Figure 2.

Internal circularization sites of DENV-1 genome, as determined by SPLASH cross-linking [19]. It is apparent that the number of internal circularization motifs in virions (red) is much higher than those identified in infected cells. A number of interactions persist in cells (blue). This may be attributed to the spatial constraints imposed by the virion shell or it may be a prerequisite for packaging. Functional assays demonstrate the importance of these motifs for viral fitness, with structure-disrupting changes causing a pronounced drop in viral activity. Compensatory mutations restore viral fitness. Several of the identified internal circularization sites show multiple interaction partners in the SPLASH experiment and structure models of the relevant regions show competing base pairs among the possible partners. It is currently unclear whether these competing interactions form in a stochastic manner or whether specific interactions are present at different stages of the viral life cycle and/or rearrange dynamically.