Extended Data Fig. 8: Secondary structure model for SL1 mutants.
From: Short- and long-range interactions in the HIV-1 5′ UTR regulate genome dimerization and packaging
Secondary structure model for SL1 mutants. Models were obtained using DMS reactivities as soft constraints for in silico folding in the Vienna RNA structure package. DMS reactivities for each nucleotide position are show in the upper barchart. Shannon entropies are shown in the lower chart. Upper arc plots show consensus structure. Lower arc plots show base pairing probabilities (green = 70-100%; blue = 40-70%; yellow = 10-40%; grey = 5-10%). DMS reactivities from monomer and dimer samples were mapped to A and C residues on SL1. Red signifies highly reactive positions that are unpaired. Pale yellow signifies unreactive positions that are base-paired. (a) A235C and (b) A239C reconfigure the SL1 lower helix and internal loop to enhance dimerization. Red arrows highlight position 239 showing a reactivity change between the A235C and A239C mutations.
