Regional fluctuation is related to RNA contacts. (A,B) Replica 2 and replica 8 with 0 mM Mg2+, dG[−], 300 K. The metastable state where P1 and P3 helices are distorted and the joint major groove is open can result from the breaking of near-junction base-pairings on P1 helix. (C,D) Two examples—with the presence of Mg2+ at 300 K (5 mM Mg2+, dG[−], and 20 mM Mg2+, dG[+], respectively). Although the number of contacts of PK is small, the dissociation of them only causes local distortion, which does not melt the PK and has little effect on global fluctuation. Distances between base pairs are measured as the distance between the N1 atom of purine bases and the N3 atom of pyrimidine bases. The distance for base stacking is defined as the distance between the center of mass of the bases.
