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. Author manuscript; available in PMC: 2010 Jul 17.
Published in final edited form as: J Mol Biol. 2009 May 3;390(3):428–442. doi: 10.1016/j.jmb.2009.04.048

Figure 2.

Figure 2

Optimized structure alignment of R2 5′ RNAs. Conserved structures are highlighted in different colors, except in the pseudoknot, where the individual helices are colored for clarity. Base pairs are indicated with matching brackets, while unpaired nucleotides are indicated by “dots”. Sites in each RNA that are strongly modified by DMS or CMCT are colored green and blue, respectively, in the nucleotide numbering, while sites that are strongly modified by NMIA are in red. Sites strongly modified by DMS or CMCT and by NMIA are orange. For R2Bm, sites strongly modified by kethoxal are also colored green. Strongly modified sites have ≥ 6 times the control intensity. Unambiguous microarray binding centers exhibiting medium (≥ 1/9 maximum intensity) or strong (≥ 1/3 maximum intensity) binding are boxed. Below the alignment, the consensus structure is indicated by “<” and “>” characters. Below that, sites with compensatory mutations are given by the boxed nucleotides and consistent mutations are indicated by the unboxed nucleotides. Note that numbering for alignment positions is at the top and differs from the numbering of each RNA. For R2Sc, R2Ch, R2Cpr and R2Spy, the nucleotide labeled 2 corresponds to nucleotides 472, 734, 482, and 433, respectively, of the full-length R2 sequence (the first G was added for increased transcription efficiency). For R2Bm, the nucleotide labeled 1 is position 650 on the full-length R2 sequence.