Fig. 4: Demonstration of interface flexibility.

a, A representation of interface flexibility related to the mobility of the peripheral 3PS segments following the Holiday junction. The upper box represents an aligned, ‘closed’ configuration that allows directional binding and the lower box represents a wider, ‘open’ configuration that is unavailable for binding. b, The probability distribution of the end-to-end arm distances at the π–π interface obtained from the oxDNA molecular dynamics simulations of the 3PS monomers. The purple area highlights the region where the arms are in a closed state and yellow is used for the open state. c, A patchy-particle model used for Monte Carlo simulations, highlighting the patch state with variable p (p = 1 for closed state and p = 0 for open state), and the P_open the probability that a patch has a state p = 0. Other model parameters defined as in the classical Kern–Frenkel model, where σ is the diameter of the hard-core repulsion, δ is the attraction range and θ_pw is the patch width. r_ij is the center-to-center distance between the two interacting particles, i and j. See Supplementary Information for details. d,e, Comparison of simulation results, bottom and experimental measurements, top of short 3PS (d) and long 3PS (e). For AFM images, the lowest intensity corresponds to background at 0 nm and the highest intensity corresponds to DNA at approximately 2 nm. The selected frames are taken from simulation trajectories with similar average ND values as in the experiments. f, An approximate state diagram as a function of the probability of open state (that is, when p = 0) and the interaction strength. The dark grey region shows the diffusion-limited aggregation regime, purple/orange shows the short-like/long-like regime and the light grey shows the gas (mostly single particles) phase. Each data point represents a set of conditions simulated, with length dimensions normalized to our short design. The state diagram was obtained for σ = 1, δ = 0.038 and θ_pw = 0.44.