Figure 3.

SHAPE analysis results in ELVd conformations with a central domain, wherein most of the nucleotides that can potentially form the hammerheads are base-paired, flanked by terminal domains with bifurcations. (A) ELVd (+) RNA folding in vitro shows minor differences in some loops with respect to one of the structures predicted in silico. (B) ELVd (−) RNA folding in vitro is also consistent with the structures predicted in silico, including 2 variations with a cruciform motif in the central domain and a rearrangement in one of the arms forming the left terminal bifurcation. Nucleotides in red, yellow and black displayed high (more that 0.85), intermediate (0.85–0.40) and low (less than 0.40) SHAPE-reactivity. Nucleotides in gray, for which the SHAPE-reactivity could not be determined, correspond to the primer binding region and adjacent positions, and to blurry positions. Other details as in the legend to Fig. 1.