Extended Data Fig. 9: Secondary structure predictions for dimer and monomer promoting mutants.
From: Short- and long-range interactions in the HIV-1 5′ UTR regulate genome dimerization and packaging
Secondary structure predictions for dimer and monomer promoting mutants targeting the polyA-SL1 and PBS-SL1 interactions. DMS reactivities and secondary structure models for polyA, SL1 and polyA-SL1. DMS reactivities for each nucleotide position are show in the upper barchart. Shannon entropies are shown in 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. Red signifies highly reactive positions that are unpaired. Pale yellow signifies unreactive positions that are base-paired. (a-c) DMS reactivities and secondary structure models for polyA-SL1 mutants. (a) dimer promoting mutant C84A-C85A folds into the canonical 5’UTR structure (b) Monomer promoting mutant U86G–A89C contains the polyA-SL1 interaction. (c) Reactivities for both mutants U86G-A89C (left hemisphere) and C84A-C85A (right hemisphere) mapped to the structures polyA, SL1, and polyA-SL1. (d) Dimer promoting mutant C218G folds into the structure containing SL1 (e) Monomer promoting mutant U220G-G221A folds into a structure containing the PBS-SL1 interaction. (f) Reactivities for both mutants U220G-G221A (left hemisphere) and C218G (right hemisphere) mapped to the structures polyA, SL1 and polyA-SL1.
