Figure 5.

Unfolding and refolding of the five-way junction. (A) Distances were monitored between O2′ atoms on C418 (h16) and G540 (h18) in the five-way junction with/without S4 (left), and in quenching simulations using Mg²⁺ and S4N (right). (B) Interactions established between the unfolded five-way junction and S4N during 50 ns of the S4N quenching simulation. The simulation starts with a single interaction (shown in bold) between Lys⁷ and A411 in the unfolded conformations of S4N and the five-way junction. Positively charged residues on S4N form salt bridges with phosphate atoms on the RNA, hydrogen bonds with 2′ oxygens on the sugar rings (^∗), and cation-π interactions with bases (†). Additional interactions between S4N and h18 close to those seen in the crystal structure are also observed.