Figure 1.

The internal representation of multi-strand secondary structures corresponds to non-nested basepairings. Left: schematic of one of the 4-strand RNA-square designs (also called tectosquare).¹ Right: Equivalent circular plot of the computer-internal representation of the RNA-square. Helices are represented as arcs. Non-nested base pairs correspond to crossing of arcs. A more detailed version of the circular representation of the RNA-square is part of the screenshot shown in Figure 5. The left part of the figure has been reprinted from Methods, 54(2), Kasprzak et al.: Use of RNA structure flexibility data in nanostructure modeling, 239–250, Copyright (2011), with permission from Elsevier.⁴¹