Fig. 3: Base pairing within nos 3′UTR homodimer is driven by regions with low sequence complementarity.

a Examples of simulated structures of monomeric nos 3′UTR at different energy states with an accompanying free energy spectrum, where each blue line represents a cluster of secondary structures generated in the simulation. Shown is a 3D conformation of nos 3′UTR corresponding to the ground state (G = 0 kcal/mol). b Intramolecular base pairing (red lines) within nos 3′UTR in a monomer state. c Simulated base accessibility of each nucleotide of nos 3′UTR in a monomer state (top; blue line) and homodimer state (bottom; magenta and green lines). d Correlation of base accessibility between homodimer and monomer state of nos 3′UTR, with a Pearson correlation coefficient (r) of 0.92. e Intramolecular base pairing (red lines) within nos 3′UTR in a homodimer state. f Simulated nos 3′UTR homodimer (magenta and green). g Intermolecular base pairing (red lines) between two nos 3′UTRs is shown in (i), with a magnified view of example interacting sequences in (ii) (yellow and purple boxes). Note that the sequence orientation in the purple box differs for visualization purposes: in (ii), it is shown from 3′ to 5′, whereas in (i), it is displayed from 5′ to 3′. The sequences within these boxes are connected by intermolecular base pairing interactions (lines). The base pairing probabilities, represented by a red color gradient, are derived from an ensemble of homodimer simulations. Therefore, some bases on one strand may pair with multiple bases on the other strand. See also Supplementary Figs. S4–S6. Source data are provided as a Source Data file.