FIGURE 1.

Enzymatic and chemical footprinting-based determination of the correct Lys1 secondary structure. (A) Enzymatic (RNase A, RNase I, and RNase T₁) cleavage and SHAPE modification of Lys1. Dotted horizontal bars represent two standard deviations from the mean cleavage intensity. Nucleotides whose intensity lies above the bar denote cleavage hits. The M-fold predicted secondary structures of lowest energy are shown. (B) Lys1.1 with M-fold predicted ΔG = −12.3 kcal/mol and percent agreement with footprinting = 43; (C) Lys1.2 with ΔG = −11.8 kcal/mol and percent agreement = 83; and (D) Lys1.3 with ΔG = −11.5 kcal/mol and percent agreement = 86. For each predicted secondary structure, open triangles indicate RNase A cleavage sites, open arrowheads indicate RNase T₁ cleavage sites, and asterisks indicate RNase I cleavage sites. Nucleotides that readily react with NMIA (SHAPE reagent), indicating flexible and single-stranded nucleotides, are marked with a crosshair.