The pattern of local and long-range base pairing within RNA. Pairing can hide a binding motif or an initiation region, making accessibility an experimentally testable regulatory variable.
Bringing separated RNA segments into proximity while an intervening segment forms a loop. Multivalent RNA-binding proteins can stabilize this geometry, with consequences for accessibility and splice-site use.
A structured RNA recognition element bound by iron regulatory proteins. In suitable 5′ contexts it controls biological translation, whereas a 3′ stability-control context can regulate RNA decay. It is not an autonomous iron-sensing riboswitch.
A regulatory mechanism in which a chemical modification changes RNA secondary structure and thereby exposes or occludes a functional element. Modification dependence of binding alone does not distinguish this mechanism from direct chemical recognition.[ref]
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Analogous problem to the secondary structure of proteins. Likely a bit simpler due to the strong tendency for complementary pairs to bind.