Figure 9.

Discovery of higher-order RNA structure. (A) Well-determined secondary structure elements across the first half of the DENV2 genome based on the lowSS metric. (B) RING correlated chemical probing analysis of three RNA elements with well-determined structures and higher-order folds. Elements are named by the gene in which they occur. (C) Effect of mutations in regions with significant RING correlations on (top) global compaction of the DENV2 RNA genome (measured by dynamic light scattering) and on (bottom) replication fitness (visualized by immunostaining of DENV2 envelope protein and nuclei). (D) Modeled three-dimensional folds of three elements in the DENV2 RNA based on RING correlations used to restrain discrete molecular dynamics simulations.