Fig. 4. Cationic depsipeptides directly interact with RNA.

a Structures of cationic peptide 12 and depsipeptide 13 used for gel mobility shift assays, and depsipeptide 14 used for circular dichroism studies. b Gel mobility shift assay with increasing concentrations (66.6–530 µM) of the FAM-labeled sequences 12 or 13 (green fluorescence) and a 5′-Cy5-U₂₀ RNA (26.6 µM, red fluorescence) in MES-TEA buffer (pH 6). A physical association between the RNA and cationic oligomers is evident as a less mobile band in the gel, which appears as orange due to co-localization of the green and red dyes, and as loss of intensity of the free RNA band. The gel was cropped at the edges for clarity. The image shown is representative of two independent experiments giving similar results. c CD spectra of RNA duplex 1 (5 μM each strand) with increasing concentrations of depsipeptide 14 (0–10 μM), indicating a concentration-dependent association. Spectra were recorded in 100 mM MES-TEA buffer (pH 6). d Plot of the change in CD signal at 266 nm as a function of increasing concentrations of depsipeptide 14. Red and blue colors of the filled circles correspond to curves of the same color in panel (c). Data were fit to a simple one-site binding model (black line) yielding an apparent K_d of ~3 μM.