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. Author manuscript; available in PMC: 2010 Jul 10.

Published in final edited form as: J Mol Biol. 2009 May 13;390(2):319–338. doi: 10.1016/j.jmb.2009.05.005

Fig. 7 — Enzymatic structure mapping of TARwt and A34U:U37A monomers and dimers. Monomeric and dimeric RNAs were prepared by native gel-purification and renaturations of monomer, as described. Sequencing lanes for G (T1) and all nucleotides (OH⁻) are provided to the left of each dataset. The secondary structures were determined using RNases A (C, U-specific) orange, T1 (G-specific) blue, T2 (single stranded-specific) green, and V1 (double strand-specific) red. Open triangles represent weaker cleavages and closed triangles stronger cleavages. RNA samples were run on 12% PAGE/1×TBE/8.3 M urea denaturing gels. For simplicity, triangles are displayed only on the lower half of dimer RNA secondary structures. (a) TARwt monomer mapped as expected, ⁴⁴,⁴⁵ while mapping of the dimer is consistent with a completely extended duplex with two 3-nt bulges. (b) A34U:U37A monomer data are consistent with an AA mismatch in the upper stem, which destabilizes the monomer. Mapping of the A34U:U37A dimer is consistent with a completely extended duplex with two [2×1] internal loops. The transition from two monomers to one dimer is annotated for both TARwt and A34U:U37A. Two-state hybridization server (UNAFold) by M. Zuker also predicts these two secondary structures well.⁴⁷

Fig. 7 — Enzymatic structure mapping of TARwt and A34U:U37A monomers and dimers. Monomeric and dimeric RNAs were prepared by native gel-purification and renaturations of monomer, as described. Sequencing lanes for G (T1) and all nucleotides (OH⁻) are provided to the left of each dataset. The secondary structures were determined using RNases A (C, U-specific) orange, T1 (G-specific) blue, T2 (single stranded-specific) green, and V1 (double strand-specific) red. Open triangles represent weaker cleavages and closed triangles stronger cleavages. RNA samples were run on 12% PAGE/1×TBE/8.3 M urea denaturing gels. For simplicity, triangles are displayed only on the lower half of dimer RNA secondary structures. (a) TARwt monomer mapped as expected, ⁴⁴,⁴⁵ while mapping of the dimer is consistent with a completely extended duplex with two 3-nt bulges. (b) A34U:U37A monomer data are consistent with an AA mismatch in the upper stem, which destabilizes the monomer. Mapping of the A34U:U37A dimer is consistent with a completely extended duplex with two [2×1] internal loops. The transition from two monomers to one dimer is annotated for both TARwt and A34U:U37A. Two-state hybridization server (UNAFold) by M. Zuker also predicts these two secondary structures well.⁴⁷