Conformational-Dependent and Independent RNA Binding to the Fragile X Mental Retardation Protein

Figure 3

Annealed BC1 RNA and unannealed BC1 RNA differ structurally. (a) Secondary structure model of BC1 RNA from M-fold. Black arrows indicate potential RNase VI cleavage sites (both sides of the stem); gray arrows mark potential RNase A cleavage sites. (b) Serial treatment of annealed and unannealed full-length BC1 RNA with RNase A starting at 1 ng as indicated. (c) Ten-fold serial treatment of annealed and unannealed full-length BC1 RNA with RNase VI starting with 0.1 units/μL (upper panel), or 0.5 units/μL (lower panel) as indicated. RNA was visualized by ethidium bromide staining. Arrows mark the major conformers that can be resolved in this system. Lane M shows 100 bp molecular weight markers.