Probing Retroviral and Retrotransposon Genome Structures: The “SHAPE” of Things to Come
Figure 5
(a) Structure of the threading intercalator, MPE. (b) Examining RNA tertiary interactions by through-space hydroxyl radical cleavage (–OH) with the threading intercalator methidiumpropyl EDTA (MPE). Once a SHAPE profile for the RNA under investigation is determined, an MPE intercalation site is introduced by replacing four consecutive nucleotides with the CGAG/C(C/U)G recognition motif. SHAPE is then repeated to determine that sequence changes are nonperturbing, after which site-directed hydroxyl radical cleavage is performed to identify neighboring sites in the RNA. Repeating this process with independent RNAs containing unique MPE intercalation sites cumulatively provides information on tertiary interactions.
