FIGURE 4.

Set of 60 hairpins that best satisfy the scoring function in Figure 3D and the best-predicted Hamiltonian path for MS2 RNA (Dykeman et al. 2011). The helix numbers are listed only for the top row (hairpins 1–10) and then the first hairpin on the left in each row. The number below the hairpin represents the first 5′ nucleotide in the helix. Hairpins are listed in 5′-3′ sequence order. Small circles indicate strong chemical modification hits on in vitro–transcribed free MS2 RNA (Fiers et al. 1976; Skripkin et al. 1990). An x marks the single chemical modification hit at A2142 that is inconsistent with the predicted hairpins. Chemical modification is allowed at helix ends, in GU pairs, adjacent to GU pairs, and adjacent to bulges and loops (Mathews et al. 2004).