Probing Retroviral and Retrotransposon Genome Structures: The “SHAPE” of Things to Come

Figure 3

Examining RNA tertiary interactions by ai-SHAPE. (a) ai-SHAPE principal, that is, hybridization of an interfering oligonucleotide (green) to one partner of the proposed RNA duplex increases acylation sensitivity of its base-paired counterpart. (b) Electropherogram of NMIA reactivity of MTE nucleotides 60–170 in the absence (blue trace) and presence of the interfering oligonucleotide 1B (yellow trace). Loop L3 has been highlighted by the red box. (c) Secondary structure map for a portion of the MusD RNA transport element MTE, illustrating the L3/IL8 kissing interaction. The sequence of the interfering oligonucleotide hybridized to IL8 is indicated in orange, while nucleotides of loop L3 and the neighboring helix that exhibited enhanced NMIA reactivity are depicted within orange boxes adapted from [30].