Fig. 2.

Protein binding to HIV-2 5′UTR. a Secondary structure model of +1–560 nt region of HIV-2 RNA [33] with the positions protected from hydroxyl radical cleavage in the presence of the HIV-2 GagΔp6, NC, and MA proteins marked. The level of protection increases with protein concentration. Closed circles indicate residues protected starting at lowest protein concentration; open circles indicate residues protected starting at intermediate protein concentration. Light grey annotates lack of data. b Sequences within binding sites and their vicinities were compared using http://weblogo.berkeley.edu/ [68]