Figure 9.
A kissing loop motif within the musD RNA transport element validated by aiSHAPE. (A) Predicted secondary structure the musD RNA transport element, including a postulated kissing loop interaction between nt 82–89 and nt 182–189. (B) The LNA-DNA chimera designed to hybridize to nt 182–189 would be expected to displace nt 82–89 and render them more susceptible to acylation. Perturbation of RNA structure outside of this region should be minimal. (C) A step plot comparing RNA reactivity values obtained in the presence and absence of the LNA-DNA chimera. A marked increase in reactivity was observed for nt 82–89 in the presence of the chimera, thus validating the kissing loop prediction. Adapted from Legiewicz et al. (2010).