FIGURE 3.

Predictions of MS2 RNA secondary structure ensembles using Crumple and Sliding Windows. Increasingly strict scoring functions reduce the conformational space of ensembles of RNA hairpins in encapsidated MS2 RNA. MS2 RNA nucleotide numbers between 415 and 3509 are along the x-axis. The bars represent nucleotides forming a hairpin that satisfies the experimental constraints as defined by a scoring function. The color of the bar shows how well the hairpin satisfies the scoring criteria. The scoring function for each ensemble A–D has progressively more detailed criteria. (A) Hairpins of 3–4 nt with at least five pairs in the stem. (B) Hairpins with an A or C in the 3′ position. (C) Hairpins with an A or U in the 5′ position of 4- or 3-nt loops, respectively. (D) Hairpin stems with bulged nucleotides preferred 2 or 3 nt below 4- or 3-nt loops, respectively.