Idealized schematic of the junction conformations.
The stacked (a) iso-I and (b) iso-II conformations predominate at modest and high salt concentrations. (c) The open conformation is mainly observed at low salt concentration and also potentially acts as an intermediary of conformational changes between iso-I and II. The colors denote the strands of the J3 junction, labeled X, R, B and H, following the convention of Lilley and co-workers39,40,41. See methods for the complete sequence. In the lower panel, the arrows highlight the inter-base distances for non-complementary bases of distinct strands at the junction center. In iso-I, the TT and CC separations are small (red arrows), while the AG distances are large (blue arrows); the opposite occurs for iso-II. The distances are essentially identical in the open conformation. We take advantage of these differences to distinguish conformations.