Figure 7.
Time-dependent conformational rearrangement of the HIV-2 RRE. Analyses were performed on a 216 nt RRE derived from HIV-2ROD by in vitro transcription. (A) Native gel electrophoresis as a function of incubation time indicates the HIV-2 RRE comprises a mixture of “open”, “intermediate”, and “closed” conformers (A–C, respectively) at short incubation times and whose ratio varies with time, with the closed conformer ultimately predominating. (B) SHAPE-derived conformations of the open, intermediate, and closed HIV-2 RRE forms, respectively. Secondary structural motifs are indicated and color-coded as follows: SL-I, red; S-IIA, dark green, SL-IIB, -IIC and adjacent connecting loops, magenta; SL-III, yellow; SL-IV, blue; SL-V, orange. Modified from Reference [64].