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. 2014 Jun;20(6):846–854. doi: 10.1261/rna.043323.113

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© 2014 Rice et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society

This article is distributed exclusively by the RNA Society for the first 12 months after the full-issue publication date (see http://rnajournal.cshlp.org/site/misc/terms.xhtml). After 12 months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.

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FIGURE 2. — Differential SHAPE analysis of the E. coli 5S rRNA. Normalized SHAPE reactivities from reactions with NMIA (top) and 1M6 (middle) are colored by nucleotide reactivity. Differential SHAPE reactivities (Steen et al. 2012) (bottom) were calculated by first scaling 1M6 to NMIA reactivities over a moving window and then subtracting 1M6 from NMIA reactivities. Strong differential reactivity enhancements (>|0.3| SHAPE units) are colored green for NMIA and blue for 1M6. These sites correspond to nucleotides with slow dynamics and those with a face available for stacking, respectively. Nucleotide positions showing strong positive-amplitude (favoring NMIA) differential reactivities are labeled.