Figure 2.

Molecular beacon only binds misfolded RNA. (A) Fluorescence of molecular beacon MB-P3 (100 nM) in the presence of 300 nM L-21 ribozyme RNA at 37°C. The beacon bound ribozyme RNA preincubated in splicing buffer with no MgCl₂ (−Mg²⁺) but not RNA folded in 6 mM MgCl₂ (+Mg²⁺) prior to addition of the beacon. (B) Fluorescence of 100 nM linear probe L-P3 in the presence of folded or unfolded L-21 ribozyme, as in (A). Curves represent best fit to $\Delta F=A\left(1-{\text{e}}^{-k_{\text{obs}}t}\right)$ for MB-P3 and $\Delta F=A{\text{e}}^{-k_{\text{obs}}t}$for L-P3. MB-P3, k_obs = 0.059 min⁻¹; L-P3, k_obs = 0.31 min⁻¹ (−Mg²⁺).