Fig. 3: Kinetic model of metal ion-induced IBS1* and dIBS1* recognition.

a Two-state binding of IBS1* (blue) and dIBS1* (orange) to the EBS1* hairpin under high monovalent ionic strength (0: exon unbound; 1: exon bound). The area of the circle is proportional to the state population (specified in percentage) and the arrow width reflects the relative rate of the transition. Binding rates, k′_on,01, are indicated as pseudo-first-order rates coefficients calculated from the trained HMM. b Three-state model with two degenerate high FRET states reflecting the coordination of Mg²⁺ to the formed tertiary contact (0: exon unbound, Mg²⁺ unbound; 1: exon bound, Mg²⁺ unbound; 2: exon bound, Mg²⁺ bound). Insets show surface representations of the RNA–RNA and RNA–DNA interaction, color coded by the electrostatic potential (red: −15 kT e⁻¹; blue 5 kT e⁻¹). Arrows indicate coordination sites for Mg²⁺. Source data are provided as a Source Data file.