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RNA’s hierarchical network-like structures from 1D to 3D. The primary (1D), secondary (2D), and tertiary (3D) structures associated with fluoride riboswitch (PDB:4NEC [81]) are shown. The RAG tree and dual graphs representing its 2D topology without and with pseudoknot, respectively, are also shown. The double-stranded or stem regions are colored green for tree topologies and red for pseudoknot formation.
