FIGURE 10.

Comparison of SHAPE-calculated and phylogenetic models of SL1^ISS. A, left, secondary structure of SL1^ISS determined by SHAPE modification and covariation analysis within the context of the entire HIV-1 genome (17). Right, alternative model of SL1^ISS determined by phylogenetic comparisons and chemoenzymatic probing of the isolated ssA7 locus (12, 13). B, NOE evidence that the upper helix of SL1^ISS folds with a structure consistent with the phylogenetic model. C, mapping of the SHAPE reactivity data onto the three-dimensional structure of SL1^ISS shows that ∼87% of the low and medium reactive nucleotides can be accommodated in regions of stable structure.