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. Author manuscript; available in PMC: 2012 Sep 6.
Published in final edited form as: Biochemistry. 2011 Aug 15;50(35):7647–7665. doi: 10.1021/bi200463p

Figure 1.

Figure 1

Isoenergetic microarray mapping and chemical mapping results for DsrA RNA, marked on (A1) structure proposed by Sledejski based only on computational analysis, (A2) structure proposed by Lease and Belfort, (A3) structure proposed by Rolle, (A4) structure predicted by RNAstructure constrained by microarray mapping data. Red squares represent sites of binding to probe (middle nucleotide of target binding region), orange squares represent two sites which can bind to the same probe. Chemical modification data are superimposed: kethoxal with triangles, CMCT with squares, and NMIA with circles. Free energy of each structure is predicted by RNAstructure 4.6. Isoenergetic microarray mapping results for (B) DsrA 38, (C) DsrA SL3, (D) complex DsrA RNA/oligonucleotide d1. The navy line shows complementary region of binding for d1. Red squares represent binding sites to probes which have the same intensity relative to DsrA RNA alone. Orange squares represent two sites which can bind to the same probe and have the same intensity relative to DsrA RNA alone. Blue squares represent additional binding sites to probes, not observed in DsrA RNA. Light-blue squares represent additional binding sites to probes, not observed in DsrA RNA, which have the possibility of binding to alternative binding sites. Yellow squares represent lack of binding to probes in the presence of d1.