Figure 3.

Crowding stabilizes native and non-native intermediates. Folding of the L9 mutant was analyzed by native PAGE in (a) dilute solution and (b) 18% PEG₁₀₀₀. Top, native PAGE was performed in the same experimental condition as SAXS. Bands were assigned as described in SI Methods. The two high mobility bands have the same response to [Mg²⁺] and were grouped. Bottom, populations of each conformer in solution calculated from native PAGE (solid lines) and the change in R_g (dashed lines). Some of the unfolded RNA in solution folds to I_U or I_C when the sample contacts the MgCl₂ in the gel running buffer. U, unfolded RNA (red); I_U, extended folding intermediates (green); I_C, compact intermediates (blue). Fitted parameters are the standard deviation from 2–3 trials. Data for L9 and other ribozymes are shown in Supplementary Figure S3.