Fig. 3.

SHAPE analysis of preQ₁-II RNA mutants. (A) Secondary structure and representative gel for the SHAPE probing of the preQ₁-II C19U mutant with BzCN. Lanes from Left to Right: control in the absence of probing reagent (DMSO lane), probing in the absence of MgCl₂ or ligand (BzCN) and presence of 5 mM Mg²⁺ ions, and 5 mM Mg²⁺ ions plus 10 μM preQ₁. (B) Same as A for preQ₁-II A11U/G12U mutant. (C) Same as A for a deletion mutant of preQ₁-II RNA with ΔP4. The region that is highly indicative of preQ₁ binding is highlighted by a red square. Secondary structures are color-coded to facilitate correlation of nucleoside positions with gel electrophoresis band shifts. Mutations and deletions highlighted by red lettering.