3-mer motifs found in the gap regions as well as ΔT_m, the T_m distance from the region-specific optimal T_m, as determined by iterated re-weighted least-squares fitting of a robust linear model. Error bars indicate 1 SD (D). Scatterplot of measured mRNA levels after gapmer knockdown versus mRNA levels captured by the linear model based on 3-mer motifs and ΔT_m. r² indicates coefficient of determination.