(A) Principal component projection of an optimized ensemble based on 3J-couplings, with estimated free energy contours revealing a structured conformational landscape containing multiple low-energy basins. (B) K-means clustering identifies five dominant conformational substates (CSs), with representative centroids indicated as red points. (C) Root mean square fluctuations of the terminal loop nucleotides within each CS relative to its centroid. (D) Three-dimensional centroid structures, substate populations, and dynamic secondary structures within each CS, where base-pairing and nucleobase stacking within each CS are visualized via color intensity (darker tones indicate higher probability across the cluster ensemble).
