Regional stability at 400 K for (A) 0 mM Mg2+, dG[−] and (B) 5 mM Mg2+, dG[−]. From left to right, the number of native hydrogen bonds formed in the region, the total number of hydrogen bonds formed in the region (both scaled by the number of native hydrogen bonds), and regional RMSD with the entire structure fit first (same as before). The native helices and PK melt in both cases giving a large deviation from the native structure of ∼15 Å; however, the variety of hydrogen bonds donor and acceptor in nucleic acid makes it possible for the RNA motifs to form nonnative hydrogen bonds as compensation and lower the energy. As shown in the first column, the number of hydrogen bond can even exceed the original number, and these newly formed hydrogen bonds can either be between the submotifs and collapse the structure, or inside the strand which makes the single strand curly.
