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. 2015 Feb 3;108(3):748–757. doi: 10.1016/j.bpj.2014.12.014

Figure 1.

Figure 1

Structure probing of VAI. (a) Secondary structure of VAI. The complementary triplets in loops 8 and 10 are depicted in red, and the conserved tetrastem 4 is depicted in green. (b) DMS probing of VAI structure. The gel includes C and A sequencing ladders, a control lane without DMS (-), and a lane with DMS (+). Artifacts arising from reverse transcriptase pause sites are marked with an asterisk. (c) SHAPE probing of VAI structure. The gel includes C and A sequencing ladders, a control lane without SHAPE reagent (-) and a lane with 1M7 (+). Artifacts arising from reverse transcriptase pause sites are marked with an asterisk. (d) DMS and SHAPE reaction sites mapped onto the secondary structure diagram of VAI. To see this figure in color, go online.