Fig. 1.

Well-determined secondary structure elements in the DENV2 RNA genome. The first half of the genome is shown (the entire genome is shown in SI Appendix, Fig. S1, panel 1). Median ex virion 1M7 SHAPE reactivities (black) and Shannon entropies (dark blue) are plotted over centered 55-nt windows. Regions with both low SHAPE and low Shannon entropy are highlighted by dark-gray shading, with light-gray shading extended to encompass entire intersecting helices. The first 12 elements (out of 24 total elements) with well-determined structures are numbered. Base pair probability arcs are colored by probability (see scale), with green arcs indicating the most probable base pairs; black arcs indicate plausible pseudoknots (PK). The minimum free-energy secondary structure (inverted black arcs) was obtained using both 1M7 and differential SHAPE reactivities as constraints (1, 12, 13). Secondary structures of elements 1–12 are colored by SHAPE reactivity; high-resolution structures are provided in SI Appendix, Fig. S1, panel 2.