A frequently occurring motif of RNA secondary structures is the so called pseudoknot. Pseudoknots exert diverse biological functions. They show catalytic activity in various ribozymes and self-splicing introns and can alter the gene expression by inducing ribosomal frameshift in many viruses.

The most simple and best characterised pseudoknot is the H-type pseudoknot. It emerges when bases from inside a hairpin loop interact with bases outside the hairpin. See figures A, B and C for the formation of a pseudoknot.

Image from: Staple DW, Butcher SE (2005) Pseudoknots: RNA Structures with Diverse Functions. PLoS Biol 3(6): e213