Figure 1: Endo I binding to Holliday junctions captures the instantaneous junction conformer and permits exchange between two isoforms (B1 and B2).

a, Schematic of junction structural dynamics before and after Endo I binding. Junction 7 (J7) comprises four arms of 11 bp. b, smFRET-time traces for unbound J7 obtained at 0 or 10 mM Ca²⁺. c, E_FRET histograms of unbound J7 at 0 or 10 mM Ca²⁺ (left) and of Endo I-bound J7 obtained in the Ca²⁺-EDTA-Ca²⁺ buffer exchange experiments (right). d, smFRET-time traces of Endo I-bound J7 at 10 mM Ca²⁺, showing the transitions between B1 and B2. Partial dissociation (PD) was observed as an intermediate (blue-shaded region) for ~30% of the transitions between B1 and B2 (right). e, Single molecule time traces of J7 showing an Endo I binding event. The blue dashed line indicates the time when 10 nM Endo I were added. The percentages were analyzed from 1,000 HJ molecules. f, Conformer exchange rates k_B1→B2 and k_B2→B1 for the four variants of Endo I obtained at 10 mM Ca²⁺. Data are means ± s.e.m of n = 1,000 HJ molecules. Error bars represent bootstrap estimates of s.e.m..